BIL160/Biology 2 Notes (Sarkar)
BIL160/Biology 2 Notes (Sarkar) BIL160
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Chapter 22 Evidences of evolution 0 evolution as descent With modi cation more narrowly as a change in the genetic composition of a population from generation to generation The pattern of evolutionary change is revealed by data from a range of scienti c disciplines including biology geol ogy physics and chemistry The process of evolution consists of the mechanisms that produce the observed pattern of change These mechanisms represent natural causes of the natural phenomena we observe Aristotle rec ognized certain af nities among organisms He concluded that lifeforms could be arranged on a ladder or scale of in creasing complexity later called the scala naturae scale of na ture Carolus Linnaeus 17071778 a Swedish physician and botanist who sought to classify life s diversity in his words for the greater glory of God Linnaeus developed the twopart or binomial format for naming species such as Homo sapiens for humans that is still used to day 0 Groupingg species into increasingly general categories 0 Darwin argued that classi ca tion should be based on evolutionary relationships ing fossils the remains or traces of organisms from the past Many fossils are found in sedimentary rocks formed from the sand and mud that settle to the bottom of seas lakes swamps and other aquatic habitat o superimposed layers of rock called strata singular stratum Paleontology the study of fossils was developed in large part by French scientist Georges Cuvier o e advocated catastrophism the principle that events in the past oc curred suddenly and were caused by mechanisms different from those operating in the present cottish geologist James Hutton 17261797 proposed that Earth s geologic features could be explained by gradual mechanisms still operating to day Charles Lyell 17971875 incorporated Hutton s think ing into his principle of uniformitarianism which stated that mechanisms of change are constant over time Lyell pro posed that the same geologic processes are operating today as in the past and at the same rate 0 Darwin agreed that if geologic change results from slow continuous actions rather than from sudden events then Earth must be much older than the widely accepted age of a few thousand years proposed a mechanism for how life changes over time Lamarck is primarily remembered today not for his visionary recognition that evolutionary change explains pat terns in fossils and the match of organisms to their environ ments but for the incorrect mechanism he proposed to explain how evolution occurs 0 Lamarck had found what appeared to be several lines of de scent each a chronological series of older to younger fossils leading to a living species He explained his ndings using two principles that were widely accepted at the time The rst was use and disuse the idea that parts of the body that are used extensively become larger and stronger while those that are not used deteriorate Among many examples he cited a giraffe stretching its neck to reach leaves on high branches The sec ond principle inheritance of acquired characteristics stated that an organism could pass these modi cations to its offspring Lamarck also thought that evolution happens because organ isms have an innate drive to become more complex Darwin rejected this idea but he too thought that variation was introduced into the evolutionary process in part through in heritance of acquired characteristics 0 Today however our un derstanding of genetics refutes this mechanism Experiments show that traits acquired by use during an individual s life are not inherited in the way proposed by Lamarck 0 After Beagle voyage natural selection a process in which individ uals that have certain inherited traits tend to survive and reproduce at higher rates than other individuals because of those traits 0 Wallace had developed a hy pothesis of natural selection nearly identical to Darwin s 0 Darwin publishes 5 The Origin of Species mOverview the unity of life the diversity of life and the match between organisms and their environments Organisms share many characteristics leading Darwin to perceive unity in life He attributed the unity of life to the descent of all organisms from an ancestor that lived in the remote past To Darwin the Linnaean hierarchy re ected the branching history of life with organisms at the vari ous levels related through descent from common ancestors Artificial Selection Natural Selection and Adaptation Darwin proposed the mechanism of natural selection to explain the observ able patterns of evolution Humans have modi ed other species over many generations by se lecting and breeding individuals that possess desired traits a process called arti cial selection Darwin then argued that a similar process occurs in nature He based his ar gument on two observations from which he drew two inferences Observation 1 Members of a popu lation often vary in their inherited traits Figure 2210 Observation 2 All species can pro duce more offspring than their environ ment can support Figure 2211 and many of these offspring fail to survive and reproduce Inference 1 Individuals whose in herited traits give them a higher proba bility of surviving and reproducing in a given environment tend to leave more offspring than other individuals Inference 2 This unequal ability of individuals to survive and reproduce will lead to the accumulation of favorable traits in the population over generations An organism s heritable traits can in uence not only its own performance but also how well its offspring cope with en vironmental challenges For example an organism might have a trait that gives its offspring an advantage in escaping preda tors obtaining food or tolerating physical conditions 0 When such advantages increase the number of offspring that survive and reproduce the traits that are favored will likely appear at a greater frequency in the next generation Thus over time natural selection resulting from factors such as predators lack of food or adverse physical conditions can lead to an increase in the proportion of favorable traits in a population How rapidly do such changes occur Darwin reasoned that if arti cial selection can bring about dramatic change in a rel atively short period of time then natural selection should be capable of substantial modi cation of species over many hun dreds of generations One subtle but important point is that although natural se lection occurs through interactions between individual organ isms and their environment individuals do not evolve Rather it is the population that evolves over time A second key point is that natural selection can amplify or diminish only those heritable traits that differ among the in dividuals in a population Thus even if a trait is heritable if all the individuals in a population are genetically identical for that trait evolution by natural selection cannot occur Third remember that environmental factors vary from place to place and over time A trait that is favorable in one place or time may be useless or even detrimental in other places or times Natural selection is always operating but which traits are favored depends on the context in which a species lives and mates The Evolution of DrugResistant Bacteria MRSA strains are resistant to multiple antibiotics probably because bacteria can ex change genes with members of their own and other species see Figure 2713 Thus the presentday multidrugresistant strains may have emerged over time as MRSA strains that were resistant to different antibiotics exchanged genes Homology A second type of evidence for evolution comes from analyzing similarities among different organisms As a result related species can have characteristics that have an underlying similarity yet function differently Similarity resulting from common ancestry is known as homology Anatomical and Molecular H omologies Of course closely related species share the features used to determine their relationship but they also share many other features Some of these shared features make little sense except in the context of evolution Such striking anatomical resemblances would be highly unlikely if these structures had arisen anew in each species Rather the underlying skeletons of the arms forelegs ippers and wings of different mammals are homologous structures that represent variations on a structural theme that was present in their common ancestor Some of the most intriguing homologies concern left over structures of marginal if any importance to the organ ism These vestigial structures are remnants of features that served a function in the organism s ancestors Another example is provided by eye remnants that are buried under scales in blind species of cave shes But molecular homologies go beyond a shared code For example organisms as dissimilar as humans and bacteria share genes inherited from a very distant common ancestor Some of these homologous genes have acquired new functions while others such as those coding for the ribosomal subunits used in protein synthesis It is also common for organisms to have genes that have lost their function even though the ho mologous genes in related species may be fully functional Like vestigial structures it appears that such inactive pseudogenes may be present simply because a common ancestor had them Homologies and Tree Thinking Some homologous characteristics such as the genetic code are shared by all species because they date to the deep ances tral past In contrast homologous characteristics that evolved more recently are shared only within smaller groups of organ isms Biologists often represent the pattern of descent from com mon ancestors and the resulting homologies with an evolutionary tree a diagram that re ects evolutionary rela tionships among groups of organisms A Dijferent Cause of Resemblance Convergent Evolution Although organisms that are closely related share characteristics because of common descent distantly related organisms can resemble one another for a different reason convergent evolution the independent evolu tion of similar features in different lin eages Mar supials are distinct from another group of mammals the eutherians few of which live in Australia o Although they evolved independently from different ancestors these two mammals have adapted to similar environments in sim ilar ways In such examples in which species share features because of convergent evolution the resemblance is said to be analogous not homologous Analogous features share similar function but not common ancestry while homolo gous features share common ancestry but not necessarily similar function The Fossil Record A third type of evidence for evolution comes from fossils Fos sils also show the evolutionary changes that have occurred in various groups of organisms Fossils can also shed light on the origins of new groups of organisms Some of these fossils provided an unexpected line of support for a hypothesis based on DNA data that cetaceans are closely related to eventoed ungulates a group that in cludes deer pigs camels and cows Collectively the recent fossil discoveries document the forma tion of new species and the origin of a major new group of mam mals the cetaceans Biogeography A fourth type of evidence for evolution comes from biogeography the geographic distribution of species The geographic distribution of organisms is in uenced by many factors including continental drift the slow movement of Earth s continents over time About 250 million years ago these movements united all of Earth s landmasses into a sin gle large cnntinent called Panoaea Wh UUllLlllUllL LTCUIULI filllgill il We can use our understanding of evolution and continental drift to predict where fossils of different groups of organisms might be found For example scientists have constructed evolu tionary trees for horses based on anatomical data We can also use our understanding of evolution to explain biogeographic data For example islands generally have many species of plants and animals that are endemic which means they are found nowhere else in the world at Is Theoretical About DarWin s View of Life Some people dismiss Darwin s ideas as just a theory However as we have seen the pattern of evolution the observation that life has evolved over time has been documented directly and is supported by a great deal of evidence In addition Darwin s explanation of the process of evolution that natural selection is the primary cause of the observed pattern of evolutionary change makes sense of massive amounts of data The effects of natural selection also can be observed and tested in nature The colloquial use of the word theory comes close to what scientists mean by a hypothesis In science a theory is more comprehensive than a hypothesis A theory such as the theory of evolution by natural selection accounts for many observations and explains and integrates a great variety of phenomena The skepticism of scientists as they continue to test theo ries prevents these ideas from becoming dogma For example although Darwin thought that evolution was a very slow process we now know that this isn t always true 1 Which of the following is not an observation or inference on which natural selection is based 2 There is heritable variation among individuals 3 Poorly adapted individuals never produce offspring 4 Species produce more offspring than the environment can support 5 Individuals whose characteristics are best suited to the en vironment generally leave more offspring than those whose characteristics are less well suited 6 Only a fraction of an individual s offspring may survive 2 Which of the following observations helped Darwin shape his concept of descent with modi cation 1 Species diversity declines farther from the equator 2 Fewer species live on islands than on the nearest continents 3 Birds can be found on islands located farther from the main land than the birds maximum nonstop ight distance 4 South American temperate plants are more similar to the tropical plants of South America than to the temperate plants of Europe 5 Earthquakes reshape life by causing mass extinctions 1 Level 2 ApplicationAnalysis 3 V1thin six months of effectively using methicillin to treat S aureus infections in a community all new infections were caused by MRSA How can this result best be explained 2 S aureus can resist vaccines 3 A patient must have become infected with MRSA from an other community 4 In response to the drug S aureus began making drug resistant versions of the protein targeted by the drug 5 Some drug resistant bacteria were present at the start of treatment and natural selection increased their frequency 6 The drug caused the S aureus DNA to change 4 The upper forelimbs of humans and bats have fairly similar skeletal structures whereas the corresponding bones in whales have very different shapes and proportions However genetic data suggest that all three kinds of organisms diverged from a common ancestor at about the same time Which of the following is the most likely explanation for these data 1 Humans and bats evolved by natural selection and whales evolved by Lamarckian mechanisms 2 Forelimb evolution was adaptive in people and bats but not in whales 3 Natural selection in an aquatic environment resulted in signi cant changes to whale forelimb anatomy 4 Genes mutate faster in whales than in humans or bats 5 Whales are not properly classi ed as mammals 5 DNA sequences in many human genes are very similar to the sequences of corresponding genes in chimpanzees The most likely explanation for this result is that l humans and chimpanzees share a relatively recent com mon ancestor 2 humans evolved from chimpanzees 3 chimpanzees evolved from humans 4 convergent evolution led to the DNA similarities 5 humans and chimpanzees are not closely related Chapter 23 The Evolution of Population Consider the medium ground nch Geospiza fortis a seed eating bird that inhabits the Galapagos Islands Figure 231 In 1977 the G fortis population on the island of Daphne Major was decimated by a long period of drought Of some 1200 birds only 180 survived Researchers Peter and Rosemary Grant observed that during the drought small soft seeds were in short supply The nches mostly fed on large hard seeds that were more plentiful Birds with larger deeper beaks were better able to crack and eat these larger seeds and they survived at a higher rate than nches with smaller beaks Since beak depth is an in herited trait in these birds the average beak depth in the next generation of G fortis was greater than it had been in the pre drought population Figure 232 The nch population had evolved by natural selection However the individual nches did not evolve Each bird had a beak of a particular size which did not grow larger during the drought Rather the proportion of large beaks in the population increased from generation to gen eration The population evolved not its individual members Focusing on evolutionary change in populations we can de ne evolution on its smallest scale called microevolution as change in allele frequencies in a population over genera tions natural selection is not the only cause of microevolution In fact there are three main mechanisms that can cause allele frequency change natural selection genetic drift chance events that alter allele frequen cies and gene ow the transfer of alleles between popula tions Genetic Variation JCllC LIL V I1 llLlUll Individual variations often re ect genetic variation differences among individuals in the composition of their genes or other DNA segments 0 some phenotypic variation is not heritable Phenotype is the product of an inher ited genotype and many environmental in uences In a human example bodybuilders alter their phenotypes dramati cally but do not pass their huge muscles on to the next genera tion 0 In general only the genetically determined part of phenotypic variation can have evolutionary consequences genetic variation provides the raw material for evolution ary change Without genetic variation evolution cannot occur Variation Within a Population Characters that vary within a population may be discrete or quantitative Discrete characters such as the purple or white ower colors of Mendel s pea plants see Figure 143 can be classi ed on an eitheror basis each plant has owers that are either purple or white Many discrete characters are deter mined by a single gene locus with different alleles that pro duce distinct phenotypes 0 However most heritable variation involves quantitative characters which vary along a contin uum within a population Heritable quantitative variation usually results from the in uence of two or more genes on a single phenotypic character For both discrete and quantitative characters biologists often need to describe how much genetic variation there is in a particular population 0 We can measure genetic variation at the wholegene level gene variability and at the molecular level of DNA nucleotide variability 0 Gene variability can be quanti ed as the average heterozygosity the average per centage of loci that are heterozygous Variation Between Populations In addition to variation observed within a population species also exhibit geographic variation differences in the ge netic composition of separate populations In certain populations some of the chromo somes have become fused However the patterns of fused chromosomes differ from one population to another Because these chromosomelevel changes leave genes intact their phe notypic effects on the mice seem to be neutral Thus the varia tion between these populations appears to have resulted from chance events drift rather than natural selection Other examples of geographic variation occur as a cline a graded change in a character along a geographic axis 0 Clines such as the one depicted in Figure 235 probably result from natural selection otherwise there would be no reason to expect a close association between the envi ronmental variable and the frequency of the allele But selec tion can only operate if multiple alleles exist for a given locus Such variation in alleles can arise in several ways Sources of Genetic Variation The genetic variation on which evolution depends originates when mutation gene duplication or other processes produce new alleles and new genes Many new genetic variants can be produced in short periods of time in organisms that repro duce rapidly Formation of New Alleles new alleles can arise by mutation a change in the nucleotide sequence of an organism s DNA A mutation is like a shot in the dark we cannot predict accurately which segments of DNA will be altered or in what way In multicellular organisms only mutations in cell lines that produce gametes can be passed to offspring But in most animals the majority of mutations occur in somatic cells and are lost when the individual dies A change of as little as one base in a gene called a point mutation can have a signi cant impact on phenotype as in sicklecell disease 0 Organisms re ect thou sands of generations of past selection and hence their pheno types generally provide a close match to their environment As a result it s unlikely that a new mutation that alters a phe notype will improve it In fact most such mutations are at least slightly harmful Also be cause of the redundancy in the genetic code even a point mutation in a gene that encodes a protein will have no effect on the protein s function if the amino acid composition is not changed And even where there is a change in the amino acid it may not affect the protein s shape and function However as will be discussed later in this chapter a mutant allele may on rare occasions actually make its bearer better suited to the environment enhancing reproductive success Altering Gene Number or Position Chromosomal changes that delete disrupt or rearrange many loci at once are usually harmful 0 However when such large scale changes leave genes intact their effects on organisms may be neutral 0 In rare cases chromosomal rearrangements may even be bene cial For example the translocation of part of one chromosome to a different chromosome could link DNA segments in a way that results in a positive effect An important source of variation begins when genes are duplicated due to errors in meiosis such as unequal crossing over slippage during DNA replication or the activities of transposable elements Duplications of large chromosome segments like other chromosomal aberrations are often harmful but the duplication of smaller pieces of DNA may not be Gene duplications that do not have severe effects can persist over generations allowing mu tations to accumulate The result is an expanded genome with new genes that may take on new functions Rapid Reproduction Mutation rates tend to be low in plants and animals averaging about one mutation in every 100000 genes per generation and they are often even lower in prokaryotes But prokaryotes typically have short generation anwm an 11IIfrf1t1rn Ania 1II1r7t7 n3n3 3 rtnmofin 17rvlt1rf1t1 1 rtrIInf1t1an l F flnnnn Av nnnmwm spans so mutations can quickly generate genetic var1at1on1n populations of these or gan1sms The same is true of viruses For instance HIV has a generation span of about two days It also has an RNA genome which has a much higher mutation rate than a typi cal DNA genome because of the lack of RNA repair mecha nisms in host cells see Chapter 19 For this reason it is unlikely that a singledrug treatment would ever be effective against HIV mutant forms of the virus that are resistant to a particular drug would no doubt proliferate in relatively short order The most effective AIDS treatments to date have been drug cocktails that combine several medications It is less likely that multiple mutations conferring resistance to all the drugs will occur in a short time period Sexual Reproduction In organisms that reproduce sexually most of the genetic variation in a population results from the unique combina tion of alleles that each individual receives from its parents Of course at the nucleotide level all the differences among these alleles have originated from past mutations and other processes that can produce new alleles But it is the mecha nism of sexual reproduction that shuf es existing alleles and deals them at random to produce individual genotypes three mechanisms contribute to this shuf ing crossing over independent assortment of chromosomes and fertilization 0 During meiosis homologous chromosomes one inherited from each parent trade some of their alleles by crossing over These homologous chromo somes and the alleles they carry are then distributed at ran dom into gametes The combined effects of these three mechanisms ensure that sexual reproduction rearranges existing alleles into fresh combinations each generation providing much of the genetic variation that makes evolution possible The HardyWeinberg equation can be used to test whether a population is evolving Although the individuals in a population must differ geneti cally for evolution to occur the presence of genetic variation does not guarantee that a population will evolve For that to happen one of the factors that cause evolution must be at work In this section we ll explore one way to test whether evo lution is occurring in a population The rst step in this process is to clarify what we mean by a population Gene Pools and Allele Frequencies A population is a group of individuals of the same species that live in the same area and interbreed producing fertile offspring Different populations of a single species may be iso lated geographically from one another thus exchanging ge netic material only rarely S We can characterize a population s genetic makeup by de scribing its gene pool which consists of all copies of every type of allele at every locus in all members of the population If only one allele exists for a particular locus in a population that allele is said to be xed in the gene pool and all individu als are homozygous for that allele Each allele has a frequency proportion in the population The HardyWeinberg Principle One way to assess whether natural selection or other factors are causing evolution at a particular locus is to determine what the genetic makeup of a population would be if it were not evolving at that locus 0 We can then compare that scenario with data from a real population If there are no differences we can conclude that the real population is not evolving If there are differences this suggests that the real population may be evolving and then we can try to gure out why H ardyWeinberg Equilibrium The gene pool of a population that is not evolving can be de scribed by the HardyWeinberg principle states that the frequencies of alleles and genotypes in a population will remain constant from generation to generation provided that only Mendelian segregation and recombination of alleles are at work Such a gene pool is in HardyWeinberg equilibrium Previously we used Pun nett squares to determine the genotypes of offspring in a ge netic cross see Figure 145 Here instead of considering the possible allele combinations from one cross consider the combination of alleles in all of the crosses in a population 0 Imagine that all the alleles for a given locus from all the indi viduals in a population were placed in a large bin 0 We can think of this bin as holding the population s gene pool for that locus Reproduction occurs by selecting alleles at ran dom from the bin somewhat similar events occur in nature when sh release sperm and eggs into the water or when pollen containing plant sperm is blown about by the wind By view ing reproduction as a process of randomly selecting and com bining alleles from the bin the gene pool we are in effect assuming that mating occurs at random that is that all malefemale matings are equally likely Conditions for H ardyWeinberg Equilibrium The HardyWeinberg principle describes a hypothetical popu lation that is not evolving But in real populations the allele and genotype frequencies often do change over time Such changes can occur when at least one of the following ve conditions of HardyWeinberg equilibrium is not met 0 1 No mutations The gene pool is modi ed if mutations alter alleles or if entire genes are deleted or duplicated O 2 Random mating If individuals mate preferentially within a subset of the population such as their close relatives inbreeding random mixing of gametes does not occur and genotype frequencies change 0 3 No natural selection Differences in the survival and reproductive success of individuals carrying differ ent genotypes can alter allele frequencies 0 4 Extremely large population size The smaller the population the more likely it is that allele frequencies will uctuate by chance from one generation to the next a process called genetic drift 0 5 No gene ow By moving alleles into or out of popula tions gene ow can alter allele frequencies Departure from these conditions usually results in evolu tionary change which as we ve already described is com mon in natural populations quot Applying the H ardyWeinberg Principle The HardyWeinberg equation is often used as an initial test of whether evolution is occurring in a population The equation also has medical applications such as estimating the percentage of a population carrying the allele for an inherited disease To apply the HardyWeinberg equation we must assume that no new PKU mutations are being introduced into the population condition 1 and that people neither choose their mates on the basis of whether or not they carry this gene nor generally mate with close relatives condition 2 We must also ignore any effects of differential survival and reproduc tive success among PKU genotypes condition 3 and assume that there are no effects of genetic drift condition 4 or of gene ow from other populations into the United States con dition 5 Natural selection genetic drift and gene ow can alter allele frequencies in a population Note again the ve conditions required for a population to be in HardyWeinberg equilibrium A deviation from any of these conditions is a potential cause of evolution New muta tions violation of condition 1 can alter allele frequencies but because mutations are rare the change from one genera tion to the next is likely to be very small Nevertheless as we ll see mutation ultimately can have a large effect on allele frequencies when it produces new alleles that strongly in u ence tness in a positive or negative way Nonrandom mat ing violation of condition 2 can affect the frequencies of homozygous and heterozygous genotypes but by itself usu ally has no effect on allele frequencies in the gene pool The three mechanisms that alter allele frequencies directly and cause most evolutionary change are natural selection genetic drift and gene ow violations of conditions 35 Natural Selection Darwin s concept of natural selec tion is based on differential success in survival and reproduc tion Individuals in a population exhibit variations in their heritable traits and those with traits that are better suited to their environment tend to produce more offspring than those with traits that are not as well suited By consistently favoring some alleles over oth ers natural selection can cause adaptive evolution evolution that results in a better match between organisms and their environment Genetic Drift The smaller the number of coin ips the more likely it is that chance alone will cause a devi ation from the predicted result In this case the prediction is an equal number of heads and tails Chance events can also cause allele frequencies to uctuate unpredictably from one generation to the next especially in small populations a process called genetic drift The Founder E ect When a few individuals become isolated from a larger popu lation this smaller group may establish a new population whose gene pool differs from the source population this is called the founder effect The founder effect might occur for example when a few members of a population are blown by a storm to a new island Genetic drift in which chance events alter allele frequencies will occur in such a case if the storm indiscriminately transports some individuals and their alleles but not others from the source population The founder effect probably accounts for the relatively high frequency of certain inherited disorders among iso lated human populations The Bottleneck E ect A sudden change in the environment such as a re or ood may drastically reduce the size of a population A severe drop in population size can cause the bottleneck effect so named because the population has passed through a bottle neck that reduces its size By chance alone certain alleles may be overrepresented among the survivors others may be underrepresented and some may be absent al together Ongoing genetic drift is likely to have substantial effects on the gene pool until the population becomes large enough that chance events have less impact But even if a population that has passed through a bottleneck ultimately recovers in size it may have low levels of genetic variation for a long period of time a legacy of the genetic drift that occurred when the population was small E ects of Genetic Drift A Summary o Genetic drift is signi cant in small populations Chance events can cause an allele to be disproportion ately over or underrepresented in the next generation Although chance events occur in populations of all sizes they tend to alter allele frequencies substantially only in small populations o Genetic drift can cause allele frequencies to change at random Because of genetic drift an allele may increase in frequency one year then decrease the next the change from year to year is not predictable Thus unlike natural selection which in a given environment consistently favors some alleles over others genetic drift causes allele frequencies to change at random overtime Genetic drift can lead to a loss of genetic variation within populations By causing allele frequencies to uc tuate randomly overtime genetic drift can eliminate alleles from a population Because evolution depends on genetic variation such losses can in uence how effectively a popula tion can adapt to a change in the environment Genetic drift can cause harmful alleles to become xed Alleles that are neither harmful nor bene cial can be lost or become xed entirely by chance through genetic drift In very small populations genetic drift can also cause alleles that are slightly harmful to become xed When this occurs the population s survival can be threatened as for the greater prairie chicken Gene Flow Natural selection and genetic drift are not the only phenom ena affecting allele frequencies Allele frequencies can also change by gene ow the transfer of alleles into or out of a population due to the movement of fertile individuals or their gametes Because alleles are exchanged between populations gene ow tends to reduce the genetic differences between populations In fact if it is extensive enough gene ow can result in two populations combining into a single population with a common gene pool Alleles transferred by gene ow can also affect how well populations are adapted to local environmental conditions Gene ow can also transfer alleles that improve the ability of populations to adapt to local conditions For example gene ow has resulted in the worldwide spread of several insecticide resistance alleles in the mosquito Calex pipiens a vector of West Nile virus and other diseases Each of these alleles has a unique genetic signature that allowed researchers to docu ment that it arose by mutation in one or a few geographic lo cations I In their population of origin these alleles increased because they provided insecticide resistance These alleles were then transferred to new populations where again their frequencies increased as a result of natural selection ene ow has become an increasingly important agent of evolutionary change in human populations Hu mans today move much more freely about the world than in the past As a result mating is more common between mem bers of populations that previously had very little contact leading to an exchange of alleles and fewer genetic differ ences between those populations Natural selection is the only mechanism that consistently causes adaptive evolution Evolution by natural selection is a blend of chance and sorting chance in the creation of new genetic variations as in mutation and sorting as natural selection favors some alleles over others Because of this favoring process the out come of natural selection is not random Instead natural se lection consistently increases the frequencies of alleles that provide reproductive advantage and thus leads to adaptive evolution In examining how natural selection brings about adaptive evolution we ll begin with the concept of relative tness and the different ways that an organism s phenotype is subject to natural selection Relative Fitness The phrases struggle for existence and survival of the ttest are commonly used to describe natural selection but these expressions are misleading if taken to mean direct com petitive contests among individuals But reproduc tive success is generally more subtle and depends on many factors besides outright battle 0 For example a barnacle that is more ef cient at collecting food than its neighbors may have greater stores of energy and hence be able to produce a larger number of eggs certain traits can lead to greater relative tness the contribution an in dividual makes to the gene pool of the next generation relative to the contributions of other individuals Directional Disruptive and Stabilizing Selection Natural selection can alter the frequency distribution of heri table traits in three ways depending on which phenotypes in a population are favored Directional selection occurs when conditions favor individuals exhibiting one extreme of a phenotypic range thereby shifting a population s frequency curve for the phenotypic character in one direction or the other Figure 23l3a Directional selection is common when a population s environment changes or when members of a population migrate to a new and different habitat For instance an increase in the relative abundance of large seeds over small seeds led to an increase in beak depth in a population of Galapagos nches see Figure 232 Disruptive selection Figure 2313b occurs when con ditions favor individuals at both extremes of a phenotypic range over individuals with intermediate phenotypes One ex ample is a population of black bellied seedcracker nches in Cameroon whose members display two distinctly different beak sizes Small billed birds feed mainly on soft seeds whereas largebilled birds specialize in cracking hard seeds It appears that birds with intermediatesized bills are relatively inef cient at cracking both types of seeds and thus have lower relative tness Stabilizing selection Figure 2313c acts against both extreme phenotypes and favors intermediate variants This mode of selection reduces variation and tends to maintain the status quo for a particular phenotypic charac ter For example the birth weights of most human babies lie in the range of 34 kg 66 88 pounds babies who are either much smaller or much larger suffer higher rates of mortality The Key Role of Natural Selection in Adaptive Evolution Such adaptations can arise gradually over time as natural selection increases the frequencies of alleles that enhance survival and reproduction As the proportion of individuals that have favorable traits increases the match between a species and its environment improves that is adaptive evo lution occurs However as we saw in Chapter 22 the physical and biological components of an organism s environment may change over time As a result what constitutes a good match between an organism and its environment can be a moving target making adaptive evolution a continuous dy namic process Sexual Selection sexual selection a form of selection in which individuals with certain inherited characteristics are more likely than other individuals to obtain mates Sexual selection can result in sexual dimorphism a difference between the two sexes in secondary sexual characteristics Figure 2315 These dis tinctions include differences in size color ornamentation and behavior In intrasexual selection meaning selection within the same sex individuals of one sex compete directly for mates of the opposite sex 0 In many species intrasexual selection oc curs among males For example a single male may patrol a group of females and prevent other males from mating with them The patrolling male may defend his status by defeating smaller weaker or less erce males in combat Y AI IA l llJ 4 z1z39 1 JZZ J l L ll 41 L l L 1 In intersexual selection also called mate choice individ uals of one sex usually the females are choosy in selecting their mates from the other sex In many cases the female s choice depends on the showiness of the male s appearance or behavior The Preservation of Genetic Variation Some of the genetic variation in populations represents neutral variation differences in DNA sequence that do not confer a selective advantage or disadvantage But varia tion is also found at loci affected by selection The tendency for direc tional and stabilizing selection to reduce variation is coun tered by mechanisms that preserve or restore it Diploidy In diploid eukaryotes a considerable amount of genetic variation is hidden from selection in the form of recessive alleles Recessive alleles that are less favorable than their dominant counterparts or even harmful in the current en vironment can persist by propagation in heterozygous indi viduals This latent variation is exposed to natural selection only when both parents carry the same recessive allele and two copies end up in the same zygote This happens only rarely if the frequency of the recessive allele is very low Het erozygote protection maintains a huge pool of alleles that might not be favored under present conditions but which could bring new bene ts if the environment changes Balancing Selection Selection itself may preserve variation at some loci Balancing selection occurs when natural selection maintains two or more forms in a population This type of selection includes het erozygote advantage and frequencydependent selection Heterozygote Advantage I ndividualswhoareheterozygous at a particular locus have greater tness than do both kinds of homozygotes they exhibit heterozygote advantage In such a case natural selection tends to maintain two or more al leles at that locus 0 Note that heterozygote advantage is de ned in terms of genotype not phenotype Thus whether heterozy gote advantage represents stabilizing or directional selection depends on the relationship between the genotype and the phenotype For example if the phenotype of a heterozygote is intermediate to the phenotypes of both homozygotes het erozygote advantage is a form of stabilizing selection heterozygote advantage occurs at the locus in humans that codes for the b polypeptide subunit of hemo globin the oxygencarrying protein of red blood cells In ho mozygous individuals a certain recessive allele at that locus causes sicklecell disease The red blood cells of people with sicklecell disease become distorted in shape or sickled under low oxygen conditions see Figure 521 as occurs in the cap illaries These sickled cells can clump together and block the ow of blood in the capillaries resulting in serious damage to organs such as the kidney heart and brain Although some red blood cells become sickled in heterozygotes not enough become sickled to cause sicklecell disease Heterozygotes for the sicklecell allele are protected against the most severe effects of malaria a disease caused by a parasite that infects red blood cells see Figure 2810 This partial protection occurs because the body destroys sickled red blood cells rapidly killing the parasites they harbor but not affecting parasites inside normal red blood cells Protec tion against malaria is important in tropical regions where the disease is a major killer FrequencyDependent Selection In frequencydependent selection the tness of a phenotype depends on how com mon it is in the population Consider the scaleeating sh Perissodus microlepis of Lake Tanganyika in Africa These sh attack other sh from behind darting in to remove a few scales from the ank of their prey Why Natural Selection Cannot Fashion Perfect Organisms Though natural selection leads to adaptation nature abounds with examples of organisms that are less than ideally engi neered for their lifestyles There are several reasons why 1 Selection can act only on existing variations Natural selection favors only the ttest phenotypes among those currently in the population which may not be the ideal traits New advantageous alleles do not arise on demand 2 Evolution is limited by historical constraints Each species has a legacy of descent with modi cation from ancestral forms Evolution does not scrap the ancestral anatomy and build each new complex structure from scratch rather evolution coopts existing structures and adapts them to new situations We could imagine that if a terrestrial animal were to adapt to an environ ment in which ight would be advantageous it might be best just to grow an extra pair of limbs that would serve as wings However evolution does not work this way in stead it operates on the traits an organism already has Thus in birds and bats an existing pair of limbs took on new functions for ight as these organisms evolved from non ying ancestors 3 Adaptations are often compromises Each organ ism must do many different things A seal spends part of its time on rocks it could probably walk better if it had legs instead of ippers but then it would not swim nearly as well We humans owe much of our versatility and ath leticism to our prehensile hands and exible limbs but these also make us prone to sprains torn ligaments and dislocations Structural reinforcement has been compro mised for agility Figure 2319 depicts another example of evolutionary compromise 4 Chance natural selection and the environment interact Chance events can affect the subsequent evolu tionary history of populations For instance when a storm blows insects or birds hundreds of kilometers over an ocean to an island the wind does not necessarily transport those individuals that are best suited to the new environ ment Thus not all alleles present in the founding popula tion s gene pool are better suited to the new environment than the alleles that are left behind In addition the en vironment at a particular location may change unpre dictably from year to year again limiting the extent to which adaptive evolution results in a close match between the organism and current environmental conditions With these four constraints evolution does not tend to craft perfect organisms Natural selection operates on a bet ter than basis We can in fact see evidence for evolution in the many imperfections of the organisms it produces LEVEL 1 KNOWLEDGECOMPREHENSION 1 Natural selection changes allele frequencies because some survive and reproduce more successfully than others a alleles c gene pools e individuals b loci d species 2 No two people are genetically identical except for identical twins The main source of genetic variation among human in dividuals is a new mutations that occurred in the preceding generation b genetic drift due to the small size of the population c the reshuf ing of alleles in sexual reproduction d geographic variation within the population e environmental effects 3 Sparrows with average sized wings survive severe storms bet ter than those with longer or shorter wings illustrating a the bottleneck effect b disruptive selection c frequency dependent selection d neutral variation e stabilizing selection 4If the nucleotide variability of a locus equals 0 what is the gene variability and number of alleles at that locus 1 gene variability 0 number of alleles 0 2 gene variability 0 number of alleles 1 3 gene variability 0 number of alleles 2 4 gene variability 0 number of alleles 2 5 Without more information gene variability and number of alleles cannot be determined 5There are 40 individuals in population 1 all with genotype A1A1 and there are 25 individuals in population 2 all with genotype A2A2 Assume that these populations are located far from each other and that their environmental conditions are very similar Based on the information given here the ob served genetic variation is most likely an example of a genetic drift b gene ow c disruptive selection d discrete variation e directional selection 6 A fruit y population has a gene with two alleles AI and A2 Tests show that 70 of the gametes produced in the population contain the A allele If the population is in Hardy Weinberg equilibrium what proportion of the ies carry both A and A2 a 07 b 049 c 021 d 042 e 009 Chapter 24 The Origin of Species That Mystery of Mysteries 0 The mystery of mysteries that captivated Darwin is Speciation the process by which one species splits into two or more species Speciation explains not only differences between species but also similarities between them the unity of life When one species splits into two the species that result share many characteristics because they are descended from this common ancestral species Speciation also forms a conceptual bridge between microevolution changes over time in allele frequencies in a population and macroevolution the broad pattern of evolution above the species level The biological species concept emphasizes reproductive isolation biologists compare not only the morphology body form of different groups of organisms but also less obvious differences in physiology biochemistry and DNA sequences The results generally con rm that mor phologically distinct species are indeed discrete groups dif fering in many ways besides their body forms The Biological Species Concept The primary de nition of species used in this textbook is the biological species concept According to this concept a species is a group of populations whose members have the potential to interbreed in nature and produce viable fertile offspring but do not produce viable fertile offspring with members of other such groups Typically gene ow occurs between the different popula tions of a species This ongoing exchange of alleles tends to hold the populations together genetically Reproductive Isolation Because biological species are de ned in terms of reproduc tive compatibility the formation of a new species hinges on reproductive isolation the existence of biological fac tors barriers that impede members of two species from interbreeding and producing viable fertile offspring Such barriers block gene ow between the species and limit the formation of hybrids offspring that result from an inter speci c mating Although a single barrier may not prevent all gene ow a combination of several barriers can effectively isolate a species gene pool These barriers can be classi ed according to whether they contribute to reproductive isolation before or after fertilization Prezygotic barriers before the zy gote block fertilization from occurring Such barriers typi cally act in one of three ways by impeding members of different species from attempting to mate by preventing an attempted mating from being completed successfully or by hindering fertilization if mating is completed successfully If a sperm cell from one species overcomes prezygotic barriers and fertilizes an ovum from another species 41 nminrn l F Irtc1l39rIt7A1tl391 I nan 1 3 flan r I7rtf13 1vnt7 rt1rfw IIf13 n 3nnlnnn3 ntnft1a 1 3 flan a variety of postzygotic barriers quotafter the zygote may contribute to reproductive isolation after the hybrid zygote is formed Habitat Isolation 0 Two species that occupy differ ent habitats within the same area may encounter each other rarely if at all even though they are not isolated by obvious physical barriers such as moun tain ranges Temporal Isolation Species that breed during differ ent times of the day different seasons or different years can not mix their gametes Behavioral Isolation Courtship rituals that attract mates and other behaviors unique to a species are effective reproductive barriers even be tween closely related species Such behavioral rituals enable mate rec0gniti0n a way to identify potential mates of the same species Mechanical Isolation Mating is attempted but mor phological differences prevent its successful completion Gametic Isolation Sperm of one species may not be able to fertilize the eggs of another species For instance sperm may not be able to sur vive in the reproductive tract of females of the other species or biochemical mechanisms may prevent the sperm from penetrating the membrane surrounding the other species eggs Reduced Hybrid Viability The genes of different parent species may interact in ways that impair the hybrid s devel opment or survival in its environment Reduced Hybrid Fertility Even if hybrids are vigorous they may be sterile If the chro mosomes of the two parent species differ in number or structure meiosis in the hybrids may fail to produce normal gametes Since the infertile hy brids cannot produce offspring when they mate with either par ent species genes cannot ow freely between the species Hybrid Breakdown Some rst generation hybrids are viable and fertile but when they mate with one another or with either parent species off spring of the next generation are feeble or sterile Limitations of the Biological Species Concept However the number of species to which this concept can be usefully applied is lim ited There is for example no way to evaluate the reproduc tive isolation of fossils The biological species concept also does not apply to organisms that reproduce asexually all or most of the time such as prokaryotes Further more in the biological species concept species are designated by the absence of gene ow But there are many pairs of species that are morphologically and ecologically distinct and yet gene ow occurs between them grizzly and polar bear 0 This observation has led some researchers to argue that the biological species concept overemphasizes gene ow and downplays the role of natural selection Because of the limita tions to the biological species concept alternative species con cepts are useful in certain situations Other De nitions of Species While the biological species concept emphasizes the separateness of species from one another due to reproductive barriers several other de nitions emphasize the unity within a species For exam ple the morphological species concept characterizes a species by body shape and other structural features characterizes a species by body shape and other structural features The mor phological species concept can be applied to asexual and sexual organisms and it can be useful even without information on the extent of gene ow The ecological species concept views a species in terms of its ecological niche the sum of how members of the species interact with the nonliving and living parts of their environment The phylogenetic species concept de nes a species as the smallest group of individuals that share a common ances tor forming one branch on the tree of life Speciation can take place with or without geographic separation Allopatric Other Country Speciation In allopatric speciation from the Greek allos other and patra homeland gene flow is interrupted when a popula tion is divided into geographically isolated subpopulations For example the water level in a lake may subside resulting in two or more smaller lakes that are now home to separated populations Al lopatric speciation can also occur without geologic remodel ing such as when individuals colonize a remote area and their descendants become geographically isolated from the parent population The Process of Allopatric S peciation 0 How formidable must a geographic barrier be to promote al lopatric speciation The answer depends on the ability of the organisms to move about B Once geographic separation has occurred the separated gene pools may diverge Different mutations arise and natu ral selection and genetic drift may alter allele frequencies in different ways in the separated populations Reproductive isolation may then arise as a byproduct of selection or drift having caused the populations to diverge genetically Thus as a byproduct of selection for avoiding predators reproductive barriers have started to form in these allopatric populations Evidence of Allopatric Speciation Many studies provide evidence that speciation can occur in allopatric populations The importance of allopatric speciation is also suggested by the fact that regions that are isolated or highly subdivided by barriers typically have more species than do otherwise similar regions that lack such features For example many unique plants and animals are found on the geographically isolated Hawaiian Islands Laboratory and eld tests also provide evidence that repro ductive isolation between two populations generally increases as the distance between them increases We need to emphasize here that although geographic iso lation prevents interbreeding between allopatric populations physical separation is not a biological barrier to reproduc tion Biological reproductive barriers such as those described in Figure 243 are intrinsic to the organisms themselves Hence it is biological barriers that can prevent interbreeding when members of different populations come into contact with one another Sympatric Same Country Speciation In sympatric speciation from the Greek syn together speciation occurs in populations that live in the same geo graphic area Although such contact and the ongo ing gene ow that results makes sympatric speciation less common than allopatric speciation sympatric speciation can occur if gene ow is reduced by such factors as polyploidy habitat differentiation and sexual selection Note that these factors can also promote allopatric speciation Polyploidy species may originate from an accident during cell division that results in extra sets of chromosomes a condition called polyploidy Polyploid speciation occasionally occurs in animals for example the gray tree frog Hyla versicolor see Figure 2316 is thought to have originated in this way How ever polyploidy is far more common in plants Two distinct forms of polyploidy have been observed in plant and a few animal populations An autopolyploid from the Greek autos self is an individual that has more than two chromosome sets that are all derived from a single species In plants for example a failure of cell di vision could double a cell s chromosome number from the diploid number 2n to a tetraploid number 4n A second form of polyploidy can occur when two differ ent species interbreed and produce hybrid offspring Most such hybrids are sterile because the set of chromosomes from one species cannot pair during meiosis with the set of chromosomes from the other species However an infertile hybrid may be able to propagate itself asexually as many plants can do In subsequent generations various mecha nisms can change a sterile hybrid into a fertile polyploid called an allopolyploid Figure 2411 The allopolyploids are fertile when mating with each other but cannot inter breed with either parent species thus they represent a new biological species Many important agricultural crops such as oats cotton potatoes tobacco and wheat are polyploids Habitat Dijferentiation Sympatric speciation can also occur when genetic factors en able a subpopulation to exploit a habitat or resource not used by the parent population Sexual Selection There is evidence that sympatric speciation can also be driven by sexual selection One hypothesis is that subgroups of the original cichlid populations adapted to different food sources and that the re sulting genetic divergence contributed to speciation in Lake Victoria But sexual selection in which typically females se lect males based on their appearance see Chapter 23 may also have been a factor Their re sults suggest that mate choice based on male breeding col oration is the main reproductive barrier that normally keeps the gene pools of these two species separate Hybrid zones reveal factors that cause reproductive isolation What happens if species with incomplete reproductive barri ers come into contact with one another One possible out come is the formation of a hybrid zone a region in which members of different species meet and mate producing at least some offspring of mixed ancestry Patterns Within Hybrid Zones What causes such a pattern of allele frequencies across a hy brid zone We can infer that there is an obstacle to gene ow otherwise alleles from one parent species would also be common in the gene pool of the other parent species Because the hybrids have poor survival and reproduction they produce few viable offspring with members of the parent species As a result hybrid individuals rarely serve as a steppingstone from which alleles are passed from one species to the other Outside the hybrid zone additional obstacles to gene ow may be provided by natural selection in the different environments in which the parent species live Hybrid Zones over Time Reproductive barriers between species may be reinforced over time limiting the formation of hybrids or weakened over time causing the separating species to fuse into one species Or hybrids may continue to be produced creating a longterm and stable hybrid zone Let s examine what studies in the eld suggest about these three possibilities Reinforcement Strengthening Reproductive Barriers When hybrids are less t than members of their parent species as in the Bombina example we might expect natural selection to strengthen prezygotic barriers to reproduction thus reducing the formation of un t hybrids Because this process involves reinforcing reproductive barriers it is called reinforcement O logical prediction is that barriers to reproduction between species should be stronger for sym patric populations than for allopatric populations Fusion Weakening Reproductive Barriers Next let s consider the case in which two species contact one another in a hybrid zone but the barriers to reproduction are not strong So much gene flow may occur that reproductive barriers weaken further and the gene pools of the two species become increasingly alike In ef fect the speciation process reverses eventually causing the two hybridizing species to fuse into a single species Stability Continued Formation of Hybrid Individuals Many hybrid zones are stable in the sense that hybrids con tinue to be produced In some cases this occurs because the hybrids survive or reproduce better than members of either parent species at least in certain habitats or years But stable hybrid zones have also been observed in cases where the hy brids are selected against an unexpected result In short sometimes the outcomes in hybrid zones match our predictions events in hybrid zones can shed light on how barriers to reproduction between closely related species change g v Anna 111 1 L11 L IJJ11Ll tax gtJ11A Axbxnv I11 11I vv Luc111Au I 1 tl1JrIrII 1J11 Lvvv 11 1JgtJ17 11A A gtJtI1gtJ Anucxnbv over time Speciation can occur rapidly or slowly and can result from changes in few or many genes For example how long does it take for new species to form And how many genes change when one species splits into two Answers to these questions are also beginning to emerge The Time Course of Speciation We can gather information about how long it takes new species to form from broad patterns in the fossil record and from studies that use morphological data including fossils or molecular data to assess the time interval between specia tion events in particular groups of organisms Patterns in the Fossil Record coined the term punctuated equilibria to describe these periods of apparent stasis punc tuated by sudden change Other species do not show a punctuated pattern instead they change more gradually over long periods of time What do punctuated and gradual patterns tell us about how long it takes new species to form Suppose that a species survived for 5 million years but most of the morphological changes that caused it to be designated a new species occurred during the rst 50000 years of its existence just 1 of its total lifetime S peciation Rates The punctuated pattern suggests that once the process of speciation begins it can be completed relatively rapidly a suggestion supported by a growing number of studies Unlike the out come of allopolyploid speciation in which there is a change in chromosome number after hybridization in these sun ow ers the two parent species and the hybrid all have the same number of chromosomes 211 34 How then did speciation occur To answer this question the researchers performed an xperiment designed to mimic events in nature 0 Their results indicated that natural selection could produce extensive genetic changes in hybrid populations over short periods of time These changes appear to have caused the hybrids to diverge reproductively from their parents and form a new species H anomalus Studying the Genetics of Speciation Studies of ongoing speciation as in hybrid zones can reveal traits that cause reproductive isolation By identifying the genes that control those traits scientists can explore a funda mental question of evolutionary biology How many genes change when a new species forms In other organisms the speciation process is in uenced by larger numbers of genes and gene interactions From Speciation to Macroevolution However as specia tion occurs again and again such differences can accumulate and become more pronounced eventually leading to the for mation of new groups of organisms that differ greatly from their ancestors as in the origin of whales from landdwelling mammals see Figure 2220 Furthermore as one group of or ganisms increases in size by producing many new species another group of organisms may shrink losing species to ex tinction The cumulative effects of many such speciation and extinction events have helped shape the sweeping evolution ary changes that are documented in the fossil record In the next chapter we turn to such largescale evolutionary changes as we begin our study of macroevolution 1 LEVEL 1 KNOWLEDGECOMPREHENSION 1 The largest unit within which gene ow can readily occur is a a population b species c genus d hybrid e phylum Allopatric speciation Sympatric speciation 2 Males of different species of the fruit y Drosophila that live in the same parts of the Hawaiian Islands have different elaborate courtship rituals These rituals involve ghting other males and making stylized movements that attract females What type of reproductive isolation does this represent a habitat isolation b temporal isolation c behavioral isolation d gametic isolation e postzygotic barriers 3 According to the punctuated equilibria model natural selection is unimportant as a mechanism of evolution given enough time most existing species will branch grad ually into new species most new species accumulate their unique features rela tively rapidly as they come into existence then change little for the rest of their duration as a species most evolution occurs in sympatric populations speciation is usually due to a single mutation LEVEL 2 APPLICATIONANALYSIS 4 Bird guides once listed the myrtle Warbler and Audubon s war bler as distinct species Recently these birds have been classi ed as eastern and western forms of a single species the yellow rumped Warbler Which of the following pieces of evi dence if true would be cause for this reclassi cation 1 Thetwoformsinterbreedofteninnatureandtheiroff spring have good survival and reproduction The two forms live in similar habitats The two forms have many genes in common The two forms have similar food requirements The two forms are very similar in coloration PP quot 5 Which of the following factors would not contribute to al lopatric speciation 2 A population becomes geographically isolated from the parent population 3 4 The separated population is small and genetic drift occurs The isolated population is exposed to different selection pressures than the ancestral population 5 Different mutations begin to distinguish the gene pools of the separated populations 6 Gene ow between the two populations is extensive 6 Plant species A has a diploid number of 12 Plant species B has a diploid number of 16 A new species C arises as an allopolyploid from A and B The diploid number for species C would probably be a 12 b 14 c 16 d 28 e 56 LEVEL 3 SYNTHESISEVALUATION 7 Suppose that a group of male pied ycatchers migrated from a region where there were no collared ycatchers to a region where both species were present see Figure 2415 Assuming events like this are Very rare which of the following scenarios is least likely 2 3 4 5 The frequency of hybrid offspring would increase Migrant pied males would produce fewer offspring than would resident pied males Pied females would rarely mate with collared males Migrant males would mate with collared females more often than with pied females The frequency of hybrid offspring would decrease Chapter 25 The History of Life on Earth Lost Worlds In this land of extreme cold where there is almost no liquid water life is sparse and small the largest fully terrestrial animal is a y that is 5 mm long But even as early Antarctic explorers strug gled to survive some of them made an astonishing discovery fossil evidence that life once thrived where it now barely ex ists Fossils reveal that 500 million years ago the ocean waters surrounding Antarctica were warm and teeming with tropical invertebrates Later the continent was covered in forests for hundreds of millions of years Fossils discovered in other parts of the world tell a similar if not quite as surprising story Past organisms were very differ ent from those presently living The sweeping changes in life on Earth as revealed by fossils illustrate macroevolution the broad pattern of evolution above the species level 0 Examples of macroevolutionary change include the emergence of terres trial vertebrates through a series of speciation events the im pact of mass extinctions on the diversity of life and the origin of key adaptations such as ight in birds Conditions on early Earth made the origin of life possible Direct evidence of life on early Earth comes from fossils of micro organisms that are about 35 billion years old Observations and experi ments in chemistry geology and physics have led scientists to propose one scenario that we ll examine here They hypothe size that chemical and physical processes on early Earth aided by the emerging force of natural selection could have pro duced very simple cells through a sequence of four main stages 1 The abiotic nonliving synthesis of small organic mol ecules such as amino acids and nitrogenous bases 2 The joining of these small molecules into macromol ecules such as proteins and nucleic acids 3 The packaging of these molecules into protocells droplets with membranes that maintained an internal chemistry different from that of their surroundings 4 The origin of selfreplicating molecules that eventually made inheritance possible Synthesis of Organic Compounds on Early Earth There is scienti c evidence that Earth and the other planets of the solar system formed about 46 billion years ago con densing from a vast cloud of dust and rocks that surrounded the young sun The collisions from meterorites generated enough heat to vaporize the available water and prevent seas from forming This early phase likely ended about 4239 billion years ago The first atmosphere was probably thick with water vapor along with various compounds released by volcanic eruptions in cluding nitrogen and its oxides carbon dioxide methane ammonia hydrogen and hydrogen sulfide As Earth cooled the water vapor condensed into oceans and much of the hy drogen escaped into space During the 19205 Russian chemist A I Oparin and British scientist J B S Haldane independently hypothesized that Earth s early atmosphere was a reducing electronadding en vironment in which organic compounds could have formed from simpler molecules The energy for this organic synthesis could have come from lightning and intense UV radiation Haldane suggested that the early oceans were a solution of organic molecules a primitive soup from which life arose Stanley Miller Harold Urey tested the Oparin Haldane hypothesis by creating laboratory conditions compa rable to those that scientists at the time thought existed on early Earth see Figure 42 His apparatus yielded a variety of amino acids found in organisms today along with other or ganic compounds 0 However it is unclear whether the atmosphere of early Earth contained enough methane and ammonia to be reducing 0 Some evidence suggests that the early atmosphere was made up primarily of nitrogen and carbon dioxide and was neither re ducing nor oxidizing electronremoving 0 Recent MillerUrey type experiments using such neutral atmospheres have also produced organic molecules MillerUreytype experiments demonstrate that the abiotic synthesis of organic molecules is possible under various as sumptions about the composition of the early atmosphere A second source of organic molecules may have been meteorites o rocks that are l 2 carbon compounds by mass Fragments of the Murchison meteorite a 45 billionyearold chondrite that fell to Australia in 1969 contain more than 80 amino acids some in large amounts These amino acids can not be contaminants from Earth because they consist of an equal mix of D and L isomers o Organisms make and use only L isomers with a few rare exceptions Recent studies have shown that the Murchison meteorite also con tained other key organic molecules including lipids simple sugars and nitrogenous bases such as uracil Abiotic Synthesis of Macromolecules The presence of small organic molecules such as amino acids and nitrogenous bases is not sufficient for the emergence of life as we know it Every cell has a vast assortment of macro molecules including enzymes and other proteins and the nu cleic acids that are essential for selfreplication Could such macromolecules have formed on early Earth A 2009 study demonstrated that one key step the abiotic synthesis of RNA monomers can occur spontaneously from simple precursor molecules 0 In addition by dripping solutions of amino acids or RNA nucleotides onto hot sand clay or rock researchers have produced polymers of these molecules 0 The polymers formed spontaneously without the help of enzymes or ribo somes 0 Unlike proteins the amino acid polymers are a com plex mix of linked and crosslinked amino acids 0 Nevertheless it is possible that such polymers may have acted as weak cata lysts for a variety of chemical reactions on early Earth Protocells All organisms must be able to carry out reproduction and en ergy processing metabolism Life cannot persist without both of these functions DNA molecules carry genetic information including the instructions needed to replicate themselves ac curately during reproduction But the replication of DNA re quires elaborate enzymatic machinery along with a copious supply of nucleotide building blocks that are provided by the cell s metabolism This suggests that self replicating molecules and a metabolismlike source of the building blocks may have appeared together in early proto cells The necessary conditions may have been met in vesicles uidfilled compartments bounded by a membrane like struc ture 0 Recent experiments show that abiotically produced vesi cles can exhibit certain properties of life including simple reproduction and metabolism as well as the maintenance of an internal chemical environment different from that of their surroundings o vesicles can form spontaneously when lipids or other organic molecules are added to water When this oc curs the hydrophobic molecules in the mixture organize into a bilayer similar to the lipid bilayer of a plasma membrane Adding substances such as montmorillonite a soft mineral clay produced by the weathering of volcanic ash greatly increases the rate of vesicle selfassembly This clay which is thought to have been common on early Earth provides sur faces on which organic molecules become concentrated in creasing the likelihood that the molecules will react with each other and form vesicles 0 Abiotically produced vesicles can re produce on their own and they can increase in size grow without dilution of their contents Vesicles also can absorb montmorillonite particles including those on which RNA and other organic molecules have become attached Finally experiments have shown that some vesicles have a selectively permeable bilayer and can perform metabolic reactions using an external source of reagents another important prerequisite for life SelfReplicating RNA and the Dawn of Natural Selection The first genetic material was most likely RNA not DNA Thomas Cech of the University of Colorado and Sidney Altman of Yale University found that RNA which plays a central role in protein synthesis can also carry out a number of enzymelike catalytic functions 0 Cech called these RNA catalysts ribozymes Some ribozymes can make comple mentary copies of short pieces of RNA provided that they are supplied with nucleotide building blocks Natural selection on the molecular level has produced ri bozymes capable of selfreplication in the laboratory 0 Unlike doublestranded DNA which takes the form of a uniform helix singlestranded RNA molecules as sume a variety of speci c threedimensional shapes mandated by their nucleotide sequences In a particular environment 0 RNA molecules with certain base sequences are more stable and replicate faster and with fewer errors than other se quences o The RNA molecule whose sequence is best suited to the surrounding environment and has the greatest ability to replicate itself will leave the most descendant molecules A vesicle with selfreplicating catalytic RNA would differ from its many neighbors that did not carry RNA or that car ried RNA without such capabilities If that vesicle could grow split and pass its RNA molecules to its daughters the daugh ters would be protocells that had some of the properties of their parent The most successful of the early protocells would have increased in number be cause they could exploit their resources effectively and pass their abilities on to subsequent generations Once RNA sequences that carried genetic information ap peared in protocells many further changes would have been possible For example RNA could have provided the template on which DNA nucleotides were assembled Doublestranded DNA is a more stable repository for genetic information than the more fragile singlestranded RNA 0 DNA also can be repli cated more accurately Accurate replication was advantageous as genomes grew larger through gene duplication and other processes and as more properties of the protocells became coded in genetic information 0 After DNA appeared perhaps RNA molecules began to take on their presentday roles as reg ulators and intermediates in the translation of genes The stage was now set for a blossoming of diverse lifeforms a change we see documented in the fossil record The fossil record documents the history of life The Fossil Record As a result the fossil record is based prima rily on the sequence in which fossils have accumulated in sedimentary rock layers called strata see Figure 223 Useful information is also provided by other types of fossils such as insects preserved in amber fossilized tree sap and mammals frozen in ice Of those fos sils that were formed many were destroyed by later geologic processes and only a fraction of the others have been discov ered As a result the known fossil record is biased in favor of species that existed for a long time were abundant and wide spread in certain kinds of environments and had hard shells skeletons or other parts that facilitated their fossilization Even with its limitations however the fossil record is a re markably detailed account of biological change over the vast scale of geologic time Furthermore as shown by the recently unearthed fossils of whale ancestors with hind limbs see Figures 2219 and 2220 gaps in the fossil record continue to be lled by new discoveries How Rocks and Fossils Are Dated How can we determine the absolute age of a fossil Note that absolute dating does not mean errorless dating but only that an age is given in years rather than relative terms such as before and after One of the most common techniques is radiometric dating which is based on the decay of ra dioactive isotopes see Chapter 2 In this process a radioac tive parent isotope decays to a daughter isotope at a fixed rate The rate of decay is expressed by the halflife the time required for 50 of the parent isotope to decay 0 Each type of radioactive isotope has a characteristic halflife which is not affected by temperature pressure or other envi ronmental variables For example carbonl4 decays relatively quickly it has a halflife of 5730 years Uranium238 decays slowly its halflife is 45 billion years For example a living or ganism contains the most common carbon isotope carbon 12 as well as a radioactive isotope carbonl4 When the organism dies it stops accumulating carbon and the amount of carbonl2 in its tissues does not change over time However the carbonl4 that it contains at the time of death slowly decays into another element nitrogenl4 Thus by measuring the ratio of carbonl4 to carbon l2 in a fossil we can determine the fossil s age 0 This method works for fossils up to about 75000 years old fossils older than that contain too little car bonl4 to be detected with current techniques Radioactive isotopes with longer halflives are used to date older fossils Determining the age of these older fossils in sedimentary rocks is challenging Organisms do not use radioisotopes with long halflives such as uranium23 8 to build their bones or shells Moreover the sedimentary rocks themselves tend to consist of sediments of differing ages The Origin of New Groups of Organisms Along with amphibians and reptiles mammals belong to the group of animals called tetrapods from the Greek tetra four and pad foot named for having four limbs o Mammals have a number of unique anatomical features that fossilize readily allowing scientists to trace their origin As detailed in Figure 256 the fossil record shows that the unique features of mammalian jaws and teeth evolved gradu ally over time in a series of steps Some of these fossils would re ect how the features of a group that dominates life today the mammals gradually arose in a previously existing group the cynodonts Others would reveal side branches on the tree of life groups of organisms that thrived for millions of years but ultimately left no descendants that survive today Key events in life s history include the origins of single celled and multicelled organisms and the colonization of land The study of fossils has helped geologists establish a geologic record of Earth s history which is divided into three eons The first two eons the Archaean and the Proterozoic together lasted approximately 4 billion years The Phanerozoic eon roughly the last half bil lion years encompasses most of the time that animals have ex isted on Earth 0 It is divided into three eras the Paleozoic Mesozoic and Cenozoic v 0 Each era represents a distinct age in the history of Earth and H39urriiri3 its d o For example the Mesozoic era is sometimes called the ColonIca1ioi1 0quot Ianuh age of reptiles because of its quotrimquoti5 Owl of mm abundance of reptilian fossils 1Lu including those of dinosaurs o The boundaries between the eras correspond to major extinction events seen in the fossil record when many forms of life disappeared and were replaced by forms that evolved from the survivors ll Mruiu393939ulir 39 UiCrlquotJquotU1L Slrflglt 39Lf t r139 P39 quot quot39J39U1 3 eullr n39y39o1ea Atrnosuheiin uxxy39giri A Figure 257 lock analogy for some key events In Earth39s hlstonr The Llouk mks Uuvm from the onum 0 Earth 416 million 39n39Bdlf The First SingleCelled Organisms The earliest direct evidence of life dating from 35 billion years ago comes from fossilized stromatolites see Figure 254 Stromatolites are layered rocks that form when certain prokaryotes bind thin lms of sediment together 0 If microbial communities complex enough to form stromatolites ex isted 35 billion years ago it is a reasonable hypothesis that singlecelled organisms originated much earlier perhaps as early as 39 billion years ago Early prokaryotes were Earth s sole inhabitants from at least 35 billion years ago to about 21 billion years ago As we will see these prokaryotes transformed life on our planet Photosynthesis and the Oxygen Revolution Most atmospheric oxygen gas O2 is of biological origin produced during the watersplitting step of photosynthesis When oxygenic photosynthesis first evolved the free O2 it produced probably dis solved in the surrounding water until it reached a high enough concentration to react with dissolved iron This would have caused the iron to precipitate as iron oxide which accumulated as sediments These sedi ments were compressed into banded iron formations red lay ers of rock containing iron oxide that are a source of iron ore today Once all of the dissolved iron had precipitated addi tional O2 dissolved in the water until the seas and lakes be came saturated with O2 After this occurred the O2 finally began to gas out of the water and enter the atmosphere This change left its mark in the rusting of ironrich terrestrial rocks a process that began about 27 billion years ago This chronology implies that bacteria similar to today s cyanobac teria oxygenreleasing photosynthetic bacteria originated well before 27 billion years ago The amount of atmospheric O2 increased gradually from about 27 to 23 billion years ago but then shot up rela tively rapidly to between 1 and 10 of its present level Figure 258 o This oxygen revolution had an enormous impact on life In certain of its chemical forms oxygen attacks chemical bonds and can inhibit enzymes and damage cells 0 As a result the rising concentration of atmospheric O2 proba bly doomed many prokaryotic groups Some species survived in habitats that remained anaerobic where we nd their de scendants living today 0 gradual rise in atmos pheric O2 levels was probably brought about by ancient cyanobacteria A few hundred million years later the rise in O2 accelerated What caused this acceleration One hypothe sis is that this rise followed the evolution of eukaryotic cells containing chloroplasts The First Eukatjyotes eukaryotic cells have more com plex organization than prokaryotic cells Eukaryotic cells have a nu clear envelope mitochondria en doplasmic reticulum and other internal structures that prokaryotes lack 0 Also unlike prokaryotic cells eukaryotic cells have a cy toskeleton a feature that enables eukaryotic cells to change their shape and thereby surround and engulf other cells Eukaryotic features 9 prokaryotic o endosymbiont theory which posits that mitochondria and plastids a gen eral term for chloroplasts and related organelles were for merly small prokaryotes that began living within larger cells 0 The term endosymbiont refers to a cell that lives within an other cell called the host cell The prokaryotic ancestors of mi tochondria and plastids probably gained entry to the host cell as undigested prey or internal parasites 0 Though such a process may seem unlikely scientists have directly observed cases in which endosymbionts that began as prey or parasites came to have a mutually beneficial relationship with the host in as little as five years we can hy pothesize how the symbiosis could have become mutually beneficial o A host that is a heterotroph an organism that eats other organisms or substances derived from them could use nutrients released from photosynthetic endosymbionts 0 And in a world that was becoming increasingly aerobic a host that was itself an anaerobe would have benefited from endosym bionts that turned the oxygen to advantage Over time the host and endosymbionts would have become a single organ ism its parts inseparable 0 Although all eukaryotes have mito chondria or remnants of these organelles they do not all have plastids 0 Thus the hypothesis of serial endosymbiosis sup poses that mitochondria evolved before plastids through a se quence of endosymbiotic events great deal of evidence supports the endosymbiotic ori gin of mitochondria and plastids o The inner membranes of both organelles have enzymes and transport systems that are homologous to those found in the plasma membranes of living prokaryotes o Mitochondria and plastids replicate by a splitting process that is similar to that of certain prokaryotes 0 each of these organelles contains a single circu lar DNA molecule that like the chromosomes of bacteria is not associated with histones or large amounts of other pro teins 0 As might be expected of organelles descended from freeliving organisms mitochondria and plastids also have the cellular machinery including ribosomes needed to tran scribe and translate their DNA into proteins 0 Finally in terms of size RNA sequences and sensitivity to certain antibiotics the ribosomes of mitochondria and plastids are more similar to prokaryotic ribosomes than they are to the cytoplasmic ri bosomes of eukaryotic cells The Origin of Multicellularity the increased complexity of the orchestra makes more variations possible Likewise the appearance of structurally complex eukaryotic cells sparked the evolution of greater morphological diversity than was possible for the simpler prokaryotic cells After the first eu karyotes appeared a great range of unicellular forms evolved The Earliest Multicellular E ukaryotes Based on comparisons of DNA se quences researchers have suggested that the common ancestor of multi cellular eukaryotes lived 15 billion years ago Why were multicellular eukaryotes limited in size and di versity until the late Proterozoic One hypothesis stems from geologic evidence indicating that a series of severe ice ages oc curred from 750 to 580 million years ago At various times dur ing this period glaciers covered all of the planet s landmasses and the seas were largely iced over 0 The snowball Earth hy pothesis suggests that most life would have been confined to areas near deepsea vents and hot springs or to equatorial re gions of the ocean that lacked ice cover o The fossil record of the first major diversification of multicellular eukaryotes be ginning about 575 million years ago corresponds roughly to the time when snowball Earth thawed The Cambrian Explosion Many presentday animal phyla appear suddenly in fossils formed early in the Cambrian period 53 5525 million years ago a phenomenon referred to as the Cambrian explosion Fossils of several animal groups sponges cnidarians sea anemones and their relatives and molluscs appear in even older rocks dating from the late Proterozoic 0 Prior to the Cambrian explosion all large animals were softbodied The fossils of large pre Cambrian animals reveal little evidence of predation Instead these animals appear to have been grazers feeding on algae suspension feeders or scavengers not hunters The Cambrian explosion changed everything 0 In a relatively short period of time 10 million years predators lived dinosaurs The Colonization of Land The colonization of land was an other milestone in the history of life There is fossil evidence that cyanobacteria and other photosyn thetic prokaryotes coated damp ter restrial surfaces well over a billion years ago However larger forms of life such as fungi plants and ani mals did not begin to colonize land until about 500 million years ago 0 This gradual evolu tionary venture out of aquatic environments was associated with adaptations that made it possible to reproduce on land and that helped prevent dehydration Plants colonized land in the company of fungi Even today the roots of most plants are associated with fungi that aid in the absorption of water and minerals from the soil see Chapter 31 These root fungi in turn obtain their organic nutrients from the plants Such mutually beneficial associa tions of plants and fungi are evident in some of the oldest fossilized roots dating this relationship back to the early spread of life onto land Although many animal groups are now represented in ter restrial environments the most widespread and diverse land animals are arthropods particularly insects and spiders and tetrapods Arthropods were the first animals to colonize land roughly 420 million years ago Tetrapods include humans although we are late arrivals on the scene The human lineage diverged from other primates around 67 million years ago and our species originated only about 195000 years ago The rise and fall of groups of organisms re ect differences in speciation and extinction rates From its beginnings life on Earth has seen the rise and fall of groups of organisms o Anaerobic prokaryotes originated our ished and then declined as the oxygen content of the atmo sphere rose 0 Billions of years later the first tetrapods emerged from the sea giving rise to several major new groups of organisms 0 One of these the amphibians went on to domi nate life on land for 100 million years until other tetrapods including dinosaurs and later mammals replaced them as the dominant terrestrial vertebrates Just as a population increases in size when there are more births than deaths the rise of a group of organisms oc curs when it produces more new species than are lost to ex tinction The reverse occurs when a group is in decline 0 plate tectonics mass extinctions and adaptive radiations Plate Tectonics Since the origin of multicellular eukaryotes roughly 15 billion years ago there have been three occasions 11 billion 600 million and 250 million years ago when most of the landmasses of Earth came together to form a supercontinent then later broke apart Each time they yielded a different configuration of con tinents theory of plate tectonics the continents are part of great plates of Earth s crust that essentially oat on the hot underlying portion of the mantle Figure 2512 Movements in the mantle cause the plates to move over time in a process called continental drift Consequences of Continental Drift continental drift alters the habitats in which organisms live About 250 million years ago plate movements brought all the previously separated land masses together into a supercontinent named Pangaea Ocean basins became deeper which lowered sea level and drained shallow coastal seas o Pangaea destroyed a considerable amount of that habitat The interior of the vast continent was cold and dry probably an even more severe environment than that of central Asia today Overall the formation of Pangaea had a tremendous impact on the physical environment and climate which drove some species to extinction and provided new opportu nities for groups of organisms that survived the crisis affects organisms is the climate change that results when a continent shifts its lo cation 0 When faced with the changes in climate that such shifts in position entail organisms adapt move to a new location or become extinct this last outcome occurred for many organisms stranded on Antarctica promotes allopatric speciation on a grand scale 0 When supercontinents break apart regions that once were connected become geographically isolated can help explain puzzles about the geographic distribution of extinct organisms 0 such as why fossils of the same species of Permian freshwater reptiles have been discovered in both Brazil and the West African na tion of Ghana Continental drift also explains much about the current distributions of organisms 0 such as why Aus tralian fauna and ora contrast so sharply with those of the rest of the world Mass Extinctions fossil record shows that the overwhelming majority of species that ever lived are now extinct o A species may become extinct for many reasons 0 Its habitat may have been de stroyed or its environment may have changed in a manner unfavorable to the species Even if physical factors in the envi ronment remain stable biological factors may change the origin of one species can spell doom for another Although extinction occurs on a regular basis at certain times disruptive global environmental changes have caused the rate of extinction to increase dramatically When this oc curs a mass extinction results in which large numbers of species become extinct throughout Earth The Big Five Mass Extinction Events These events are par ticularly well documented for the decimation of hardbodied animals that lived in shallow seas the organisms for which the fossil record is most complete In each mass extinction 50 or more of Earth s marine species became extinct Two mass extinctions the Permian and the Cretaceous have received the most attention 0 The Permian mass extinc tion which de nes the boundary between the Paleozoic and Mesozoic eras 251 million years ago claimed about 96 of marine animal species and drastically altered life in the ocean Terrestrial life was also affected For example 8 out of 27 known orders of insects were wiped out o The Permian mass extinction occurred at the time of enor mous volcanic eruptions in what is now Siberia o the eruptions may have produced enough car bon dioxide to warm the global climate by an estimated 6 C 0 Reduced temperature differences between the equator and the poles could have slowed the mixing of ocean water which in turn could have led to a widespread drop in oxygen concentrations o The resulting lowoxygen condition called ocean anoxia would have suffocated oxygenbreathers and promoted the growth of anaerobic bacteria that emit a poi sonous metaboli byproduct hydrogen H2S gas 0 As this gas bubbled into the atmosphere it could have caused further extinctions by directly killing land plants and ani mals and by initiating chemical reactions that destroy the ozone layer a shield that ordinarily protects organisms from lifethreatening levels of UV radiation The Cretaceous mass extinction occurred about 655 mil lion years ago and marks the boundary between the Mesozoic and Cenozoic eras o extinguished more than half of all marine species and eliminated many families of terrestrial plants and animals including all dinosaurs except birds 0 One clue to a possible cause of the Cretaceous mass extinction is a thin layer of clay enriched in iridium that separates sediments from the Mesozoic and Cenozoic eras Iridium is an element that is very rare on Earth but common in many of the mete orites and other extraterrestrial objects that occasionally fall to Earth 0 Walter Alvarez and the late Luis Alvarez proposed that this clay is fallout from a huge cloud of debris that billowed into the atmosphere when an asteroid or large comet collided with Earth This cloud would have blocked sunlight and se verely disturbed the global climate for several months Is a Sixth Mass Extinction Under Way human actions such as habi tat destruction are modifying the global environment to such an extent that many species are threatened with extinction This question is difficult to answer in part because it is hard to document the total number of extinctions occurring today Even so it is clear that losses to date have not reached those of the big five mass extinctions in which large percentages of Earth s species became extinct Indeed the fossil record indicates that over the last 500 million years extinction rates have tended to increase when global temperatures were high Consequences of Mass Extinctions Mass extinctions have significant and longterm effects By eliminating large numbers of species a mass extinction can reduce a thriving and complex ecological community to a pale shadow of its former self And once an evolutionary lin eage disappears it cannot reappear The course of evolution is changed forever 0 Consider what would have happened if the early primates living 66 million years ago had died out in the Cretaceous mass extinction Humans would not exist and life on Earth would differ greatly from what it is today Mass extinctions can also alter ecological communities by changing the types of organisms found in them 0 A rise in the number of predator species can increase both the pressures faced by prey and the competition among predators for food mass ex tinctions can curtail lineages with highly advantageous fea tures Adaptive Radiations The fossil record indicates that the diversity of life has increased over the past 250 million years This increase has been fueled by adaptive radiations periodsof evolutionary change in which groupsof organisms form many new specieswhose adaptations allow them to fill different ecological roles or niches in their communities 0 Largescale adaptive radiations occurred after each of the big five mass extinctions when survivors became adapted to the many vacant ecological niches 0 Adaptive radia tions have also occurred in groups of organisms that possessed major evolutionary innovations such as seeds or armored body coverings or that colonized regions in which they faced little competition from other species Worldwide Adaptive Radiations Fossil evidence indicates that mammals underwent a dramatic adaptive radiation after the extinction of terrestrial dinosaurs 655 million years ago Early mammals may have been restricted in size and diversity because they were eaten or outcompeted by the larger and more diverse dinosaurs With the disappearance of the dinosaurs except for birds mammals expanded greatly in both diversity and size filling the ecological roles once occu pied by terrestrial dinosaurs The history of life has also been greatly altered by radia tions in which groups of organisms increased in diversity as they came to play entirely new ecological roles in their com munities 0 Examples include the rise of photosynthetic prokaryotes the evolution of large predators in the Cambrian explosion and the radiations following the colonization of land by plants insects and tetrapods 0 Each of these last three radiations was associated with major evolutionary innova tions that facilitated life on land 0 The radiation of land plants for example was associated with key adaptations such as stems that support plants against gravity and a waxy coat that protects leaves from water loss the diversification of land plants stimulated a series of adaptive radiations in in sects that ate or pollinated plants one reason that insects are the most diverse group of animals on Earth today Regional Adaptive Radiations Striking adaptive radiations have also occurred over more lim ited geographic areas 0 Such radiations can be initiated when a few organisms make their way to a new often distant location in which they face relatively little competition from other or ganisms o The Hawaiian archipelago is one of the world s great showcases of this Major changes in body form can result from changes in the sequences and regulation of developmental genes seek to understand the intrinsic biological mechanisms that underlie changes seen in the fossil record For this we turn to genetic mechanisms of change paying particular attention to genes that in uence development Effects of Developmental Genes evodevo research at the inter face between evolutionary biology and developmental biology is illuminating how slight genetic divergences can produce major morphological differences between species Genes that control development in uence the rate timing and spatial pattern of change in an organism s form as it de velops from a zygote into an adult Changes in Rate and Timing striking evolutionary transformations are the result of heterochrony from the Greek hetero different and chronos time an evolutionary change in the rate or timing of devel opmental events 0 an organism s shape depends in part on the relative growth rates of different body parts during development Changes to these rates can alter the adult form substantially as seen in the contrasting shapes of human and chimpanzee skulls Heterochrony can also alter the timing of reproductive de velopment relative to the development of nonreproductive or gans o If reproductive organ development accelerates compared to other organs the sexually mature stage of a species may re tain body features that were juvenile structures in an ancestral species a condition called paedomorphosis 0 Such an evolutionary alteration of developmental timing can produce animals that appear very different from their ancestors even though the overall genetic change may be small Indeed recent evidence indicates that a change at a single locus was probably sufficient to bring about paedomorphosis in the axolotl salamander al though other genes may have contributed as well Changes in Spatial Pattern Substantial evolutionary changes can also result from alter ations in genes that control the placement and spatial organ ization of body parts For example master regulatory genes called homeotic genes described in Chapters 18 and 21 determine such basic features as where a pair of wings and a pair of legs will develop on a bird or how a plant s ower parts are arranged The products of one class of homeotic genes the Hox genes provide positional information in an animal embryo This information prompts cells to develop into structures ap propriate for a particular location Changes in Hox genes or in how they are expressed can have a profound impact on morphology For example among crustaceans a change in the location where two Hox genes Ubx and Scr are expressed correlates with the conversion of a swimming appendage to a feeding appendage Large effects are also seen in snakes where changes in how two Hox genes HoxC6 and H0xC8 are expressed suppresses limb formation The Evolution of Development The 565millionyearold fossils of Ediacaran animals in Figure 254 suggest that a set of genes sufficient to produce complex animals existed at least 30 million years before the Cambrian explosion Adaptive evolution by natural selection provides one answer to this question As we ve seen throughout this unit by sorting among differences in the sequences of proteinencoding genes selection can improve adaptations rapidly o In addition new genes created by gene duplication events can take on a wide range of new metabolic and structural functions Thus adap tive evolution of both new and existing genes may have played a key role in shaping the great diversity of life Changes in Genes New developmental genes arising after gene duplication events very likely facilitated the origin of novel morphological forms But since other genetic changes also may have occurred at such times it can be difficult to establish causal links between ge netic and morphological changes that occurred in the past This difficulty was sidestepped in a recent study of develop mental changes associated with the divergence of sixlegged insects from crustaceanlike ancestors that had more than six legs 0 When expressed the Ubx gene suppresses leg formation in insects but not in crustaceans To examine the workings of this gene researchers cloned the Ubx gene from Drosophila and Artemia Next they genetically engineered fruit y embryos to express either the Drosophila Ubx gene or the Artemia Ubx gene throughout their bodies The Drosophila gene suppressed 100 of the limbs in the embryos as expected whereas the Artemia gene suppressed only 15 o By inserting these hybrid genes into fruit y embryos one hybrid gene per embryo and observing their effects on leg development the researchers were able to pinpoint the exact amino acid changes responsible for the suppression of additional limbs in insects In so doing this study provided evidence linking a particular change in the nucleotide se quence of a developmental gene to a major evolutionary change the origin of the sixlegged insect body plan Changes in Gene Regulation Changes in the nucleotide sequence or regulation of develop mental genes can result in morphological changes that harm the organism Moreover a change in the nu cleotide sequence of a gene may affect its function wherever the gene is expressed In contrast changes in the regulation of gene expression can be limited to a single cell type Thus a change in the regulation of a develop mental gene may have fewer harmful side effects than a change to the sequence of the gene This line of reasoning has prompted researchers to suggest that changes in the form of organisms may often be caused by mutations that affect the regulation of developmental genes not their sequences Evolution is not goal oriented What does our study of macroevolution tell us about how evo lution works Moreover to paraphrase the Nobel Prize winning geneticist Francois Jacob evolution is like tinkering a process in which new forms arise by the slight modification of existing forms Even large changes like the ones that produced the first mammals or the sixlegged body plan of insects can result from the modification of exist ing structures or existing developmental genes Over time such tinkering has led to three key features of the natural world l striking ways in which or ganisms are suited for life in their environments 2 the many shared characteristics of life 3 the rich diversity of life Evolutionary Novelties Francois J acob s view of evolution harkens back to Darwin s concept of descent with modification 0 As new species form novel and complex structures can arise as gradual modifica tions of ancestral structures 0 In many cases complex struc tures have evolved in increments from simpler versions that performed the same basic function 0 Eg How could the human eye have evolved in gradual increments Throughout their evolutionary history eyes retained their basic function of vision But evolutionary novelties can also arise when structures that originally played one role gradu ally acquire a different one Structures that evolve in one context but become coopted for another function are sometimes called exaptations to distinguish them from the adaptive ori gin of the original structure 0 Note that the concept of exapta tion does not imply that a structure somehow evolves in anticipation of future use 0 Natural selection cannot predict the future it can only improve a structure in the context of its current utility 0 Novel features such as the new jaw hinge and ear bones of early mammals can arise gradually via a se ries of intermediate stages each of which has some function in the organism s current contex Evolutionary Trends Extracting a single evolutionary progression from the fos sil record can be misleading however it is like describing a bush as growing toward a single point by tracing only the branches that lead to that twig o For example by selecting cer tain species from the available fossils it is possible to arrange a succession of animals intermediate between Hyracotherium and living horses that shows a trend toward large singletoed species 0 However if we consider all fossil horses known today this apparent trend vanishes Branching evolution can result in a real evolutionary trend even if some species counter the trend One model of long term trends proposed by Steven Stanley views species as analogous to individuals Specia tion is their birth extinction is their death and new species that diverge from them are their offspring 0 Stanley suggests that just as populations of individual organ isms undergo natural selection species undergo species selection 0 The species that endure the longest and generate the most new offspring species determine the direction of major evolutionary trends 0 The species selection model sug gests that differential speciation success plays a role in macroevolution similar to the role of differential reproduc tive success in microevolution Evolutionary trends can also result directly from natural selection 0 For example when horse ancestors invaded the grasslands that spread during the midCenozoic there was strong selection for grazers that could escape predators by running faster This trend would not have occurred without open grasslands Whatever its cause an evolutionary trend does not imply that there is some intrinsic drive toward a particular pheno type Evolution is the result of the interactions between or ganisms and their current environments if environmental conditions change an evolutionary trend may cease or even reverse itself The cumulative effect of these ongoing interac tions between organisms and their environments is enor mous LEVEL 1 KNOWLEDGECOMPREHENSION 1 Fossilized stromatolites 1 all date from 27 billion years ago 2 formed around deepsea vents 3 resemble structures formed by bacterial communities that are found today in some warm shallow salty bays 4 provide evidence that plants moved onto land in the com pany of fungi around 500 million years ago 5 contain the first undisputed fossils of eukaryotes and date from 21 billion years ago 2 The oxygen revolution changed Earth s environment dramati cally Which of the following took advantage of the presence of free oxygen in the oceans and atmosphere a the evolution of cellular respiration which used oxygen to help harvest energy from organic molecules b the persistence of some animal groups in anaerobic habitats c the evolution of photosynthetic pigments that protected early algae from the corrosive effects of oxygen d the evolution of chloroplasts after early protists incor porated photosynthetic cyanobacteria e the evolution of multicellular eukaryotic colonies from communities of prokaryotes 3 Which factor most likely caused animals and plants in India to differ greatly from species in nearby southeast Asia a The species became separated by convergent evolution b The climates of the two regions are similar c India is in the process of separating from the rest of Asia d Life in India was wiped out by ancient volcanic eruptions e India was a separate continent until 45 million years ago 4 Adaptive radiations can be a direct consequence of four of the following five factors Select the exception 1 vacant ecological niches genetic drift colonization of an isolated region that contains suitable habitat and few competitor species evolutionary innovation an adaptive radiation in a group of organisms such as plants that another group uses as food 3939gt 5 Which of the following steps has not yet been accomplished by scientists studying the origin of life a synthesis of small RNA polymers by ribozymes b abiotic synthesis of polypeptides cformation of molecular aggregates with selectively perme able membranes d formation of protocells that use DNA to direct the poly merization of amino acids e abiotic synthesis of organic molecules LEVEL 2 APPLICATIONANALYSIS 7 A genetic change that caused a certain Hox gene to be ex pressed along the tip of a vertebrate limb bud instead of far ther back helped make possible the evolution of the tetrapod limb This type of change is illustrative of l the in uence of environment on development 2 paedomorphosis 3 a change in a developmental gene or in its regulation that altered the spatial organization of body parts 4 heterochrony 5 gene duplication 8 A swim bladder is a gasfilled sac that helps fish maintain buoyancy The evolution of the swim bladder from lungs of an ancestral fish is an example of a an evolutionary trend b exaptation c changes in Hox gene expression d paedomorphosis e adaptive radiation Chapter 26 Phylogeny and the Tree of Life Investigating the Tree of Life how do biologists distinguish and categorize the millions of species on Earth An understanding of evolutionary relationships suggests one way to address these questions We can decide in which container to place a species by comparing its traits with those of potential close relatives our emphasis will shift from the process of evolution the evolutionary mechanisms described in Unit Four to its pattern observations of evolution s products over time To set the stage for surveying life s diversity in this chapter we consider how biologists trace phylogeny the evolution ary history of a species or group of species To construct phylogenies biologists utilize systematics a discipline focused on classifying organisms and determin ing their evolutionary relationships Systematists use data ranging from fossils to molecules and genes to infer evolu tionary relationships Phylogenies show evolutionary relationships an organism is likely to share many of its genes metabolic pathways and structural proteins with its close relatives We ll consider practical applications of such in formation at the close of this section but first we ll examine how organisms are named and classified the scientific disci pline of taxonomy Binomial Nomenclature To avoid ambiguity when communicating about their re search biologists refer to organisms by Latin scientific names The twopart format of the scientific name commonly called a binomial was instituted in the 18th century by Carolus Linnaeus The first part of a binomial is the name of the genus plural genera to which the species be longs The second part called the specific epithet is unique for each species within the genus Hierarchical Classification Linnaeus also grouped them into a hierarchy of increasingly inclusive categories The first grouping is built into the binomial Species that appear to be closely related are grouped into the same genus For example the leopard Pcmthera pardus belongs to a genus that also in cludes the African lion Pcmthera leo the tiger Pcmthera tigris and the jaguar Pcmthera orzca Beyond genera taxonomists employ progressively more comprehensive categories of clas sification The taxonomic system named after Linnaeus the Linnaean system places related genera in the same family families into orders orders into classes classes into phyla singular phylum phyla into kingdoms and more recently kingdoms into domains the named taxonomic unit at any level of the hierarchy is called a taxon plural taxa Linking Classification and Phylogeny The evolutionary history of a group of organisms can be repre sented in a branching diagram called a phylogenetic tree One reason for misclassification might be that over the course of evolution a species has lost a key feature shared by its close relatives If DNA or other new evidence indicates that such a mistake has occurred the or ganism may be reclassified to accurately re ect its evolutionary history Another issue is that while the Linnaean system may distinguish groups such as mammals reptiles birds and other classes of vertebrates it tells us nothing about these groups evolutionary relationships to one another A system called PhyloCode for example only names groups that include a common ancestor and all of its descendants 0 While PhyloCode would change the way taxa are defined and recognized the taxonomic names of most species would remain the same But groups would no longer have ranks attached to them such as family or class Also some com monly recognized groups would become part of other groups previously of the same rank 0 Although PhyloCode is controversial many systematists are adopting the phylogenetic approach on which it is based Whether groups are named according to PhyloCode or ac cording to Linnaean classification a phylogenetic tree repre sents a hypothesis about evolutionary relationships These relationships often are depicted as a series of dichotomies or twoway branch points Each branch point represents the divergence of two evolutionary lineages from a common an cestor o sister taxa groups of or ganisms that share an immediate common ancestor o rooted which means that a branch point within the tree often drawn farthest to the left represents the most recent common ancestor of all taxa in the tre o basal taxon refers to a lineage that diverges early in the his tory of a group 0 polytomy a branch point from which more than two de scendant groups emerge A polytomy signifies that evolution ary relationships among the taxa are not yet clear What We Can and Cannot Learn from Phylogenetic Trees First they are intended to show patterns of descent not phe notypic similarity 0 Although closely related organisms often resemble one another due to their common ancestry they may not if their lineages have evolved at different rates or faced very different environmental conditions For example even though crocodiles are more closely related to birds than to lizards see Figure 2217 they look more like lizards because morphology has changed dramatically in the bird lineage Second the sequence of branching in a tree does not nec essarily indicate the actual absolute ages of the particular species 0 Generally unless given specific information about what the branch lengths in a phylogenetic tree mean for example that they are proportional to time we should in terpret the diagram solely in terms of patterns of descent No assumptions should be made about when particular species evolved or how much change occurred in each lineage Third we should not assume that a taxon on a phyloge netic tree evolved from the taxon next to it Applying Phylogenies Understanding phylogeny can have practical applications Consider maize corn which originated in the Americas and is now an important food crop worldwide From a phylogeny of maize based on DNA data researchers have been able to iden tify two species of wild grasses that may be maize s closest living relatives These two close relatives may be useful as reservoirs of beneficial alleles that can be transferred to cultivated maize by crossbreeding or genetic engineering Phylogenies are inferred from morphological and molecular data To infer phylogeny systematists must gather as much infor mation as possible about the morphology genes and bio chemistry of the relevant organisms It is important to focus on features that result from common ancestry because only such features re ect evolutionary relationships Morphological and Molecular Homologies Recall that phenotypic and genetic similarities due to shared ancestry are called homologies In the same way genes or other DNA sequences are homologous if they are de scended from sequences carried by a common ancestor In general organisms that share very similar morphologies or similar DNA sequences are likely to be more closely related than organisms with vastly different structures or sequences In some cases however the morphological divergence be tween related species can be great and their genetic diver gence small or vice versa 0 But despite these striking phenotypic dif ferences the silverswords genes are very similar Based on these small molecular divergences scientists estimate that the silversword group began to diverge 5 million years ago which is also about the time when the oldest of the current islands formed Sorting Homology from Analogy A potential red herring in constructing a phylogeny is similar ity due to convergent evolution called analogy rather than to shared ancestry homology convergent evolution occurs when similar environmental pressures and natural selection produce similar analogous adaptations in organisms from different evolutionary line ages Distinguishing between homology and analogy is critical in reconstructing phylogenies To see why consider bats and birds both of which have adaptations that enable ight This superficial resemblance might imply that bats are more closely related to birds than they are to cats which cannot y But a closer examination reveals that a bat s wing is far more similar to the forelimbs of cats and other mammals than to a bird s wing Analogous structures that arose inde pendently are also called homoplasies from the Greek meaning to mold in the same way Besides corroborative similarities and fossil evidence an other clue to distinguishing between homology and analogy is the complexity of the characters being compared The more elements that are similar in two complex structures the more likely it is that they evolved from a common ancestor The same argument applies to comparisons at the gene level Genes are sequences of thousands of nucleotides each of which represents an in herited character in the form of one of the four DNA bases A adenine G guanine C cytosine or T thymine If genes in two organisms share many portions of their nu cleotide sequences it is likely that the genes are homologous Evaluating Molecular Homologies Comparisons of DNA molecules often pose technical chal lenges for researchers The first step after sequencing the mol ecules is to align comparable sequences from the species being studied If the species are very closely related the sequences probably differ at only one or a few sites In contrast compa rable nucleic acid sequences in distantly related species usually have different bases at many sites and may have dif ferent lengths This is because insertions and deletions accu mulate over long periods of time uppose for example that certain noncoding DNA se quences near a particular gene are very similar in two species except that the first base of the sequence has been deleted in one of the species The effect is that the remaining sequence shifts back one notch A comparison of the two sequences that does not take this deletion into account would overlook what in fact is a very good match Such molecular comparisons reveal that many base substi tutions and other differences have accumulated in the com parable genes of an Australian mole and a North American mole The many differences indicate that their lineages have diverged greatly since their common ancestor thus we say that the living species are not closely related Just as with morphological characters it is necessary to dis tinguish homology from analogy in evaluating molecular simi larities for evolutionary studies In the rest of this unit you will see how our understanding of phy logeny has been transformed by molecular systematics the discipline that uses data from DNA and other molecules to determine evolutionary relationships Shared characters are used to construct phylogenetic trees the first step is to distinguish homologous features from analogous ones since only homology re ects evolutionary history Next we must choose a method of inferring phylogeny from these homologous char acters A widely used set of methods is known as cladistics Cladistics In the approach to systematics called cladistics common an cestry is the primary criterion used to classify organisms Using this methodology biologists attempt to place species into groups called clades each of which includes an ancestral species and all of its descendants Clades like taxonomic ranks are nested within larger clades for example the cat group Felidae represents a clade within a larger clade Carnivora that also includes the dog group Canidae However a taxon is equivalent to a clade only if it is monophyletic from the Greek meaning single tribe signi fying that it consists of an ancestral species and all of its descen dants see Figure 26l0a Contrast this with a paraphyletic beside the tribe group which consists of an ancestral species and some but not all of its descendants or a polyphyletic many tribes group which includes taxa with different ancestors Shared Ancestral and Shared Derived Characters As a result of descent with modification organisms both share characteristics with their ancestors and differ from them 0 For ex ample all mammals have backbones but a backbone does not distinguish mammals from other vertebrates because all verte brates have backbones o The backbone predates the branching of mammals from other vertebrates Thus for mammals the back bone is a shared ancestral character a character that origi nated in an ancestor of the taxon o In contrast hair is a character shared by all mammals but not found in their ancestors Thus in mammals hair is considered a shared derived character an evolutionary novelty unique to a clade Note that it is a relative matter whether a particular character is considered ancestral or derived A backbone can also qualify as a shared derived character but only at a deeper branch point that distinguishes all vertebrates from other animals Inferring Phylogenies Using Derived Characters Shared derived characters are unique to particular clades Be cause all features of organisms arose at some point in the his tory of life it should be possible to determine the clade in which each shared derived character first appeared and to use that information to infer evolutionary relationships As a basis of comparison we need to select an out group An outgroup is a species or group of species from an evolutionary lineage that is known to have diverged before the lineage that includes the species we are studying the ingroup A suitable outgroup can be determined based on evidence from morphology paleontology embryonic develop ment and gene sequences By comparing members of the ingroup with each other and with the outgroup we can determine which characters were derived at the various branch points of vertebrate evolu tion For example all of the vertebrates in the ingroup have backbones This character was present in the ancestral verte brate but not in the outgroup Phylogenetic Trees with Proportional the lengths of the tree s branches do not indicate the degree of evolution ary change in each lineage Furthermore the chronology rep resented by the branching pattern of the tree is relative earlier versus later rather than absolute how many millions of years ago But in some tree diagrams branch lengths are proportional to amount of evolutionary change or to the times at which particular events occurred These equal spans of chronological time can be repre sented in a phylogenetic tree whose branch lengths are pro portional to time Such a tree draws on fossil data to place branch points in the context of geologic time Additionally it is possible to combine these two types of trees by labeling branch points with information about rates of ge netic change or dates of divergence Maximum Parsimony and Maximum Likelihood As the growing database of DNA sequences enables us to study more species the difficulty of building the phyloge netic tree that best describes their evolutionary history also grows According to the principle of maximum parsimony we should first investigate the simplest explanation that is consis tent with the facts The parsimony principle is also called Occam s razor after William of Occam a 14thcentury English philosopher who advocated this minimalist prob lemsolving approach of shaving away unnecessary com plications In the case of trees based on morphology the most parsimonious tree requires the fewest evolutionary events as measured by the origin of shared derived morpho logical characters For phylogenies based on DNA the most parsimonious tree requires the fewest base changes The principle of maximum likelihood states that given certain probability rules about how DNA sequences change over time a tree can be found that re ects the most likely se quence of evolutionary events Maximumlikelihood meth ods are complex but as a simple example let us return to the phylogenetic relationships between a human a mushroom and a tulip Phylogenetic Trees as Hypotheses This is a good place to reiterate that any phylogenetic tree rep resents a hypothesis about how the various organisms in the tree are related to one another The best hypothesis is the one that best fits all the available data A phylogenetic hypothesis may be modified when new evidence compels systematists to revise their trees Indeed while many older phylogenetic hy potheses have been supported by new morphological and molecular data others have been changed or rejected Thinking of phylogenies as hypotheses also allows us to use them in a powerful way We can make and test predic tions based on the assumption that a phylogeny our hypothesis is correct However fossilized dinosaur eggs and nests have provided evidence supporting the predic tion of brooding in dinosaurs An organism s evolutionary history is documented in its genome molecular systematics using comparisons of nucleic acids or other molecules to deduce relatedness is a valuable approach for tracing evolu tionary history The molecular approach helps us understand phylogenetic relationships that cannot be determined by nonmolecular methods such as comparative anatomy For ex ample molecular systematics helps us uncover evolutionary relationships between groups that have little common ground for morphological comparison such as animals and fungi And molecular methods allow us to reconstruct phylogenies among groups of presentday organisms for which the fossil record is poor or lacking entirely Different genes evolve at different rates even in the same evolutionary lineage As a result molecular trees can repre sent short or long periods of time depending on which genes are used Therefore comparisons of DNA sequences in these genes are useful for investigating re lationships between taxa that diverged hundreds of millions of years ago Gene Duplications and Gene Families What does molecular systematics reveal about the evolution ary history of genome change Consider gene duplication which plays a particularly important role in evolution because it increases the number of genes in the genome providing more opportunities for further evolutionary changes Molecu lar techniques now allow us to trace the phylogenies of gene duplications and the in uence of these duplications on genome evolution These molecular phylogenies must account for repeated duplications that have resulted in gene families groups of related genes within an organism s genome Accounting for such duplications leads us to dis tinguish two types of homologous genes orthologous genes and paralogous genes 0 Orthologous genes from the Greek orthos exact are those found in different species and their di vergence traces back to the speciation events that produced the species 0 The cytochrome c genes which code for an electron transport chain protein in humans and dogs are orthologous 0 Note that orthologous genes can only diverge after specia tion has taken place that is after the genes are found in sep arate gene pools For example although the cytochrome c genes in humans and dogs serve the same function the gene s sequence in humans has diverged from that in dogs in the time since these species last shared a common ancestor In paralogous genes from the Greek para in parallel the homology results from gene duplication hence multiple copies of these genes have diverged from one another within a species 0 Paralogous genes on the other hand can diverge within a species because they are present in more than one copy in the genome Genome Evolution Now that we can compare the entire genomes of different or ganisms including our own two patterns have emerged First lineages that diverged long ago can share orthologous genes 0 Eg though the human and mouse lineages diverged about 65 million years ago 99 of the genes of humans and mice are orthologous 0 And 50 of human genes are orthologous with those of yeast despite 1 billion years of divergent evolution 0 explain why disparate organisms never theless share many biochemical and developmental pathways Second the number of genes a species has doesn t seem to increase through duplication at the same rate as perceived phe notypic complexity o Humans have only about four times as many genes as yeast a singlecelled eukaryote even though unlike yeast we have a large complex brain and a body with more than 200 different types of tissues 0 Evidence is emerging that many human genes are more versatile than those of yeast A single human gene can encode multiple proteins that per form different tasks in various body tissues 0 Unraveling the mechanisms that cause this genomic versatility and phenotypic variation is an exciting challenge Molecular clocks help track evolutionary time One goal of evolutionary biology is to understand the rela tionships among all organisms including those for which there is no fossil record However if we attempt to determine the timing of molecular phylogenies that extend beyond the fossil record we must rely on an assumption about how change occurs at the molecular level Molecular Clocks They relied on the concept of a molecular clock a yardstick for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates 0 The assumption underlying the molecular clock is that the number of nu cleotide substitutions in orthologous genes is proportional to the time that has elapsed since the species branched from their common ancestor divergence time o In the case of par alogous genes the number of substitutions is proportional to the time since the ancestral gene was duplicated We can calibrate the molecular clock of a gene that has a reliable average rate of evolution by graphing the num ber of genetic differences for example nucleotide codon or amino acid differences against the dates of evolution ary branch points that are known from the fossil record Of course no gene marks time with complete precision In fact some portions of the genome appear to have evolved in irregular bursts that are not at all clocklike And even those genes that seem to act as reliable molecular clocks are accu rate only in the statistical sense of showing a fairly smooth average rate of change Furthermore the same gene may evolve at different rates in different groups of organisms And even among genes that are clocklike the rate of the clock may vary greatly from one gene to another some genes evolve a million times faster than others Neutral Theory The observed regularity of change that enables us to use some genes as molecular clocks raises the possibility that many of the changes in these sequences result from mutations that have be come fixed in a population by genetic drift and that the changes are selectively neutral neither beneficial nor detrimental Motoo Kimura Jack King and Thomas Jukes independ ently published papers describing this neutral theory that much evolutionary change in genes and proteins has no effect on fitness and therefore is not in uenced by natural se lection 0 many new mutations are harmful and are removed quickly But if most of the rest are neutral and have little or no effect on fitness then the rate of molecular change should indeed be regular like a clock Dif ferences in the clock rate for different genes are a function of how important a gene is o If the exact sequence of amino acids that a gene specifies is essential to survival most of the mutational changes will be harmful and only a few will be neutral 0 As a result such genes change only slowly But if the exact sequence of amino acids is less critical fewer of the new mutations will be harmful and more will be neutral Such genes change more quickly Problems with Molecular Clocks Applyi molecular clocks do not run as smoothly as neutral theory predicts Many irregularities are likely to be the result of natural selection in which certain DNA changes are favored over others Consequently some scientists question the utility of molecular clocks for timing evolution some scientists question the utility of molecular clocks for timing evolution Their skepticism is part of a broader debate about the extent to which neutral ge netic variation can account for some kinds of DNA diversity But because the direction of natural selection may change repeatedly over long periods of time and hence may average out some genes experiencing selection can nevertheless serve as approximate markers of elapsed time Another question arises when researchers attempt to ex tend molecular clocks beyond the time span documented by the fossil record Although some fossils are more than 3 bil lion years old these are very rare These estimates assume that the clocks have been constant for all that time Such es timates are highly uncertain problems may be avoided by calibrating molecular clocks with many genes rather than just one or a few genes as is often done By using many genes uctua tions in evolutionary rate due to natural selection or other factors that vary over time may average out Despite the broad period of time covered nearly 600 million years and the fact that natural selection proba bly affected some of these genes their estimates of diver gence times agreed closely with fossilbased estimates ng a Molecular Clock The Origin of HIV Researchers have used a molecular clock to date the origin of HIV infection in humans Phylogenetic analysis shows that HIV the virus that causes AIDS is descended from viruses that infect chimpanzees and other primates When did HIV jump to humans There is no simple answer because the virus has spread to humans more than once The multiple origins of HIV are re ected in the variety of strains genetic types of the virus HIV s genetic material is made of RNA and like other RNA viruses it evolves quickly To pin point the earliest HIVl M infection researchers compared samples of the virus from various times during the epidemic including a sample from 1959 A comparison of gene se quences showed that the virus has evolved in a clocklike fash ion New information continues to revise our understanding ofthe tree oflife different lineage of legless lizards than did snakes is one ex ample of how systematics is used to reconstruct the evolu tionary relationships of life s diverse forms In recent decades we have gained insight into even the very deepest branches of the tree of life through molecular systematics From Two Kingdoms to Three Domains Even with the discovery of the di verse microbial world the twokingdom system persisted o Noting that bacteria had a rigid cell wall taxonomists placed them in the plant kingdom o Eukaryotic unicellular organisms with chloroplasts were also considered plants o Fungi too were classified as plants partly because most fungi like most plants are unable to move about never mind the fact that fungi are not photosynthetic and have little in common structurally with plants 0 In the twokingdom system uni cellular eukaryotes that move and ingest food protozoans were classified as animals 0 Those such as Euglena that move and are photosynthetic were claimed by both botanists and zoologists and showed up in both kingdoms five kingdoms Monera prokaryotes Protista a di verse kingdom consisting mostly of unicellular organisms Plantae Fungi and Animalia o This system highlighted the two fundamentally different types of cells prokaryotic and eukary otic and set the prokaryotes apart from all eukaryotes by plac ing them in their own kingdom Monera However phylogenies based on genetic data soon began to reveal a problem with this system Some prokaryotes differ as much from each other as they do from eukaryotes Such diffi culties have led biologists to adopt a threedomain system The three domains Bacteria Archaea and Eukarya are a taxonomic level higher than the kingdom level The domain Bacteria contains most of the currently known prokaryotes including the bacteria closely related to chloro plasts and mitochondria The second domain Archaea con sists of a diverse group of prokaryotic organisms that inhabit a wide variety of environments Some archaea can use hydro gen as an energy source and others were the chief source of the natural gas deposits that are found throughout Earth s crust The threedomain system highlights the fact that much of the history of life has been about singlecelled organisms The two prokaryotic domains consist entirely of singlecelled organisms and even in Eukarya only the branches shown in red plants fungi and animals are dominated by multicellu lar organisms Of the five kingdoms previously recognized by taxonomists most biologists continue to recognize Plantae Fungi and Animalia but not Monera and Protista The king dom Monera is obsolete because it would have members in two different domains A Simple Tree of All Life In this tree the first major split in the history of life occurred when bacteria diverged from other organisms If this tree is correct eukaryotes and archaea are more closely related to each other than either is to bacteria This reconstruction of the tree of life is based largely on se quence comparisons of rRNA genes which code for the RNA components of ribosomes Because ribosomes are fundamen tal to the workings of the cell rRNA genes have evolved so slowly that homologies between distantly related organisms can still be detected making these genes very useful for de termining evolutionary relationships between deep branches in the history of life Comparisons of complete genomes from the three domains show that there have been substantial movements of genes be tween organisms in the different domains Figure 2622 These took place through horizontal gene transfer a process in which genes are transferred from one genome to an other through mechanisms such as exchange of transposable elements and plasmids viral infection see Chapter 19 and perhaps fusions of organisms Because phylogenetic trees are based on the assumption that genes are passed verti cally from one generation to the next the occurrence of such horizontal transfer events helps to explain why trees built using different genes can give inconsistent results Is the Tree of Life Really a Ring argued that horizontal gene transfer was so common that the early history of life should be represented as a tangled network of connected branches not a simple di chotomously branching tree Others have suggested that relationships among early organisms are best represented by a ring not a tree these researchers hypoth esized that eukaryotes arose as a fusion between an early bac terium and an early archaean an evolutionary relationship that cannot be depicted in a tree of life but can be depicted in a ring of life LEVEL 1 KNOWLEDGECOMPREHENSION 1 In Figure 264 which similarly inclusive taxon descended from the same common ancestor as Canidae 7 The relative lengths of the frog and mouse branches in the phylogeny in Figure 2612 indicate that l 3939gt 4 S33 4 5 frogs evolved before mice mice evolved before frogs the genes of frogs and mice have only coincidental homoplasies the homolog has evolved more slowly in mice the homolog has evolved more rapidly in mice Three living species X Y and Z share a common ancestor T as do extinct species U and V A grouping that consists of species T X Y and Z but not U or V makes up a a valid taxon d a paraphyletic group b a monophyletic clade e a polyphyletic group c an ingroup with species U as the outgroup In a comparison of birds and mammals having four limbs is a shared ancestral character a shared derived character a character useful for distinguishing birds from mammals an example of analogy rather than homology 5 a character useful for sorting bird species To apply parsiomony to constructing a phylogenic tree quotS tquot choose the tree that assumes all evolutionary changes are equally probable 2 choose the tree in which the branch points are based on as many shared derived characters as possible base phylogenetic trees only on the fossil record as this provides the simplest explanation for evolution choose the tree that represents the fewest evolutionary changes in either DNA sequences or morphology choose the tree with the fewest branch points LEVEL 2 APPLICATIONANALYSIS 5 6 Based on this tree which statement is not correct Salamander Iaf2 ice j The salamander lineage is a basal taxon 2 Salamanders are a sister group to the group containing lizards goats and humans 3 Salamanders are as closely related to goats as to humans 4 Lizards are more closely related to salamanders than to humans 5 The group highlighted by shading is paraphyletic If you were using cladistics to build a phylogenetic tree of cats which of the following would be the best outgroup a lion b domestic cat c wolf d leopard e tiger 7 The relative lengths of the frog and mouse branches in the phylogeny in Figure 2612 indicate that 2 frogs evolved before mice 3 mice evolved before frogs 4 the genes of frogs and mice have only coincidental homoplasies 5 6 the homolog has evolved more slowly in mice the homolog has evolved more rapidly in mice Chapter 27 Bacteria and Archaea Masters of Adaptation many other prokaryotes can tolerate ex treme conditions Examples include Deinococcus radiodurans which can survive 3 million rads of radiation 3000 times the dose fatal to humans and Picrophilus oshimae which can grow at a pH of 003 acidic enough to dissolve metal Other prokaryotes live in environments that are too cold or too hot for most other organisms Prokaryotic species are also very well adapted to more nor mal habitats the lands and waters in which most other species are found Their ability to adapt to a broad range of habitats helps explain why prokaryotes are the most abundant organisms on Earth The number of prokaryotes in a handful of fertile soil is greater than the number of people who have ever lived In this chapter we ll examine the adaptations diversity and enormous ecological impact of these tiny organisms Structural and functional adaptations contribute to prokaryotic success Most prokaryotes are unicellular although the cells of some species remain at tached to each other after cell division Prokaryotic cells typi cally have diameters of 055 um much smaller than the 10100 um diameter of many eukaryotic cells One notable exception T hiomargarita namibiensis can be 750 um across bigger than the dot on this i Finally although thy are unicellular and small prokaryotes are well organized achieving all of an organism s life functions within a single cell CellSurface Structures A key feature of nearly all prokaryotic cells is the cell wall which maintains cell shape protects the cell and prevents it from bursting in a hypotonic environment In a hypertonic environment most prokaryotes lose water and shrink away from their wall plasmolyze like other walled cells Such water losses can inhibit cell reproduction Thus salt can be used to preserve foods because it causes prokary otes to lose water preventing them from rapidly multiplying The cell walls of prokaryotes differ in structure from those of eukaryotes In eukaryotes that have cell walls such as plants and fungi the walls are usually made of cellulose or chitin see Chapter 5 In contrast most bacterial cell walls contain peptidoglycan a polymer composed of modified sugars crosslinked by short polypeptides This molecular fab ric encloses the entire bacterium and anchors other molecules that extend from its surface Archaeal cell walls contain a vari ety of polysaccharides and proteins but lack peptidoglycan Using a technique called the Gram stain scientists can classify many bacterial species into two groups based on differences in cell wall composition Samples are first stained with crystal violet dye and iodine then rinsed in alcohol and finally stained with a red dye such as safranin Grampositive bacteria have simpler walls with a relatively large amount of peptidoglycan Gram negative bacteria have less peptidoglycan and are structurally more complex with an outer membrane that contains lipopolysaccharides carbohydrates bonded to lipids Gram staining is a valuable tool in medicine for quickly de termining if a patient s infection is due to gram negative or to grampositive bacteria This information has treatment impli cations The lipid portions of the lipopolysaccharides in the walls of many gramnegative bacteria are toxic causing fever or shock Furthermore the outer membrane of a gram negative bacterium helps protect it from the body s defenses Gramnegative bacteria also tend to be more resistant than grampositive species to antibiotics because the outer mem brane impedes entry of the drugs However certain gram positive species have virulent strains that are resistant to one or more antibiotics The effectiveness of certain antibiotics such as penicillin de rives from their inhibition of peptidoglycan crosslinking The resulting cell wall may not be functional particularly in grampositive bacteria Such drugs destroy many species of pathogenic bacteria without adversely affecting human cells which do not have peptidoglycan The cell wall of many prokaryotes is surrounded by a sticky layer of polysaccharide or protein This layer is called a capsule if it is dense and wellde ned Figure 274 or a slime layer if it is less well organized Both kinds of sticky outer lay ers enable prokaryotes to adhere to their substrate or to other individuals in a colony Some capsules and slime layers protect against dehydration and some shield pathogenic prokaryotes from attacks by their host s immune system Some prokaryotes stick to their substrate or to one another by means of hairlike appendages called fimbriae Fimbriae are usually shorter and more numerous than pili singular pilus appendages that pull two cells together prior to DNA transfer from one cell to the other see Figure 2712 pili are sometimes referred to as sex pili Motility About half of all prokaryotes are capable of taxis a directed movement toward or away from a stimulus They may move toward nutrients or oxygen posi tive chemotaxis or away om a toxic substance negative chemotaxis Of the various structures that enable prokaryotes to move the most common are agella Figure 276 Flagella singu lar agellum may be scattered over the entire surface of the cell or concentrated at one or both ends Prokaryotic agella differ greatly from eukaryotic agella They are onetenth the width and are not covered by an extension of the plasma membrane see Figure 624 The agella of prokaryotes are also very different in their molecular composition and their mechanism of propulsion Among prokaryotes bacterial and archaeal agella are similar in size and rotation mechanism but they are composed of different proteins Overall these structural and molecular comparisons suggest that the a gella of bacteria archaea and eukaryotes arose independ ently Since the agella of organisms in the three domains perform similar functions but probably are not related by common descent it is likely that they are analogous not ho mologous structures Evolutionary Origins of Bacterial Flagella three main parts the motor hook and filament that are themselves com posed of 42 different kinds of proteins bacterial agella originated as simpler structures that were modi ed in a stepwise fashion over time bacterial genomes indicate that only half of the agellum s protein components appear to be neces sary for it to function the others are inessential or not encoded in the genomes of some species Two other proteins in the motor are ho mologous to proteins that function in ion transport The proteins that comprise the rod hook and lament are all related to each other and are descended from an ancestral protein that formed a piluslike tube These findings suggest that the bac terial agellum evolved as other proteins were added to an ancestral secretory sys tem This is an example of exaptation the process in which existing structures take on new functions through descent with modi cation Internal Organization and DNA The cells of prokaryotes are simpler than those of eukaryotes in both their inter nal structure and the physical arrange ment of their DNA Prokaryotic cells lack the complex compartmentalization found in eukary otic cells However some prokaryotic cells do have specialized membranes that perform metabolic functions he genome of a prokaryote is structurally different from a eukaryotic genome and in most cases has considerably less DNA In the majority of prokaryotes the genome consists of a circular chromosome with many fewer proteins than found in the linear chromosomes of eukaryotes unlike eukaryotes prokaryotes lack a membranebounded nucleus their chromosome is located in the nucleoid a region of cytoplasm that appears lighter than the surround ing cytoplasm in electron micrographs In addition to its single chromosome a typical prokaryotic cell may also have much smaller rings of independently replicating DNA molecules called plasmids see Figure 278 most carrying only a few genes 0 Differences prokaryotic ribosomes are slightly smaller than eukaryotic ribosomes and differ in their protein and RNA content These differences allow certain antibiotics such as erythromycin and tetracycline to bind to ribosomes and block protein synthesis in prokaryotes but not in eukary otes As a result people can use these antibiotics to kill or in hibit the growth of bacteria without harming themselves Reproduction and Adaptation Prokaryotes are highly successful in part because of their po tential to reproduce quickly in a favorable environment By binary ssion see Figure 1212 a single prokaryotic cell di vides into 2 cells which then divide into 4 8 16 and so on Under optimal conditions many prokaryotes can divide every 13 hours some species can produce a new generation in only 20 minutes The cells eventually exhaust their nutrient supply poison themselves with metabolic wastes face competition from other microorganisms or are consumed by other organisms reproduction in prokaryotes draws attention to three key features of their biology They are small they repro duce by binary fission and they have short generation times As a result prokaryotic populations can consist of many trillions of individuals far more than populations of multicellular eukaryotes such as plants and animals The ability of some prokaryotes to withstand harsh condi tions also contributes to their success Certain bacteria for example develop resistant cells called endospores when they lack an essential nutrient The original cell produces a copy of its chromo some and surrounds it with a tough multilayered structure forming the endospore Water is removed from the endospore and its metabolism halts The original cell then lyses releasing the endospore Finally in part because of their short generation times prokaryotic populations can evolve substantially in short pe riods of time The ability of prokaryotes to adapt rapidly to new conditions highlights the point that although the structure of their cells is simpler than that of eukaryotic cells prokaryotes are not primitive or inferior in an evolutionary sense For over 35 billion years prokaryotic populations have responded successfully to many different types of environmental challenges one reason for this is that their populations harbor high levels of genetic diversity on which selection can act Rapid reproduction mutation and genetic recombination promote genetic diversity in prokaryotes genetic variation is a prerequisite for natural selection to occur in a population The diverse adaptations exhibited by prokaryotes suggest that their popu lations must have considerable genetic variation and they do three factors that give rise to high levels of genetic diversity in prokaryotes rapid re production mutation and genetic recombination Rapid Reproduction and Mutation In sexually reproducing species the generation of a novel allele by a new mutation is rare for any particular gene Instead most of the genetic variation in sexual populations results from the way existing alleles are arranged in new combinations during meiosis and fertilization Prokaryotes do not reproduce sexually so at first glance their extensive genetic variation may seem puzzling In fact this variation can result from prokaryotes rapid reproduction and mutation Consider a prokaryote reproducing by binary fission After repeated rounds of division most of the offspring cells are ge netically identical to the original parent cell However if errors occur during DNA replication such as insertions deletions or basepair substitutions some of the offspring cells may dif fer genetically The key point is that new mutations though rare can in crease genetic diversity quickly in species with short genera tion times and large populations This diversity in turn can lead to rapid evolution Individuals that are genetically better equipped for their environment tend to survive and reproduce more prolifically than less fit individuals Genetic Recombination Although new mutations are a major source of variation in prokaryotic populations additional diversity arises from genetic recombination the combining of DNA from two sources In eukaryotes the sexual processes of meiosis and fertilization combine DNA from two individuals in a single zygote But meiosis and fertilization do not occur in prokaryotes Instead three other mechanisms transformation transduction and conjugation can bring together prokaryotic DNA from differ ent individuals When the individuals are mem bers of different species this movement of genes from one organism to another is called horizontal gene transfer Transformation and Transduction In transformation the genotype and possibly phenotype of a prokaryotic cell are altered by the uptake of foreign DNA from its surroundings o a harmless strain of Streptococcus pneumoniae can be transformed into pneumonia causing cells if the cells are placed in a medium containing DNA from a pathogenic strain This transforma tion occurs when a nonpathogenic cell takes up a piece of DNA carrying the allele for pathogenicity and replaces its own allele with the foreign allele an exchange of homologous DNA segments The cell is now a recombinant Its chromo some contains DNA derived from two different cells In transduction phages from bacteriophages the viruses that infect bacteria carry prokaryotic genes from one host cell to another In most cases transduction results from accidents that occur during the phage replicative cycle A virus that carries prokaryotic DNA may not be able to replicate because it lacks some or all of its own ge netic material However the virus can attach to another prokaryotic cell a recipient and inject prokaryotic DNA ac quired from the first cell the donor If some of this DNA is then incorporated into the recipient cell s chromosome by DNA recombination a recombinant cell is formed Conjugation and Plasmids In a process called conjugation DNA is transferred between two prokaryotic cells usually of the same species that are temporarily joined In bacteria the DNA transfer is always oneway One cell donates the DNA and the other receives it In E coli a pilus of the donor cell attaches to the recipient The pilus then retracts pulling the two cells together much like a grappling hook The next step is thought to be the formation of a temporary mating bridge between the two cells through which the donor may transfer DNA to the recipient This is an unsettled issue however and recent evidence indicates that DNA may pass directly through the pilus which is hollow In either case the ability to form pili and donate DNA dur ing conjugation results from the presence of a particular piece of DNA called the F factor F for fertility The F factor of E coli consists of about 25 genes most required for the production of pili The F factor can exist either as a plasmid or as a segment of DNA within the bacterial chromosome The F Factor as a Plasmid The F factor in its plasmid form is called the F plasmid Cells containing the F plasmid desig nated F cells function as DNA donors during conjugation Cells lacking the F factor designated F function as DNA re cipients during conjugation The F condition is transferable in the sense that an F cell converts an F cell to F if a copy of the entire F plasmid is transferred The F Factor in the Chromosome Chromosomal genes can be transferred during conjugation when the donor cell s F factor is integrated into the chromosome A cell with the F factor built into its chromosome is called an H cell for high equency of recombination Like an F cell an Hfr cell functions as a donor during conjugation with an F cell When chromosomal DNA from an Hfr cell enters an F cell homolo gous regions of the Hfr and F chromosomes may align allow ing segments of their DNA to be exchanged This results in the production of a recombinant bacterium that has genes derived from two different cells a new genetic variant on which evo lution can act RPlasmidsandAntibioticResistance Duringthel950sinJapan physicians started noticing that some hospital patients with bacterial dysentery which produces severe diarrhea did not re spond to antibiotics that had generally been effective in the past Apparently resistance to these antibiotics had evolved in certain strains of Shigella the bacterium that causes the disease Sometimes mutation in a chromosomal gene of the pathogen can confer resistance For example a muta tion in one gene may make it less likely that the pathogen will transport a particular antibiotic into its cell Mutation in a dif ferent gene may alter the intracellular target protein for an an tibiotic molecule reducing its inhibitory effect In other cases bacteria have resistance genes which code for enzymes that specifically destroy or otherwise hinder the effectiveness of certain antibiotics such as tetracycline or ampicillin Such re sistance genes are carried by plasmids known as R plasmids R for resistance Exposing a bacterial population to a specific antibiotic whether in a laboratory culture or within a host organism will kill antibioticsensitive bacteria but not those that hap pen to have R plasmids with genes that counter the antibi otic Under these circumstances we would predict that natural selection would cause the fraction of the bacterial population carrying genes for antibiotic resistance to in crease and that is exactly what happens The medical conse quences are also predictable As you ve read resistant strains of pathogens are becoming more common making the treat ment of certain bacterial infections more difficult The prob lem is compounded by the fact that many R plasmids like F plasmids have genes that encode pili and enable DNA transfer from one bacterial cell to another by conjugation Making the problem still worse some R plasmids carry as many as ten genes for resistance to that many antibiotics Diverse nutritional and metabolic adaptations have evolved in prokaryotes The extensive genetic variation found in prokaryotic popula tions is re ected in the diverse nutritional adaptations of prokaryotes Like all organisms prokaryotes can be categorized by how they obtain energy and the carbon used in building the organic molecules that make up cells Every type of nutri tion observed in eukaryotes is represented among prokaryotes along with some nutritional modes unique to prokaryotes In fact prokaryotes have an astounding range of metabolic adap tations much broader than that found in eukaryotes Organisms that obtain energy from light are called phototrophs and those that obtain energy from chemicals are called chemotrophs Organisms that need only CO2 in some form as a carbon source are called autotrophs In contrast heterotrophs require at least one organic nutrient such as glucose to make other organic compounds Combining possi ble energy sources and carbon sources results in four major modes of nutrition The Role of Oxygen in Metabolism Prokaryotic metabolism also varies with respect to oxygen O2 Obligate aerobes must use O2 for cellular respiration see Chapter 9 and cannot grow without it Obligate anaerobes on the other hand are poisoned by O2 Some ob ligate anaerobes live exclusively by fermentation others ex tract chemical energy by anaerobic respiration in which substances other than O2 such as nitrate ions NO3 or sul fate ions SO42 accept electrons at the downhill end of electron transport chains Facultative anaerobes use O2 if it is present but can also carry out fermentation or anaerobic res piration in an anaerobic environment Nitrogen Metabolism Nitrogen is essential for the production of amino acids and nucleic acids in all organisms Whereas eukaryotes can ob tain nitrogen from only a limited group of nitrogen com pounds prokaryotes can metabolize nitrogen in a wide variety of forms some cyanobacteria and some methanogens a group of archaea convert atmospheric ni trogen N2 to ammonia NH3 a process called nitrogen fixation The cells can then incorporate this fixed nitro gen into amino acids and other organic molecules In terms of their nutrition nitrogenfixing cyanobacteria are some of the most selfsufficient organisms since they need only light CO2 N2 water and some minerals to grow Nitrogen fixation by prokaryotes has a large impact on other organisms For example nitrogenfixing prokaryotes can increase the nitrogen available to plants which cannot use tmospheric nitrogen but can use the nitrogen compounds that the prokaryotes produce from ammonia Chapter 55 dis cusses this and other essential roles that prokaryotes play in the nitrogen cycles of ecosystems Table 271 Maior Nutritional Modes Mode Energy Source Carbon Source Types oi Organisms AUTOTROPH Photoautotroph Light C0 HCO or Photosynthetic prokaryotes related compound for example cyanobacteria plants certain protists for example algae Chemoautotroph Inorganic cherni C0 HCO or Unique to certain prokaryotes cals such as HS related compound for example Sun39 ol39obus39 NH or Fe 39 1 HETEROTROPH Photoheterotroph Light Organic Unique to certain aquatic compounds and saltloving vprolcaryotes for example Flquothodohacter Chi39orofi ex39u39s Chemoheterotroph Organic Organic Many prokaryotes for exam compounds compounds pie CbsrridTium and protists fungi animals some plants Metabolic Cooperation Cooperation between prokaryotic cells allows them to use en vironmental resources they could not use as individual cells In some cases this cooperation takes place between specialized cells of a filament the eyanobacterium Anabaena has genes that encode proteins for photosynthesis and for ni trogen xation but a single cell cannot carry out both processes at the same time The reason is that photosynthesis produces 02 which inactivates the enzymes involved in nitro gen fixation Instead of living as isolated cells Anabaena forms filamentous chains Most cells in a lament carry out only photosynthesis while a few specialized cells called heteroeysts sometimes called heterocytes carry out only nitrogen xation Each heteroeyst is surrounded by a thickened cell wall that restricts entry of 02 produced by neighboring photosynthetic cells Inter cellular connections allow heteroeysts to transport fixed nitrogen to neighboring cells and to receive carbohydrates Metabolic cooperation between dif ferent prokaryotic species often occurs in surfacecoating colonies known as bio lms Cells in a bio lm secrete sig naling molecules that recruit nearby cells causing the colonies to grow Channels in the biofilm allow nutrients to reach cells in the interior and wastes to be ex pelled Bio lms are common in nature but they can cause problems by con taminating industrial products and medical equipment and contributing to tooth decay and more serious health problems Altogether damage caused by biofilms costs billions of dollars annually In another example of cooperation between prokaryotes sulfateconsuming bacteria coexist with methane consuming archaea in ballshaped aggregates on the ocean oor The baete ria appear to use the archaea s waste products such as organic compounds and hydrogen In turn the bacteria produce sulfur compounds that the archaea use as oxidizing agents when they consume methane in the absence of oxygen This partnership has global ramifications Each year these archaea consume an estimated 300 billion kilograms of methane a major contribu tor to the greenhouse effect see Chapter 55 Molecular systematics is illuminating prokaryotic phylogeny prokaryotic phylogeny comparing these characteristics shape motility nutri tional mode and response to Gram staining does not reveal a clear evolutionary history Ap plying molecular systematics to the investigation of prokaryotic phylogeny however has led to some dramatic conclusions Lessons from Molecular Systematics Using small subunit ribosomal RNA as a marker for evolutionary relation ships Carl Woese and his colleagues concluded that many prokaryotes once classified as bacteria are actually more closely related to eukaryotes and belong in a domain of their own Ar chaea One lesson from studying prokaryotic phylogeny is that the genetic diversity of prokaryotes is immense today entire prokaryotic genomes can be obtained from environmental samples using metagenomics molecular systematics is the apparent significance of horizontal gene transfer in the evolution of prokaryotes Over hundreds of millions of years prokaryotes have acquired genes from even distantly related species and they continue to do so today As a result signifi cant portions of the genomes of many prokaryotes are actu ally mosaics of genes imported from other species Archaea share certain traits with bacteria and other traits with eukaryotes Table 272 A Comparison of the Three Domains of Life CHARACTERISTIC DOMAIN Bacteria Archaea Eukarya Nuclear envelope Absent Absent Present Membraneenclosed Absent Absent Present organelles Peptidoglycan in Present Absent Absent cell wall Membrane lipids Unbranched Some Unbranched hydrocarbons branched hydrocarbons hydrocarbons RNA polymerase One kind Several kinds Several kinds initiator amino acid Formy Methionine Methionine for protein synthesis methionine lntrons in genes Very rare Present in Present in some genes many genes Response to the Growth Growth not Growth not antibiotics inhibited inhibited inhibited streptomycin and chloramphenicol Histones associated Absent Present in Present with DNA some species Circular Present Present Absent chromosome Growth at temp No Some species No eratures P l00 C Archaea live in en vironments so extreme that few other organisms can survive there Such organisms are called extremophiles meaning lovers of extreme conditions from the Greek philos lover and include extreme halophiles and extreme thermophiles Extreme halophiles from the Greek halo salt live in highly saline environments such as the Great Salt Lake and the Dead Sea see Figure 271 Some species merely tolerate salinity while others require an environment that is several times saltier than seawater which has a salinity of 35 For example the proteins and cell wall of Halobacterium have un usual features that improve function in extremely salty envi ronments but render these organisms incapable of survival if the salinity drops below 9 Extreme thermophiles from the Greek thermos hot thrive in very hot environments Figure 2716 For example archaea in the genus Sulfolobus live in sulfurrich volcanic springs as hot as 90 C At temperatures this high the cells of most organisms die because for example their DNA does not remain in a double helix and many of their proteins denature Sulfolobus and other extreme thermophiles avoid this fate be cause their DNA and proteins have adaptations that make them stable at high temperatures One extreme thermophile that lives near deepsea hot springs called hydrothermal vents is informally known as strain 121 since it can reproduce even at 121 C Another extreme thermophile Pyrococcus furiosus is used in biotechnology as a source of DNA polymerase for the PCR technique see Chapter 20 Other archaea live in more moderate environments Con sider the methanogens archaea that release methane as a by product of their unique ways of obtaining energy Many methanogens use CO2 to oxidize H2 a process that produces both energy and methane waste Among the strictest of anaer obes methanogens are poisoned by O2 Other species of methanogens inhabit the anaerobic environment within the guts of cattle termites and other herbivores playing an essential role in the nutrition of these animals Methanogens also have an important applica tion as decomposers in sewage treatment facilities Bacteria include the vast majority of prokaryotic species of which most people are aware from the pathogenic species that cause strep throat and tuberculosis to the beneficial species used to make Swiss cheese and yogurt Every major mode of nutrition and metabolism is represented among bacteria and even a small taxonomic group of bacteria may contain species exhibiting many different nutritional modes As we ll see the diverse nutritional and metabolic capabilities of bacteria and archaea are behind the great impact of these tiny organisms on Earth and its life TABLE OF BACTERIA TYPES Prokaryotes play crucial roles in the biosphere prokaryotes are so impor tant to the biosphere that if they were to disappear the prospects of survival for many other species would be dim Chemical Recycling The atoms that make up the organic molecules in all living things were at one time part of inorganic substances in the soil air and water Sooner or later those atoms will return there Ecosystems depend on the continual recycling of chem ical elements between the living and nonliving components of the environment and prokaryotes play a major role in this process For example chemoheterotrophic prokaryotes func tion as decomposers breaking down dead organisms as well as waste products and thereby unlocking supplies of carbon nitrogen and other elements Without the actions of prokary otes and other decomposers such as fungi all life would cease Prokaryotes also convert some molecules to forms that can be taken up by other organisms Cyanobacteria and other au totrophic prokaryotes use CO2 to make organic compounds such as sugars which are then passed up through food chains Cyanobacteria also produce atmospheric O2 and a variety of prokaryotes fix atmospheric nitrogen N2 into forms that other organisms can use to make the building blocks of pro teins and nucleic acids Under some conditions prokaryotes can increase the availability of nutrients that plants require for growth such as nitrogen phosphorus and potassium Prokaryotes can also decrease the availability of key plant nutrients this occurs when prokaryotes immobilize nutrients by using them to synthesize molecules that remain within their cells Thus prokaryotes can have complex effects on soil nutrient concentrations Ecological Interactions Prokaryotes play a central role in many ecological interac tions Consider symbiosis from a Greek word meaning living together an ecological relationship in which two species live in close contact with each other Prokaryotes often form symbiotic associations with much larger organisms In general the larger organism in a symbiotic relationship is known as the host and the smaller is known as the symbiont There are many cases in which a prokaryote and its host participate in mutualism an ecological interaction between two species in which both benefit Other interactions take the form of commensalism an eco logical relationship in which one species benefits while the other is not harmed or helped in any significant way Finally some prokaryotes engage in parasitism an ecological relationship in which a parasite eats the cell contents tissues or body uids of its host as a group parasites harm but usually do not kill their host at least not immediately unlike a predator Parasites that cause dis ease are known as pathogens many of which are prokaryotic The very existence of an ecosystem can depend on prokary otes o Hydrothermal vents the energy that sup ports the community is derived from the metabolic activities of chemoautotrophic bacteria These bacteria harvest chemical energy from compounds such as hydrogen sulfide H2S that are released from the vent An active hydrothermal vent may support hundreds of eukaryotic species but when the vent stops releasing chemicals the chemoautotrophic bacteria can not survive As a result the entire vent community collapses Prokaryotes have both beneficial and harmful impacts on humans bestknown prokaryotes tend to be the bacteria that cause illness in humans these pathogens represent only a small fraction of prokaryotic species Mutualistic Bacteria As is true for many other eukaryotes human wellbeing can de pend on mutualistic prokaryotes our intestines are home to an estimated 500 l000 species of bacteria their cells outnumber all human cells in the body by a factor of ten Different species live in different portions of the intestines and they vary in their ability to process different foods Many of these species are mutualists digesting food that our own intes tines cannot break down Signals from the bacterium activate human genes that build the network of intestinal blood vessels necessary to absorb nutrient molecules Other signals induce human cells to produce antimicrobial compounds to which B thetaiotaomicron is not susceptible Pathogenic Bacteria Bacteria cause about half of all human diseases Some bacterial diseases are transmitted by other species such as eas or ticks Pathogenic prokaryotes usually cause illness by producing poisons which are classified as exotoxins or endotoxins Exotoxins are proteins secreted by certain bacteria and other organisms The exotoxin stimulates intestinal cells to release chloride ions into the gut and water follows by osmosis In another exam ple the potentially fatal disease botulism is caused by botu linum toxin an exotoxin secreted by the grampositive bacterium Clostridium botulinum as it ferments various foods including improperly canned meat seafood and vegetables Endotoxins are lipopolysaccharide components of the outer membrane of gramnegative bacteria In contrast to ex otoxins endotoxins are released only when the bacteria die and their cell walls break down Endotoxinproducing bacte ria include species in the genus Salmonella such as Salmonella typhi which causes typhoid fever You might have heard of food poisoning caused by other Salmonella species that are frequently found in poultry However resistance to antibi otics is currently evolving in many bacterial strains As you read earlier the rapid reproduction of bacteria enables cells carrying resistance genes to quickly give rise to large popula tions as a result of natural selection and these genes can also spread to other species by horizontal gene transfer Horizontal gene transfer can also spread genes associated with virulence turning normally harmless bacteria into potent pathogens E coli for instance is ordinarily a harmless sym biont in the human intestines but pathogenic strains that cause bloody diarrhea have emerged Pathogenic bacteria also pose a potential threat as weapons of bioterrorism For example endospores of Bacillus anthracis sent through the mail in 2001 caused 18 people to develop in halation anthrax which was fatal in 5 of the cases Such scenar ios have stimulated more research on pathogenic prokaryotic species in the hope of developing new vaccines and antibiotics Prokaryotes in Research and Technology we reap many benefits from the meta bolic capabilities of both bacteria and archaea For example humans have long used bacteria to convert milk to cheese and yogurt In recent years our greater understanding of prokaryotes has led to an explosion of new applications in biotechnology Bacteria may soon figure prominently in a major industry plastics Globally each year about 350 billion pounds of plas tic are produced from petroleum and used to make toys stor age containers soft drink bottles and many other items These products degrade slowly creating environmental prob lems Bacteria can now be used to make natural plastics o PHA polyhydroxyalkanoate which they use to store chemical energy The FHA they produce can be extracted formed into pellets and used to make durable biodegradable plastics Another way to harness prokaryotes is in bioremediation the use of organisms to remove pollutants from soil air or water For example anaerobic bacteria and archaea decompose the organic matter in sewage converting it to material that can be used as landfill or fertilizer after chemical sterilization Other bioremediation applications include cleaning up oil spills Figure 2721b and precipitating radioactive material such as uranium out of groundwater humans can now modify bacteria to produce vitamins antibiotics hormones and other products Researchers are seeking to reduce fossil fuel use by engineering bacteria that can pro duce ethanol from various forms of biomass including agri cultural waste switchgrass municipal waste such as paper products that are not recycled and corn The usefulness of prokaryotes largely derives from their di verse forms of nutrition and metabolism All this metabolic versatility evolved prior to the appearance of the structural novelties that heralded the evolution of eukaryotic organisms to which we devote the remainder of this unit LEVEL 1 KNOWLEDGECOMPREHENSION 1 Genetic variation in bacterial populations cannot result from a transduction d mutation b transformation e meiosis c conjugation 2 Photoautotrophs use a light as an energy source and CO2 as a carbon source b light as an energy source and methane as a carbon source c N2 as an energy source and CO2 as a carbon source d CO2 as both an energy source and a carbon source e H2S as an energy source and CO2 as a carbon source 3 Which of the following statements is not true a b c d e Archaea and bacteria have different membrane lipids Both archaea and bacteria generally lack membrane enclosed organelles The cell walls of archaea lack peptidoglycan Only bacteria have histones associated with DNA OnlysomearchaeauseCO2tooxidizeH2releasingmethane 4 Which of the following involves metabolic cooperation among prokaryotic cells a binary fission b endospore formation c endotoxin release d biofilms e photoautotrophy 5Bacteria perform the following ecological roles Which role typically does not involve symbiosis a skin commensalist d gut mutualist b decomposer e pathogen c aggregate with methaneconsuming archaea 6Plantlike photosynthesis that releases 02 occurs ina cyanobacteria d actinomycetes b chlamydias e chemoautotrophic bacteria c archaea Chapter 28 Protists Protists along with plants animals and fungi are classified as eukaryotes they are in domain Eukarya one of the three do mains of life As you explore this material bear in mind that the organisms in most eukaryotic lineages are protists and most protists are unicellular Thus life differs greatly from how most of us commonly think of it The large multicellular organisms that we know best plants animals and fungi are the tips of just a few branches on the great tree of life Structural and Functional Diversity in Protists protists exhibit more structural and functional diversity than any other group of eukaryotes there are some colo nial and multicellular species Singlecelled protists are justifi ably considered the simplest eukaryotes but at the cellular level many protists are very complex the most elaborate of all cells In multicellular organisms essential biological func tions are carried out by organs Unicellular protists carry out the same essential functions but they do so using subcellu lar organelles not multicellular organs ertain protists also rely on organelles not found in most other eukaryotic cells such as contractile vac uoles that pump excess water from the protistan cell see Figure 716 Protists are more nutritionally diverse than other eukary ote groups 0 Some protists are photoautotrophs and contain chloroplasts Some are heterotrophs absorbing organic molecules or ingesting larger food particles Still other pro tists called mixotrophs combine photosynthesis and heterotrophic nutrition Reproduction and life cycles also are highly varied among protists 0 Some protists are only known to reproduce asexu ally others can also reproduce sexually or at least employ the sexual processes of meiosis and fertilization All three basic types of sexual life cycles see Figure 136 are represented among protists along with some variations that do not quite fit any of these types Endosymbiosis in Eukaryotic Evolution There is abundant evidence that much of protist di versity has its origins in endosymbiosis the process in which certain unicellular organisms engulf other cells which become endosymbionts and ultimately organelles in the host cell 0 structural biochemical and DNA sequence data indicate that the first eukaryotes acquired mitochondria by engulfing an aerobic prokaryote specifically an alpha proteobacterium The early origin of mitochondria is supported by the fact that all eu karyotes studied so far have either mitochondria or modified versions of them a lineage of heterotrophic eukaryotes acquired an additional endosymbiont a photosynthetic cyanobacterium that then evolved into plastids 0 this plastidbearing lineage gave rise to two lineages of photosynthetic protists or algae red algae and green algae This hypothesis is supported by the observation that the DNA of plastid genes in red algae and green algae closely resembles the DNA of cyanobacteria 0 Transport proteins in these membranes are homologous to proteins in the inner and outer membranes of cyanobacterial endosymbionts providing further support for the hypothesis On several occasions during eukaryotic evolution red algae and green algae underwent secondary endosymbiosis They were ingested in the food vacuoles of heterotrophic eukaryotes and became endosymbionts themselves Also consistent with the hypothesis that chlorarachniophytes evolved from a eukaryote that engulfed another eukaryote their plastids are surrounded by four membranes The two inner membranes originated as the inner and outer membranes of the ancient cyanobacterium The third membrane is derived from the engulfed alga s plasma membrane and the outermost membrane is derived from the heterotrophic eukaryote s food vacuole In some other protists plastids acquired by secondary endosymbiosis are surrounded by three membranes indicating that one of the original four membranes was lost during the course of evolution Five Supergroups of Eukaryotes Diversity of plastids produced by endosymbiosis Studies of plastidbearing eukaryotes suggest that plastids evolved from a gramnegative cyanobacterium that was engulfed by an ancestral heterotrophic eukaryote primary endosymbiosis That ancestor then diversi ed into red algae and green algae some of which were subsequently engulfed by other eukaryotes secondary endosymbiosis Many of the socalled amitochondriate protists have been shown to have mitochondria though reduced ones and some of these organ isms are now classified in entirely different groups For example microsporidians once considered amitochondriate protists are now classified as fungi The ongoing changes in our understanding of the phy logeny of protists pose challenges to students and instructors alike Hypotheses about these relationships are a focus of sci entific activity changing rapidly as new data cause previous ideas to be modified or discarded Because the root of the eukaryotic tree is not known all five supergroups are shown as diverging simulta neously from a common ancestor We know that is not cor rect but we do not know which organisms were the first to diverge from the others In addition while some of the groups in Figure 283 are well supported by morphological and DNA data others are more controversial OTo cells 0quot corrpatblc OMeosis of mcronucle 9 V00 quot iU0 JC39039 if 015 C0 ntjyg Strains a gv15ig39o pvodJCCS four haploid disirtegrate ll C ren air ing 39TIC39O b 39 sde and artiall fuse ni 1 ii 1 nucleus in each cell c aides b rritosis lv 1Cl 0 uc c 1 eac cc 39 39 39 i I jgij j j 39 V O 0 Orrwcessvpvap V 03910 rmcroruc eus a M o 399 quot 39 d quot I 2 39 W Haplold 1 w Diplood micronudeus LO lIdbi39 micronudeus 14 mates 39 a J 39 I he original Dipioid 1 lICFO39FlUCi3939US miamudeus I oiisimegrales e 5 quot 6 me cels separate 39 l l 0 39wo rourds 0quot quot quot V I binary fission yield 0 i 39 39 quot39 0 Th39 T 39 d5 0 MC tquotquot39 Conjugation four daughter CH5 nacle become of PTIOSIS produce f Tl390r1l39ClCI fuse macronuclev eight microviuclei 539 quot39 MC t d d t reproduction onguga ion an repro uc ion Excavates include protists with modified mitochondria and protists with unique agella We begin this tour with Excavata the excavates a clade recently proposed based on morphological studies of the cytoskeleton Some members of this diverse group also have an excavated feeding groove on one side of the cell body The excavates include the diplomonads the parabasalids and the euglenozoans Molecular data indicate that each of these three groups is monophyletic but the data have nei ther confirmed nor strongly refuted the monophyly of the excavate supergroup Although many excavates share certain unique cytoskeletal features we cannot yet tell whether that is because the excavates are monophyletic or because the common ancestor of eukaryotes had those features one of the more controversial of the five supergroups Diplomonads and Parabasalids The protists in these two groups lack plastids and have modi fied mitochondria found in anaerobic environments Diplomonads have modi ed mitochondria called mz39t0 somes These organelles lack functional electron transport chains and hence cannot use oxygen to help extract energy from carbohydrates and other organic molecules Instead diplomonads get the energy they need from anaerobic bio chemical pathways two equalsized nuclei and multiple agella Recall that eukaryotic agella are extensions of the cytoplasm consisting of bundles of microtubules cov ered by the cell s plasma membrane They are quite different from prokaryotic agella which are fila ments composed of the globular protein agellin attached to the cell surface Many diplomonads are parasites An infamous example is Giardia intestinalis also known as Giardia lamblia see Figure 283 which inhabits the intestines of mammals Parabasalids also have reduced mitochondria called hydrogenosomes these organelles generate some energy anaero bically releasing hydrogen gas as a byproduct The bestknown parabasalid is T richomonas vaginalis a sexually transmitted par asite that infects some 5 million people each year In females if the vagina s normal acidity is disturbed T vaginalis can outcom pete beneficial microorganisms there and infect the vagina T vaginalis has a gene that allows it to feed on the vaginal lining promoting infection Studies suggest that the protist acquired this gene by horizontal gene transfer from bacterial parasites in the vagina Euglenozoans belong to a diverse clade that includes predatory heterotrophs photosynthetic autotrophs and parasites The main morphological feature that distin guishes protists in this clade is the presence of a rod with ei ther a spiral or a crystalline structure inside each of their agella two beststudied groups of eugleno zoans are the kinetoplastids and the euglenids Kinetoplastids single large mitochon drion that contains an organized mass of DNA called a kinetoplast These protists include species that feed on prokary otes in freshwater marine and moist terrestrial ecosystems as well as species that parasitize animals plants and other pro tists kinetoplastids in the genus T rypcmosoma in fect humans and cause sleeping sickness a neurological disease that is invariably fatal if not treated The infection occurs via the bite of a vector carrier organism the African tsetse y The surface of a trypanosome is coated with millions of copies of a single protein However before the host s immune system can recognize the protein and mount an attack new generations of the parasite switch to another surface protein with a different molecular struc ture Frequent changes in the surface protein prevent the host from developing immunity Euglenids has a pocket at one end of the cell from which one or two agella emerge Many species of the euglenid Euglena are mixotrophs In sunlight they are auto trophic but when sunlight is unavailable they can become heterotrophic absorbing organic nutrients from their envi ronment Many other euglenids engulf prey by phagocytosis Chromalveolates may have originated by secondary endosymbiosis supergroup Chromalveolata the chromalveolates a large extremely diverse clade of protists has recently been proposed based on two lines of evidence First some though not all DNA sequence data suggest that the chromalveolates form a monophyletic group Second some data support the hypothesis that the chromalveolates originated more than a billion years ago when a common ancestor of the group en gulfed a singlecelled photosynthetic red alga Because red algae are thought to have originated by primary endosym biosis see Figure 282 such an origin for the chromalveo lates is referred to as secondary endosymbiosis Many species in the clade have plastids whose structure and DNA indicate that they are of red algal origin Others have reduced plastids that seem to be derived from a red algal endosymbiont Still other species lack plastids altogether yet some of these species have plastid genes in their nuclear DNA Such data have led researchers to suggest that the common ancestor of the chromalveolates had plastids of red algal origin but that later some evolutionary lineages within the group lost the plastids chromalveolates are perhaps the most controversial of the five supergroups Alveolates group of protists whose monophyly is well supported by molecular systematics Structurally species in this group have membranebounded sacs alveoli just under the plasma membrane function of alveoli is unknown researchers hypothesize that they may help stabilize the cell surface or regulate the cell s water and ion content nclude three subgroups a group of agellates the dino agellates a group of parasites the apicomplexans and a group of protists that move using cilia the ciliates Dino agellates characterized by cells that are rein forced by cellulose plates Two agella located in grooves in this armor make dino agellates from the Greek dinos whirling spin as they move through the water Dino agellates are abundant components of both marine and freshwater plankton communities of mostly microscopic or ganisms that drift in currents near the water s surface These dino agellates include some of the most important species of phytoplankton photosynthetic plankton which include pho tosynthetic bacteria as well as algae However many photo synthetic dino agellates are mixotrophic and roughly half of all dino agellates are purely heterotrophic Apicomplexans all apicomplexans are parasites of animals and some cause serious human diseases The parasites spread through their host as tiny infectious cells called sporozoites Apicomplexans are so named because one end the apex of the sporozoite cell contains a complex of organelles specialized for penetrating host cells and tissues apicomplex ans are not photosynthetic recent data show that they retain a modified plastid apicoplast most likely of red algal origin intricate life cycles with both sexual and asexual stages Those life cycles often require two or more host species for completion F malaria Ciliates a large varied group of protists named for their use of cilia to move and feed may completely cover the cell surface or may be clustered in a few rows or tufts rows of tightly packed cilia function collectively in locomotion Other ciliates scurry about on leglike structures constructed from many cilia bonded together distinctive feature of ciliates is the presence of two types of nuclei tiny micronuclei and large macronuclei A cell has one or more nuclei of each type Genetic variation results from conjugation a sexual process in which two individu als exchange haploid micronuclei but do not reproduce Ciliates generally reproduce asexually by bi nary fission during which the existing macronucleus disinte grates and a new one is formed from the cell s micronuclei Each macronucleus typically contains multiple copies of the ciliate s genome Genes in the macronucleus control the everyday functions of the cell such as feeding waste re moval and maintaining water balance Stramenopiles major subgroup of the chromalveolates is the stramenopiles protists that include some of the most im portant photosynthetic organisms on the planet as well as several clades of heterotrophs heir name from the Latin stramen straw and pilos hair refers to their characteristic a gellum which has numerous fine hairlike projections In most stramenopiles this hairy agellum is paired with a shorter smooth nonhairy agellum our groups of stramenopiles diatoms golden algae brown algae and oomycetes Smooth flaxgellurr Diatoms unicellular algae that have a unique glasslike wall made of hydrated silica silicon dioxide embedded in an organic matrix wall consists of two parts that overlap like a shoe box and its lid These walls provide effective pro tection from the crushing jaws of predators Live diatoms can withstand pressures as great as 14 million kgm2 equal to the pressure under each leg of a table supporting an elephant strength comes from the delicate lacework of holes and grooves in their walls diatoms are a highly diverse group of protists They are a major component of phytoplankton both in the ocean and in lakes The abundance of diatoms in the past is also evident in the fossil record where massive accumulations of fossilized diatom walls are major constituents of sediments known as diatomaceous earth These sediments are mined for their qual ity as a ltering medium and for many other uses expect that since diatoms are so widespread and abundant their photosynthetic activity would affect global carbon dioxide levels and this is indeed the case diatoms are eaten by a variety of protists and invertebrates but during a bloom many escape this fate When these uneaten diatoms die their bodies sink to the ocean oor Diatoms that sink to the ocean oor are not very likely to be broken down by bacteria and other decomposers Hence the carbon in their bodies re mains there rather than being released as carbon dioxide as the decomposers respire The overall effect of these events is that carbon dioxide absorbed by diatoms during photosyn thesis is transported or pumped to the ocean oor With an eye toward reducing global warming by lowering atmo spheric carbon dioxide levels some scientists advocate pro moting diatom blooms by fertilizing the ocean with essential nutrients such as iron Golden Algae characteristic color of golden algae results from their yellow and brown carotenoids The cells of golden algae are typically bi agellated with both agella attached near one end of the cell components of freshwater and marine plankton While all golden algae are photosyn thetic some species are mixotrophic These mixotrophs can absorb dissolved organic compounds or ingest food parti cles including living cells by phagocytosis Most species are unicellular but some such as those in the freshwater genus Dinobryon are colonial Figure 2814 If environmental conditions deteriorate many species form protective cysts that can survive for decades Brown Algae largest and most complex algae are brown algae All are multicellular and most are marine Brown algae are espe cially common along temperate coasts where the water is cool They owe their characteristic brown or olive color to the carotenoids in their plastids seaweeds are brown algae include species that have the most complex multicellular anatomy of all algae some even have specialized tissues and organs that resemble those in plants But morphological and DNA evidence indi cates that the similarities evolved independently in the algal and plant lineages and are thus analogous not homologous hallus plural thalli from the Greek thallos sprout refers to an algal body that is plantlike Unlike the body of a plant however a thallus lacks true roots stems and leaves A typical thallus consists of a rootlike holdfast which anchors the alga and a stemlike stipe which sup ports lea ike blades 0 blades provide most of the alga s photosynthetic surface Some brown algae are equipped with gas filled bubbleshaped oats which help keep the blades up near the water surface Beyond the inter tidal zone in deeper waters live giant seaweeds known as kelps 0 cell walls are composed of cellulose and gelforming polysaccharides that help cush ion the thalli from waves and reduce drying when the algae are exposed important commodities for humans Some species are eaten such as Laminaria Japanese kombu which is used in soups In addition the gelforming substance in the cell walls of brown algae called algin is used to thicken many processed foods including pudding and salad dressing Alternation of Generations variety of life cycles have evolved among the multicellular algae The most complex life cycles include an alternation of generations the alternation of multicellular haploid and diploid forms and diploid forms Although haploid and diploid conditions alternate in all sexual life cycles human gametes for exam ple are haploid the term alternation of generations applies only to life cycles in which both haploid and diploid stages are multicellular o The diploid individual is called the sporophyte because it produces spores The spores are haploid and move by means of agella they are called zoospores The zoospores develop into haploid multicellular male and female gametophytes which produce gametes The union of two gametes fertilization or syngamy results in a diploid zygote which matures and gives rise to a new multicellular sporophyte In Laminaria the two generations are heteromorphic meaning that the sporophytes and gametophytes are struc turally different Other algal life cycles have an alternation of isomorphic generations in which the sporophytes and ga metophytes look similar to each other although they differ in chromosome number 9 71 39p39ol39 vice 39c m 39 o1r 391 39cr 115 zcl11 tfc I w x 1 39u Inam 172 4114 3911 39n39cltxy 39c lu5 39uI39lt39 QC Ilxx 3939 usu39o 39 l39wl l 1 ivumlx urto scararqm 2 40 Q 3arargm gttdLcc nu nzzc Hus S r ui Spurophylr In 39Iquoto 39nsum 439 lt1 39 rc39t39aIIy 2lultc cut 6 3c39 t39f 3 Iquot39r dew 3 on s 3939 M3939 39J39quotquotquot Iquotquotquotquot quot J I m quotH H mt ml mt cnalc qan c olquot cs Ire ym39n39ns cw vu Y 5arcarytcs 39aquot c t39l39 1 Y i H n3939u n2 39ia mwlx I39M 39lt M H mHh q39 3 1t 1al o5 qamctpquot39 c quot39 3 Ii e 39 l739v quot 4quot 939 jlr1L fIr rin V J i 9 I zit Hvv 39 V l quoto quot quot39 T 39 or1 cnalc carrc gt39wt39 Crojuzc cogs V quot39 I391quot rIquotl 39o Inc 1 cquoto u In I o lo ma o ey quot gg 39m39n39I39o Fljcjs wzuW A I w Him m391a39t39t an 39 39crm trc satquot mm 3 059quotquot st zc spar c539l c39 rpm vq tn E I 1 Jr 39 egg 39II nIY3939 1 viii 4039quot u quotw v439I A Figure 2816 the me cycle ol the brown alga lalnlnorlo an example ol alternation of generalloln Oomycetes WIater Molds and Their Relatives nclude the water molds the white rusts and the downy mildews Based on their morphology these organisms were previously classified as fungi However there are key differences between oomycetes and fungi 0 Among the differences oomycetes typi cally have cell walls made of cellulose whereas the walls of fungi consist mainly of another polysaccharide chitin Data from molecular systematics have confirmed that oomycetes are not closely related to fungi Their superficial similarity is a case of convergent evolution In both oomycetes and fungi the high surfacetovolume ratio of filamentous structures en hances the uptake of nutrients from the environment oomycetes descended from plastidbearing an cestors they no longer have plastids and do not perform photosynthesis Instead they typically acquire nutrients as decomposers or parasites Most water molds are decom posers that grow as cottony masses on dead algae and ani mals mainly in freshwater habitats he ecological impact of oomycetes can be significant For example the oomycete Phytophthora infestans causes potato late blight which turns the stalk and stem of potato plants to black slime Late blight contributed to the devastating Irish famine of the 19th century in which a million people died and at least that many were forced to leave Ireland molecular biologists have isolated DNA from a specimen of P infestans preserved from the Irish potato blight of the 1840s Genetic studies show that in recent decades this oomycete has acquired genes that make it more aggressive and more resistant to pes ticides Rhizarians are a diverse group of protists defined by DNA similarities clade Rhizaria has recently been proposed based on re sults from molecular systematics Although its members vary greatly in morphology DNA evidence suggests that rhizarians are a monophyletic group Many species in Rhizaria are among the organisms re ferred to as amoebas Amoebas were formerly defined as protists that move and feed by means of pseudopodia ex tensions that may bulge from almost anywhere on the cell sur face An amoeba moves by extending a pseudopodium and anchoring the tip more cytoplasm then streams into the pseudopodium based on molecular systematics it is now clear that amoebas do not constitute a monophyletic group but are dispersed across many distantly related eukaryotic taxa Most of those that belong to the clade Rhizaria are dis tinguished morphologically from other amoebas by having threadlike pseudopodia Rhizarians include three groups that we ll examine here radiolarians forams and cercozoans Radiolarians Forams have delicate intricately symmetrical internal skeletons that are generally made of sil ica The pseudopodia of these mostly marine protists radiate from the central body and are reinforced by bundles of microtubules The microtubules are covered by a thin layer of cytoplasm which engulfs smaller microorgan isms that become attached to the pseudopodia Cytoplasmic streaming then carries the captured prey into the main part of the cell After radiolarians die their skeletons settle to the sea oor where they have accumulated as an ooze that is hundreds of meters thick in some locations or forams are named for their porous shells called tests Foram tests con sist of a single piece of organic material hardened with cal cium carbonate The pseudopodia that extend through the pores function in swimming test formation and feeding Many forams also derive nourishment from the photosyn thesis of symbiotic algae that live within the tests found in both the ocean and fresh water Most species live in sand or attach themselves to rocks or algae but some are abundant in plankton Ninety percent of all identified species of forams are known from fossils Along with the calciumcontaining remains of other protists the fossilized tests of forams are part of marine sediments including sedimentary rocks that are now land for mations Foram fossils are excellent markers for correlating the ages of sedimentary rocks in different parts of the world other protists the fossilized tests of forams are part of marine sediments including sedimentary rocks that are now land for mations Foram fossils are excellent markers for correlating the ages of sedimentary rocks in different parts of the world Cercozoans First identified in molecular phylogenies the cercozoans form a large group that contains most of the amoeboid and agellated protists that feed with threadlike pseudopodia Cercozoan protists are common in marine freshwater and soil ecosystems Most cercozoans are heterotrophs Many are parasites of plants animals or other protists many others are predators The predators include the most important consumers of bac teria in aquatic and soil ecosystems along with species that eat other protists fungi and even small animals One small group of cercozoans the chlorarachniophytes mentioned earlier in the discussion of secondary endosymbiosis are mixotrophic These organisms ingest smaller protists and bacteria as well as perform photosynthesis At least one other cercozoan Paulinella chromatophora is an autotroph deriving its energy from light and its carbon from carbon dioxide This species has a distinctive sausageshaped internal structure where photosynthesis is performed structures were derived from a cyanobacterium although not the same cyanobacterium from which all other plastids were derived Red algae and green algae are the closest relatives of land plants molecular systematics and studies of cell structure support the following scenario More than a billion years ago a heterotrophic protist acquired a cyanobacterial endosymbiont and the photosynthetic de scendants of this ancient protist evolved into red algae and green algae 475 million years ago the lineage that produced green algae gave rise to land plants Together red algae green algae and land plants make up the fourth eu karyotic supergroup which is called Archaeplastida Ar chaeplastida is a monophyletic group that descended from the ancient protist that engulfed a cyanobacterium diversity of their closest algal relatives red algae and green algae Red Algae 6000 known species of red algae rhodophytes from the Greek rhodos red are reddish owing to a photosyn thetic accessory pigment called phycoerythrin which masks the green of chlorophyll pecies adapted to more shallow water have less phycoerythrin As a result red algal species may be greenish red in very shallow water bright red at moderate depths and almost black in deep water Some species lack pigmentation altogether and function heterotrophically as parasites on other red algae Red algae are the most abundant large algae in the warm coastal waters of tropical oceans Their accessory pigments including phycoerythrin allow them to absorb blue and green light which penetrate relatively far into the water Most red algae are multicellular Although none are as big as the giant brown kelps the largest multicellular red algae are included in the informal designation seaweeds You may have eaten one of these multicellular red algae Porphyra Japanese nori as crispy sheets or as a wrap for sushi see Figure 2820 Red algae have especially diverse life cycles and alternation of generations is common But unlike other algae they have no agellated stages in their life cycle and depend on water currents to bring gametes to gether for fertilization Green Algae grassgreen chloroplasts of green algae have a structure and pigment composition much like the chloroplasts of land plants Molecular systematics and cellular morphology leave little doubt that green algae and land plants are closely re lated In fact some systematists now advocate including green algae in an expanded plant kingdom Viridiplantae from the Latin viridis green Phylogenetically this change makes sense since otherwise the green algae are a para phyletic group divided into two main groups the charo phytes and the chlorophytes o charophytes are the algae most closely related to land plants second group the chlorophytes from the Greek chloros green includes more than 7000 species Most live in fresh water but there are also many marine and some terres trial species simplest chlorophytes are unicellular organ isms such as Chlamydomonas which resemble gametes or zoospores of more complex chlorophytes Various species of unicellular chlorophytes live in aquatic habitats as phyto plankton or inhabit damp soil Some live symbiotically within other eukaryotes contributing part of their photosyn thetic output to the food supply of their hosts some live in snow photosynthesis Larger size and greater complexity evolved in chloro phytes by three different mechanisms 1 The formation of colonies of individual cells as seen in Volvox see Figure 283 and in filamentous forms that con tribute to the stringy masses known as pond scum 2 The formation of true multicellular bodies by cell divi sion and differentiation as in Ulva 3 The repeated division of nuclei with no cytoplasmic divi sion as in Caulerpa Most chlorophytes have complex life cycles with both sexual and asexual reproductive stages Nearly all species of chlorophytes reproduce sexually by means of bi agellated ga metes that have cupshaped chloroplasts 6 quot 39 I m 39 quot 1quot quot39 l quot4pa or we rc er 39391c39139 039 r ztrc39 cc 39 cwco 39139C 1r nLc O 39 LF3939139l 391quotIllquot39Zu 4 u I 1m39ovlisuuI1 u I 1 r 5QC 39139 039 39v39vlr21392i39gt V39 I II now I 4lt39 39 quotquot1quotquot X 393939 l lquotquotn39ni 1 me I Lu I cr lira mi 1 3939wr1c1uc quotc39c I v I quot c T 39 3 39 39139 l39lrl39t J O Cr 0 Ira c v39cr cc 3 zicvcioz X s H rc ar cc malls 3 3939 cr quotrc39qc as 1 1 I w 39m IquotquotJ Hs1In39o39s l39I39 39w mwI v 9 quotJ quot lh zc5r39 dcvc p 3912 m rc 55519 ntun 3 C ZCHS REFPIIODLKTION Q 39 REPRODUCTION o I Q U I I 3 I quotJ 4 V O39 39l 39 39r I39 c 39crc1Lcs 39 I I 4 39 o a 39 10 ll n39lI II391l39 39 uo39 0 4 2 Y I I I I Lquotccrac 390 39Lquotc39 r1t39a39 oquotr 1c E 39 3 I 39c1r cc 2 rru sc39rc pLzuc on quot CH1 V Wm V re 2 am o zuml I39M 39rot39s quotV 93 quotrc39r A Figure 2322 The life cycle ol Onlamydomoncs I n unlcollulnr thlorophyto 4sl mm x u 39 O 39 39 lt hnquotvu 1 39 I n39L 1 x 3039 L xIgI f1i 39I39 197 lt3J3 vquot1W1 quot n3939v i3939 39rc 45 39orc2 fat mp 1 LUVv39 39 an Cn39rY1i1 39kquotJd u ng Lrddufnfm l nrw JJ39u3391h quot L39i 5 quotC 3 39 393 C c3r391 r 9 fhuf m rv1w39 ul n wvxTn a139 ha hr fu m n39 x wl1 391 n2 39 4 O39l39vquotO39 lt39 Ilt un Unikonts include protists that are closely related to fungi and animals recently proposed extremely diverse super group of eukaryotes that includes animals fungi and some protists There are two major clades of unikonts the amoebo zoans and the opisthokonts animals fungi and closely re lated protist groups The close relationship be tween amoebozoans and opisthokonts is more controversial Support for this close relationship is provided by comparisons of myosin proteins and by several studies based on hundreds of genes but not by other studies based on single genes Another controversy involving the unikonts concerns the root of the eukaryotic tree Recall that the root of a phyloge netic tree anchors the tree in time Branch points close to the root are the oldest At present the root of the eukaryotic tree is uncertain thus we do not know which group of eukary otes was the first to diverge from other eukaryotes According to their hypothesis the unikonts were the first eukaryotes to diverge from other eukaryotes This hypothesis proposes that animals and fungi belong to an earlydiverging group of eukaryotes while protists that lack typical mitochondria such as the diplomonads and parabasalids diverged much later in the history of life This idea remains controversial and will require more supporting ev idence to be widely accepted Amoebozoans amoebozoans form a clade that is well supported by molecular data This clade includes many species of amoebas that have lobe or tubeshaped rather than thread like pseudopodia Amoebozoans include slime molds gym namoebas and entamoebas Slime Molds once thought to be fungi because like fungi they produce fruiting bodies that aid in spore dispersal However the resemblance between slime molds and fungi ap pears to be another example of evolutionary convergence Molecular systematics places slime molds in Amoebozoa and suggests that they descended from unicellular ancestors Slime molds have diverged into two main branches plasmodial slime molds and cellular slime molds distinguished in part by their unique life cycles Many plasmodial slime molds are brightly colored often yellow or orange Figure 2824 At one stage in their life cycle they form a mass called a plasmodium which may grow to a diameter of many centimeters Don t con fuse a slime mold s plasmodium with the genus Plasmodium which includes the parasitic apicomplexan that causes malaria Despite its size the plasmodium is not multicellular it is a sin gle mass of cytoplasm that is undivided by plasma membranes and that contains many nuclei This supercell is the product of mitotic nuclear divisions that are not followed by cytokinesis Within the plasmodium cytoplasm streams first one way then the other in pulsing ows that are beautiful to watch through a microscope This cytoplasmic streaming apparently helps distribute nutrients and oxygen The plasmodium ex tends pseudopodia through moist soil leaf mulch or rotting logs engulfing food particles by phagocytosis as it grows Cellular Slime Molds The life cycle of the protists called cellular slime molds can prompt us to question what it means to be an individual organism The feeding stage of these organisms consists of solitary cells that function individ ually but when food is depleted the cells form an aggregate that functions as a unit 01 the for quotq quotsl1quot 39 s39 l391 39n139Irm yr L39fquot39J fquot11r oh 139I Iml IIoquot 3 W i 60 W Go um 39639 39 rquotdz or OL39bl39 duzfon 239quot 39m1oEx rrr39 trfr v r max lt39 u39u 3 lt39ru39n r Ix mizt f39M1 39 gtn39p U Ow Y are rc393939 p v H l 0 390 I 9 mov atquot39 L J 39vxw39lt 1 3 mi lt m39 ur a g I 0 z3939 1quotu391r39 JD tquot39 511 lt 39 3939 391 1 39139 oquot39Jlt R H1 3939IquotVi39 I2quot quot I 39 u391 gt 1 Alum I 39 I 3cO quotQ d m391 n39 39 III I39 H quot39ltz39v a srxum 0 I 7 7 RIPRODUCIIOH 5 3 1L dLrqO 1 339 uf m 1 o3939 u q H X1 1 W quot mi 39r1 39 amp amrv1 392 1239 31 39 39r V 3 3 quot391 0 lt5 AS XUAt RFPIIODUCTION 0 0 We 39Ii 391ptquot5 flquot 9quotfI ll39H39 vquoto a F aplo 1rquot139 39 l39 39quot39o quot39 39c39u IQ 1 o39nloquot3939 J hi 391Hquot3915 n 1 quot u39nquothM quotIC39L39CJ l39 quot quot5n0 1 2 r39s 39739 Hf nquot1lI39l u I iuiz 9 quot 2 3 like acrquotjatt Ijscc hc1 O Ihc aggregate 39v39 39t5 o39 1 wquot 1 m tquot3939 ts Some 0 th 13939llS1 IL39139i1fhquotr i 1l nl39 3919 1 IquotquotII P Gymnamoebas Gymnamoebas constitute a large and varied group of amoebo zoans These unicellular protists are ubiquitous in soil as well as freshwater and marine environments Most are heterotrophs that actively seek and consume bacteria and other protists Entamoebas Whereas most amoebozoans are freeliving those that be long to the genus Entamoeba are parasites They infect all classes of vertebrate animals as well as some invertebrates Humans are host to at least six species of Entamoeba but only one E histolytica is known to be pathogenic E histolytica causes amebic dysentery and is spread via contaminated drinking water food or eating utensils Responsible for up to 100000 deaths worldwide every year the disease is the third leading cause of death due to eukaryotic parasites after malaria see Figure 2810 and schistosomiasis see Figure 3311 Opisthokonts Opisthokonts are an extremely diverse group of eukaryotes that includes animals fungi and several groups of protists The nucleariids and choano agellates illustrate why scientists have abandoned the former kingdom Protista A monophyletic group that included these singlecelled eukary otes would also have to include the multicellular animals and fungi that are closely related to them Protists play key roles in ecological communities Most protists are aquatic and they are found almost any where there is water including moist terrestrial habitats such as damp soil and leaf litter In oceans ponds and lakes many protists are bottomdwellers that attach to rocks and other substrates or creep through the sand and silt Other protists are important constituents of plankton Symbiotic Protists Many protists form symbiotic associations with other species For example photosynthetic dino agellates are foodproviding sym biotic partners of the coral polyps that build coral reefs Coral reefs are highly diverse ecological communities That diversity ultimately depends on corals and on the mutualistic protist symbionts that nourish them Corals support reef diversity by providing food to some species and habitat to many others wooddigesting protists that inhabit the gut of many termite species Symbiotic protists also include parasites that have compro mised the economies of entire countries Consider the malaria causing protist Plasmodium Income levels in countries hard hit by malaria are 33 lower than in similar countries free of the disease Protists can have devastating effects on other species too Among species that par asitize plants the oomycete protist Phytophthora ramorum has emerged as a major new forest pathogen This species causes sudden oak death SOD a disease that has killed millions of oaks and other trees in California and Oregon Photosynthetic Protists Many protists are important producers organisms that use energy from light or inorganic chemicals to convert carbon dioxide to organic compounds Producers form the base of ecological food webs In aquatic communities the main pro ducers are photosynthetic protists and prokaryotes All other organisms in the community depend on them for food either directly by eating them or indirectly by eating an organism that ate a producer 30 of the world s photosynthesis is performed by di atoms dino agellates multicellular algae and other aquatic protists Photosynthetic prokaryotes contribute another 20 and land plants are responsible for the remaining 50 Because producers form the foundation of food webs factors that affect producers can dramatically affect their entire com munity In aquatic environments photosynthetic protists are often held in check by low concentrations of nitrogen phos phorus or iron A pressing question is how global warming will affect pro tists and other producers Satellite data indicate that the growth and biomass of photosynthetic protists and prokary otes have declined in many regions as sea surface temperatures have increased If sustained these changes would likely have farreaching effects on marine ecosystems fishery yields and the global carbon cycle see Chapter 55 Global warming can also affect producers on land but there the base of food webs is occupied not by protists but by land plants Key Morphological Key ConceptI Eukaryote Supergroup Major Groups Characteristics Specific Examples C 0 N C E 1 28 2 lplom s and Modirfied mitochondria grgg anas 39 raba Excavates include protists with modified mitochondria and protists with unique ll 9 3 PP 5303958l Euglenozoans Spiral or crystalline rod l39rypanosomo What avidnaee indicates that the excavate mnetoplamds inside age a Eugkm arm a dude Elug enids quot quot 283 39 1 339fT im 39SL39l i39i2 ZlT 2i quoti3939Zn iff a Z quot l l l I r Chromalveolates may have originated by Apicomplexans Paramecium secondary endosymbiosis pp 582589 Clllates If illmmalwalata uriginatal by secondary gt endasywnbiasis what can be a39n39erred about Stramenoplles Hairy and smooth lllagellla Phytophthora quot A the plastids of its numbers Explain Diatoms l aminan a Col39den algae Brown algae Oomycetes C 0 N C E PT 28 4 Radlolarlans gsng zgrogliigh at339aetairc1lllOm HexacmIl39um T 39 Rhizarians are a diverse group of protists central body defined by DNA similarities pp 589590 What am the main subgroups of rhizarians V 039 Wat quotquot5395 hm 5quotb3quot390quotP5 05 d 39 397 Fofillli Amoebas with threadllilce Cibbigmna 39 pseudopodia and a porous shell g Ceftolollls Amoebas and flagellated protists Pauinella 39 with threadlike pseudopodia g C 0 N c E 1 28 5 Red algae celtSeyhi mentJ PorpllTyra 39 l l Red algae and green algae are the closest relatlives rlof ladpants pp 590592 Green algae Planttype chllorop39asts Chlarnydomonas Arc aep asti a Um On what basis do some systematists place k o land plants in the same supurxmup Land plants See Chapters 29 and 30 lvlosses lems conifers Arclzarplastidal as red and gem algae quot W l39lquotl9 Fgtl3 15 3 m 28 6 l l k 2 39 Unikonts include protists that are closely Gymnamoebas Drttwstelium related to fungi and animals pp 593596 5 339 b35 i a My whim rt mm quotrun mmquot Oplstholtonts Higlhl variable see Nuclleariids mt quotab U k m P 395 539 gmups quot1 39quot 0quot Chapters 3l 34 choanoflagellates animals fungi Chapter 29 Plant Diversity 1 How plants colonized land The Greening of Earth Geochemical evidence suggests that thin coatings of cyanobacteria existed on land about 12 billion years ago But it was only within the last 500 million years that small plants as well as fungi and animals joined them ashore Finally by about 385 million years ago some plants appeared that could grow much taller leading to the forma tion of the first forests Land plants evolved from green algae Morphological and Molecular Evidence Many key traits of land plants also appear in some protists pri marily algae For example plants are multicellular eukaryotic photosynthetic autotrophs as are brown red and certain green algae Plants have cell walls made of cellulose and so do green algae dino agellates and brown algae And chloroplasts with chlorophylls a and b are present in green algae euglenids and a few dino agellates as well as in plants However the charophytes are the only algae that share the following four distinctive traits with land plants strongly suggesting that they are the closest relatives of plants Rings of cellulosesynthesizing proteins The cells of both land plants and charophytes have distinctive circular rings of proteins in the plasma membrane Figure 292 These protein rings synthesize the cellulose microfibrils of the cell wall In contrast noncharophyte algae have linear sets of proteins that synthesize cellulose Peroxisome enzymes The peroxisomes see Figure 619 of both land plants and charophytes contain enzymes that help minimize the loss of organic products resulting from photorespiration see Chapter 10 Structure of agellated sperm In species of land plants that have agellated sperm the structure of the sperm closely resembles that of charophyte sperm Formation of a phragmoplast Particular details of cell division occur only in land plants and certain charophytes including the genera Chara and Coleochaete For example in land plants and certain charophytes a group of micro tubules known as the phragmoplast forms between the daughter nuclei of a dividing cell A cell plate then develops in the middle of the phragmoplast across the midline of the dividing cell see Figure 1210 The cell plate in turn gives rise to a new cross wall that separates the daughter cells Adaptations Enabling the Move to Land species of charophyte algae inhabit shallow waters around the edges of ponds and lakes where they are subject to occasional drying In such environments natural selection fa vors individual algae that can survive periods when they are not submerged in water In charophytes a layer of a durable polymer called sporopollenin prevents exposed zygotes from drying out A similar chemical adaptation is found in the tough sporopollenin walls that encase the spores of plants The bright sun light was unfiltered by water and plankton the atmosphere offered more plentiful carbon dioxide than did water the soil by the water s edge was rich in some mineral nutrients and initially there were relatively few herbivores and pathogens Derived Traits of Plants adaptations that appear to have emerged after land plants diverged from their algal relatives facilitated sur vival and reproduction on dry land inn algae ANCESTRAL hlurrmh quotus lt ALGA 3 5 2 E 5 an hmnJh39quotu5 quot39 8 1 339 lt E11ur39rxul Iy39e 3 A Figure 294 Three possible quotplantquot kingdoms V Alternation of generations 0The gametophyte produces five generalized steps haploid gametes by mitosis K9 s H o l I Pf quotI C3Jl39l39lE 18 ill39Ugtlll dpl 0 r W another plan Dlplom Rm QThe spores Mitosi Mitosis develop into multicellular t gametophytes T W0 93quotquot 93 Same Gdwete unite fertilization and form a diploid zygote Zygote OThe zygote develops Mitosis into a multicellular diploid sporophyte OThe sporophyte produces haploid spores by meiosis Suompiiyte A l2rIII A quotquot39 Charophyte algae lack the four key traits of land plants described in this figure alternation of generations with an associated trait of multicellular dependent embryos walled spores produced in sporangia multicellular gametangia and apical meristems This suggests that these four traits were absent in the ancestor common to land plants and charophytes but instead evolved as derived traits of land plants Alternation of Generations and Multicellular Dependent Embryos each generation gives rise to the other a process that is called alternation of generations This type of reproductive cycle evolved in various groups of algae but does not occur in the charophytes the algae most closely related to land plants Take care not to confuse the alternation of generations in plants with the haploid and diploid stages in the life cycles of other sexually reproducing organisms see Figurel36 In humans for example meiosis produces haploid gametes that unite forming diploid zygotes that divide and become multicellular The haploid stage is represented only by singlecelled gametes In contrast alternation of generations is distinguished by the fact that the life cycle in cludes both multicellular haploid organisms and multicellular diploid organisms The multicellular haploid gametophyte gameteproducing plant is named for its production by mito sis of haploid gametes eggs and sperm that fuse during fertil ization forming diploid zygotes Mitotic division of the zygote produces a multicellular diploid sporophyte sporeproducing plant Meiosis in a mature sporophyte produces haploid spores reproductive cells that can develop into a new haploid organism without fusing with another cell Mitotic division of the spore cell produces a new multicellular gametophyte and the cycle begins again Walled Spores Produced in Sporangia Plant spores are haploid reproductive cells that can grow into multicellular haploid gametophytes by mitosis The polymer sporopollenin makes the walls of plant spores tough and resistant to harsh environments This chemical adaptation enables spores to be dispersed through dry air without harm The sporophyte has multicellular organs called sporangia singular sporangium that produce the spores Within a spo rangium diploid cells called sporocytes or spore mother cells undergo meiosis and generate the haploid spores The outer tis sues of the sporangium protect the developing spores until they are released into the air Multicellular sporangia that produce spores with sporopolleninenriched walls are key terrestrial adaptations of land plants Multicellular Gametangia distinguishing early land plants from their algal ancestors was the production of gametes within multicellular organs called gametangia The female gametangia are called archegonia singular archegonium Each archegonium is a pear shaped organ that produces a single nonmotile egg retained within the bulbous part of the organ the top for the species shown here The male gametangia called antheridia singular cmtheridium produce sperm and release them into the environment In many groups of presentday plants the sperm have agella and swim to the eggs through water droplets or a film of water Each egg is fer tilized within an archegonium where the zygote develops into an embryo Apical Meristems Light and CO2 are mainly available above ground water and mineral nutrients are found mainly in the soilthe soil Though plants cannot move from place to place their roots and shoots can elongate increasing exposure to environmental resources This growth in length is sustained throughout the plant s life by the activity of apical meristems localized regions of cell division at the tips of roots and shoots Cells produced by apical meristems differentiate into the outer epidermis which protects the body and vari ous types of internal tissues Shoot apical meristems also generate leaves in most plants Thus the com plex bodies of plants have specialized below and aboveground organs Also Cuticle the epidermis in many species has a covering the cuticle which consists of wax and other polymers Permanently exposed to the air land plants run a far greater risk of desiccation drying out than their algal an cestors The cuticle acts as waterproofing helping prevent ex cessive water loss from the aboveground plant organs while also providing some protection from microbial attack Finally many land plants produce molecules called secondary compounds so named because they are products of secondary metabolic pathways side branches off the primary metabolic pathways that produce the lipids carbohydrates amino acids and other compounds common to all organisms Secondary compounds include compounds called alkaloids terpenes tannins and avonoids Various alkaloids terpenes and tan nins have a bitter taste strong odor or toxic effect that helps defend a plant against herbivores and parasites Flavonoids ab sorb harmful UV radiation and some related compounds deter attack by pathogens Humans also benefit from second ary compounds in plants many of which are used in spices medicines and other products The Origin and Diversification of Plants One way to distinguish groups of plants is whether or not they have an extensive system of vascular tissue cells joined into tubes that transport water and nutrients throughout the plant body Most presentday plants have a complex vascular tissue system and are therefore called vascular plants Plants that do not have an extensive transport system liverworts mosses and hornworts are described as nonvascular plants even though some mosses do have simple vascular tissue Non vascular plants are often informally called bryophytes from the Greek bryon moss and phyton plant Vascular plants which form a clade that comprises about 93 of all extant plant species can be categorized further into smaller clades Two of these clades are the lycophytes club mosses and their relatives and the pterophytes ferns and their relatives The plants in each of these clades lack seeds which is why collectively the two clades are often infor mally called seedless vascular plants However notice in Figure 297 that seedless vascular plants are paraphyletic not monophyletic Groups such as the seedless vascular plants are sometimes referred to as a grade a collection of organisms that share a key biological feature Grades can be informative by grouping organisms according to features such as lack of seeds But members of a grade unlike members of a clade do not nec essarily share the same ancestry A third clade of vascular plants consists of seed plants which represent the vast majority of living plant species A seed is an embryo packaged with a supply of nutrients inside a protective coat Seed plants can be divided into two groups gymnosperms and angiosperms based on the absence or presence of enclosed chambers in which seeds mature Gymnosperms from the Greek gymnos naked and sperm seed are grouped together as naked seed plants because their seeds are not enclosed in chambers Living gym nosperm species the most familiar of which are the conifers probably form a clade Angiosperms from the Greek cmgion container are a huge clade consisting of all owering plants Angiosperm seeds develop inside chambers called ovaries which originate within owers and mature into fruits Nearly 90 of living plant species are angiosperms Oongzn of land plants about 135 myajn Qongm of vascular uianuts ahawt 425 rn y39a3939 OOrugn of enant seed olams about 305 mya p 39a393939 39ts E E 2 n V vs 3 ANCESTRAL I39 153amps amp 395 GREEN ALGA 3 E Iquot O 391 W 03915 at yccaquotrytm ICJD rnosaes U 11 V lt sake 391 ussc soquotwor1si W gs E 5 U 0 y g I Pte39 o39wte Iferrus U 1 f1quotvtlt39v nunr5 rvfl d E u 8 at 1 I E39 I V 39 I U 439 39lvTTquot1CS393EquotT S 4 r it n 9 1 2 quotI39 3 Ds23EquotPs g 3 I I T 530 am 400 350 300 so is Mosses and other A Figure 297 Highlights of plant evolution he m3939gew showquot were narrates a lean rug 3913939ut1ess 332Jt 13938 CDFIE we to e de2ateo The Millions 0 ea39s ago I rr39yaI nonvascular plants have life cycles dominated by gametophytes 39elatc3915h 35 e1wae391 quotant C1quotCJ 3 he c1uttex2 T was 391xna1e g39oJns vm se euc at zrwary 39elat o391sos nonvascular plants bryophytes are repre sented today by three phyla of small herbaceous nonwoody plants liverworts phylum Hepatophyta mosses phylum Bryophyta and hornworts phylum An thocerophyta Liverworts and hornworts are named for their shapes plus the suffix wort from the AngloSaxon for herb Mosses are familiar to many people although some plants commonly called mosses are not really mosses at all Bryoph yte Gametophytes Unlike vascular plants in all three bryophyte phyla the hap loid gametophytes are the dominant stage of the life cycle That is they are usually larger and longerliving than the sporophytes as shown in the moss life cycle Sporophytes are typically present only part of the time When bryophyte spores are dispersed to a favorable habi tat such as moist soil or tree bark they may germinate and grow into gametophytes Germinating moss spores for ex ample characteristically produce a mass of green branched onecellthick filaments known as a protonema A protonema has a large surface area that enhances absorption of water and minerals In favorable conditions a protonema produces one or more buds Each of these budlike growths has an apical meristem that generates a gameteproducing structure known as a gametophore gamete bearer Together a protonema and one or more gametophores make up the body of a moss gametophyte A second constraint on the height of many bryophytes is the absence of vascular tissue which would en able longdistance transport of water and nutrients The thin structure of bryophyte organs makes it possible to distribute materials for short distances without specialized vascular tis sue However some mosses have conducting tissues in the center of their stems The gametophytes are anchored by delicate rhizoids which are long tubular single cells in liverworts and horn worts or filaments of cells in mosses Unlike roots which are found in vascular plant sporophytes rhizoids are not composed of tissues Bryophyte rhizoids also lack specialized conducting cells and do not play a primary role in water and mineral absorption Each archegonium produces one egg whereas each antherid ium produces many sperm Some bryophyte gametophytes are bisexual but in mosses the archegonia and antheridia are typi cally carried on separate Bryoph female and male gametophytes Fla gellated sperm swim through a lm of water toward eggs entering the archegonia in response to chemical attractants yte Sporophytes Although bryophyte sporophytes are usually green and photo synthetic when young they cannot live independently They remain attached to their parental gametophytes from which they absorb sugars amino acids minerals and water A typi cal bryophyte sporophyte consists of a foot a seta and a spo rangium Embedded in the archegonium the foot absorbs nutrients from the gametophyte The seta plural setae or stalk conducts these materials to the sporangium also called a capsule which uses them to produce spores by meiosis One capsule can generate up to 50 million spores Moss and hornwort sporophytes are often larger and more complex than those of liverworts Both moss and hornwort sporophytes also have specialized pores called stomata sin gular stoma which are also found in all vascular plants These pores support photosynthesis by allowing the exchange of CO2 and O2 between the outside air and the sporophyte in terior see Figure 103 Stomata are also the main avenues by which water evaporates from the sporophyte In hot dry con ditions the stomata close minimizing water loss The Ecological and Economic Importance of Mosses In northern conif erous forests species such as the feather moss Pleurozium har bor nitrogenfixing cyanobacteria that increase the availability of nitrogen in the ecosystem Other mosses in habit such extreme environments as mountaintops tundra and deserts Many mosses are able to live in very cold or dry habitats because they can survive the loss of most of their body water then rehydrate when moisture is available Few vascular plants can survive the same degree of desiccation Peat has long been a fuel source in Europe and Asia and it is still harvested for fuel today notably in Ireland and Canada Peat moss is also useful as a soil conditioner and for packing plant roots during shipment because it has large dead cells that can absorb roughly 20 times the moss s weight in water Peatlands cover 3 of Earth s land surface and contain roughly 30 of the world s soil carbon Globally an estimated 450 billion tons of organic carbon is stored as peat Current overharvesting of Sphagnum may reduce peat s beneficial ecological effects and contribute to global warming by releasing stored CO2 In ad dition if global temperatures continue to rise the water levels of some peatlands are expected to drop Such a change would expose peat to air and cause it to decompose thereby releas ing additional stored CO2 and contributing further to global warming Ferns and other seedless vascular plants were the first plants to grow tall Origins and Traits of Vascular Plants Unlike the nonvascular plants these species had branched sporophytes that were not de pendent on gametophytes for nutrition their branching made possible more complex bodies with multiple sporangia As plant bodies became in creasingly complex competition for space and sunlight prob ably increased The ancestors of vascular plants already had some derived traits of today s vascular plants but they lacked roots and some other adaptations that evolved later Life Cycles with Dominant Sporophytes mong living vascular plants however the sporophyte diploid generation is the larger and more complex plant in the alternation of generations V Flgure 2913 I39he Ife cyde of a fern Em ii the abi liIy39 Io disperse by wind evolved in o fem how might its life cycle be affected 0 Soorangia release soores Vlost fern species oroduce a single tyne of socre tnat develops into a oisexual pnotosyntnetic gametcohyte I 0 Eacn gametoohyte de39eloos soermoroducing c39gans called anthevidza and eggDroducirg c39gans called arcnegcnia Althougn this simplified diagram snows a sperm fertilizing an egg f39oquotn the same garnetcohyte in most fern soecaes a garnetoohyte orcduces sperm and eggs at different times Tne39efo39e tyoicali39 an egg from one gametopnyte is fertilized by a soerm from anotner gaquotetop39ne Kev I Ha oiil ijnfl V 0 39 Dialuia 2n 0 Q g 9 Pqn m Sckgrg Young HTlt39liE T d UNIquot I 391 some in ganr etDlll391tE39 OJ 0 sziersal 39 quot39 39 iHhioia Sl 4 39 39 H u 39 1 quotHUE dE 39 508 of mature gametoDI391u e ijnfl Mature New 39ooraatnvte 2n 39 soorounyte 39 zygome 2nji O Soerm use agella T ug to swim to eggs in the 9 On the undevside archegonia An attractant of the spc39oon3939te39s secreted by arcnegonia reorcduie 193595 GaTemDh m nelps direct tne soerm are spots called sori 39 5 Each sous is a CD519 of 5paga p a O A zygote develops into a new spcvopnyte and tne young olant grows out from an andieheag young lea39 arcnegcniuquot of its oarent the gametoonyte Transport in Xylem and Phloem ascular plants have two types of vascular tissue xylem and phloem Xylem conducts most of the water and minerals The xylem of most vascular plants includes tracheids tube shaped cells that carry water and minerals up from roots Because nonvascular plants lack tracheids vascular plants are sometimes referred to as tracheophytes The water conducting cells in vascular plants are lignz ed that is their cell walls are strengthened by the polymer lignin The tis sue called phloem has cells arranged into tubes that dis tribute sugars amino acids and other organic products In addition the spores of tall plants could disperse farther than those of short plants enabling tall species to colonize new environments rapidly Overall the ability to grow tall was a major evolutionary innovation that gave vascular plants a competitive edge over nonvascular plants 7 Roots Lignified vascular tissue also provides benefits below ground Instead of the rhizoids seen in bryophytes roots evolved in the sporophytes of almost all vascular plants Roots are organs that absorb water and nutrients from the soil Roots also anchor vas cular plants hence allowing the shoot system to grow taller Evolution of Leaves Leaves increase the surface area of the plant body and serve as the primary photosynthetic organ of vascular plants In terms of size and complexity leaves can be classified as either micro phylls or megaphylls All of the lycophytes the oldest lineage of presentday vascular plants and only the lycophytes have microphylls small usually spineshaped leaves sup ported by a single strand of vascular tissue Almost all other vascular plants have megaphylls leaves with a highly branched vascular system a few species have reduced leaves that appear to have evolved from megaphylls According to one model of leaf evolution microphylls originated from sporangia located on the side of the stem Megaphylls by contrast may have evolved from a series of branches lying close together on a stem As one of these branches came to grow above or overtop the others the lower branches became attened and developed webbing that joined them to one another These joined branches thus became a leaf attached to the branch that overtopped them Sporophylls and Spore Variations milestone in the evolution of plants was the emergence of sporophylls modified leaves that bear sporangia Sporophylls vary greatly in structure For example fern sporophylls produce clusters of sporangia known as sori singular sorus usually on the undersides of the sporophylls see Figure 2913 In many lycophytes and in most gymnosperms groups of sporophylls form conelike structures called strobil Most seedless vascular plant species are homosporous They have one type of sporangium that produces one type of spore which typically develops into a bisexual gametophyte as in most ferns In contrast a heterosporous species has two types of sporangia and produces two kinds of spores Megasporangia on megasporophylls produce megaspores which develop into female gametophytes microsporangia on microsporophylls produce the comparatively smaller microspores which develop into male gametophytes All seed plants and a few seedless vascular plants are heterosporous The following diagram compares the two conditions Homosporous spore production I39vDCaH39v a 739 Eggs bisemal I garretcucwryte quot Sperm Sporangium Sungle ons3orooh1 M 39I391eof spore Heterosporous spore production Meqasco39anvu m39 F l Meqassccme ETTGE gt E on rnegasoorophyi garTe 0 co yte 995 Mu39tspcrang mm H M I 4 on m crossoroohy1 Mlcmsc we a E 59939 gan etc yte The Significance of Seedless Vascular Plants With the evolution of vascular tis sue roots and leaves these plants accelerated their rate of pho tosynthesis dramatically increasing the removal of CO2 from the atmosphere Scientists estimate that CO2 levels dropped by as much as a factor of five during the Carboniferous causing global cooling that resulted in widespread glacier formation Ancient CO2 levels can be estimated in several ways These in clude counting the number of stomata in fossil leaves data from living species show that this number increases as CO2 lev els drop and measuring carbon isotope levels in fossils of plankton Different methods yield similar results suggesting that reconstructions of past climates are accurate The seedless vascular plants that formed the first forests eventually became coal In the stagnant waters of Carbonifer ous swamps dead plants did not completely decay This or ganic material turned to thick layers of peat later covered by the sea Marine sediments piled on top and over millions of years heat and pressure converted the peat to coal I Coal was crucial to the Industrial Revolution Chapter 31 FUNGI Fungi are heterotrophs that feed by absorption Nutrition and Ecology Like animals fungi are heterotrophs They cannot make their own food as plants and algae can But unlike animals fungi do not ingest eat their food Instead a fungus absorbs nutri ents from the environment outside of its body Many fungi accomplish this task by secreting powerful hydrolytic en zymes into their surroundings These enzymes break down complex molecules to smaller organic compounds that the fungi can absorb into their bodies and use Other fungi use enzymes to penetrate the walls of cells enabling the fungi to absorb nutrients from the cells This is diversity of food sources corresponds to the varied roles of fungi in ecological communitities with different species living as decomposers parasites or mutualists I De composer fungi break down and absorb nutrients from non living organic material such as fallen logs animal corpses and the wastes of living organisms I Parasitic fungi absorb nu trients from the cells of living hosts Some parasitic fungi are pathogenic including many species that cause diseases in plants I Mutualistic fungi also absorb nutrients from a host or ganism but they reciprocate with actions that benefit the host F The versatile enzymes that enable fungi to digest a wide range of food sources are not the only reason for their ecolog ical success Another important factor is how their body structure increases the efficiency of nutrient absorption Body Structure The most common fungal body structures are multicellular fila ments and single cells yeasts Many species can grow as both filaments and yeasts but even more grow only as filaments rel atively few species grow only as yeasts Yeasts often inhabit moist environments including plant sap and animal tissues where there is a ready supply of soluble nutrients such as sugars and amino acids The morphology of multicellular fungi enhances their ability to grow into and absorb nutrients from their surroundings he bodies of these fungi typically form a network of tiny filaments called hyphae singu lar hypha Hyphae consist of tubular cell walls surrounding the plasma mem brane and cytoplasm of the cells Un like plant cell walls which contain cellulose fungal cell walls are strength ened by chitin This strong but exible nitrogencontaining polysaccharide is also found in the external skeletons of insects and other arthropods ungal hyphae form an interwoven mass called a mycelium plural mycelia that infiltrates the material on which the fungus feeds A mycelium s structure maximizes its surfacetovolume ratio making feeding very efficient Specialized Hyphae in Mycorrhizal Fungi Some fungi have specialized hyphae that allow them to feed on living animals Figure 314a Other fungal species have specialized hyphae called haustoria which the fungi use to extract nutrients from or exchange nutrients with their plant hosts Figure 314b Mutually beneficial relationships be tween such fungi and plant roots are called mycorrhizae the term means fungus roots Mycorrhizal fungi fungi that form mycorrhizae can im prove delivery of phosphate ions and other minerals to plants because the vast mycelial networks of the fungi are more efficient than the plants roots at acquiring these minerals from the soil In exchange the plants supply the fungi with organic nutrients such as carbohydrates There are two main types of mycorrhizal fungi Ectomycorrhizal fungi from the Greek ektos out form sheaths of hyphae over the surface of a root and typically grow into the extracellular spaces of the root cortex see Figure 3713a Arbuscular mycorrhizal fungi from the Latin arbor tree extend branching hyphae through the root cell wall and into tubes formed by invagination pushing inward of the root cell plasma membrane Mycorrhizae are enormously important in natural ecosys tems and agriculture Almost all vascular plants have mycor rhizae and rely on their fungal partners for essential nutrients Many studies have demonstrated the significance of mycor rhizae by comparing the growth of plants with and without them see Figure 3714 Foresters commonly inoculate pine seedlings with mycorrhizal fungi to promote growth In the ab sence of human intervention mycorrhizal fungi colonize soils by dispersing haploid cells called spores that form new mycelia after germinating Fungi produce spores through sexual or asexual life cycles Most fungi propagate themselves by producing vast numbers of spores either sexually or asexually Spores can be carried long distances by wind or water If they land in a moist place where there is food they germinate producing new mycelia To appreciate how effective spores are at dispersing leave a slice of melon exposed to the air Even without a visible source of spores nearby within a week or so you will likely observe fuzzy mycelia growing from the microscopic spores that have Kev l Li39f ii quotI I H 1quotquotw2 39 1 L fiquotquot42 39uI quotI39 39739 1 339 r39quot quotf 39 rp mu SEXUAL 39 quotquot39 0 nmzooucnou 00 ASEXUAI e 2 0 RI PIIODUCYIOPI LI j 4 I3 1 39 A figure 315 Clnornlllod INC cycle of lungl VA 7 39n u39xT a39 T m 39quot39Hquot39r39 I oquot ff 3 ltn1I an 1 5s3939i39ul I 39 u 39 39oquot quot39 1 up 39r I ltogt l r39u39lt r39x l m l fallen onto the melon Sexual Reproduction The nuclei of fungal hyphae and the spores of most fungal species are haploid although many fungi have transient diploid stages that form during sexual life cycles In fungi sex ual reproduction often begins when hyphae from two mycelia release sexual signaling molecules called pheromones If the mycelia are of different mating types the pheromones from each partner bind to receptors on the other and the hyphae extend toward the source of the pheromones When the hy phae meet they fuse In species with such a compatibility test this process contributes to genetic variation by prevent ing hyphae from fusing with other hyphae from the same mycelium or another genetically identical mycelium The union of the cytoplasms of two parent mycelia is known as plasmogamy In most fungi the haploid nuclei con tributed by each parent do not fuse right away Instead parts of the fused mycelium contain coexisting genetically different nu clei Such a mycelium is said to be a heterokaryon meaning different nuclei In some species the different nuclei may even exchange chromosomes and genes in a process similar to crossing over see Chapter 13 In other species the haploid nu clei pair off two to a cell one from each parent Such a mycelium is dikaryotic meaning two nuclei As a dikary otic mycelium grows the two nuclei in each cell divide in tan dem without fusing Because these cells retain two separate haploid nuclei they differ from diploid cells which have pairs of homologous chromosomes within a single nucleus Hours days or in some fungi even centuries may pass between plasmogamy and the next stage in the sexual cycle karyogamy During karyogamy the haploid nuclei contributed by the two par ents fuse producing diploid cells Zygotes and other transient structures form during karyogamy the only diploid stage in most fungi Meiosis then restores the haploid condition leading to the formation of spores that enable the fungus to disperse The sexual processes of karyogamy and meiosis generate extensive genetic varia tion a prerequisite for natural selection Asexual Reproduction Many fungi can reproduce both sexually and asexually Some 20000 fungal species are only known to reproduce asexually As with sexual reproduction the processes of asexual repro duction vary widely among fungi Many fungi reproduce asexually by growing as filamentous fungi that produce haploid spores by mitosis such species are known informally as molds if they form visible mycelia Depending on your housekeeping habits you may have ob served molds in your kitchen forming furry carpets on fruit bread and other foods Figure 316 Molds typically grow rapidly and produce many spores asexually enabling the fungi to colonize new sources of food Many species that produce such spores can also reproduce sexually if they happen to con tact a member of their species of a different mating type Other fungi reproduce asexually by growing as singlecelled yeasts Instead of producing spores asexual reproduction in yeasts oc curs by ordinary cell divi sion or by the pinching of small bud cells off a parent cell Figure 317 As already mentioned some fungi that grow as yeasts can also grow as filamentous mycelia de pending on the availability of nutrients Many yeasts and filamen tous fungi have no known sexual stage in their life cycle Since early mycologists biologists who study fungi classified fungi based mainly on their type of sexual structure this posed a problem Mycologists have traditionally lumped all fungi lack ing sexual reproduction into a group called deuteromycetes from the Greek deutero second and mycete fungus When ever a sexual stage is discovered for a socalled deuteromycete the species is reclassified in a particular phylum depending on the type of sexual structures it forms In addition to searching for sexual stages of such unassigned fungi mycologists can now use genetic techniques to classify them CONCEPI Hmql hmr radiated Into 1 dlwnn set of Innmqm pp 641648 funqal Dtstimyuhhtnq futons o Phylum Mocpholoqy and lilo Cycles 0139ruquotTri4l39x39a39vy ma 7394xvLao1 upxn39 chytrldu 39 439o rmnom 439csstant Iva as Czmrg un zygote lung as st u1l stut LDquotTn fDquot YI39CD13 Ibu9l or wtmquotwar adlllttlainr fozmemuzl LrH39 ILlquotxl mycorrhlad quot9 AsIx I391V x I39TA quotPKLJ xpzxrws ru mxnrvs xjascolnycctcs or borne ntcmalry n 15 Ill lungl ra IN an i wax 39Ilquot1ltlt3939 rll awxzmi sgmrM I rmmlia pndoct1 A llIsialixxznrn xxM Ldmr4H mi may hmly A o basldlnmycotn flnnl39nnn1n I x I39Ilir39IiHl I r39 dub fungi rnamv on 1 3 ma cmu1ucr wxzm xpzxnvs 39ixvIx39rlu x svn rr39o The ancestor of fungi was an aquatic singlecelled agellated protist As a result system atists now recognize that fungi and animals are more closely related to each other than either group is to plants or most other eukaryotes The Origin of Fungi fungi evolved from a agellated ancestor While the majority of fungi lack agella some of the earliestdiverging lineages of fungi the chytrids discussed later in this chapter do have agella Moreover most of the protists that share a close common ancestor with animals and fungi also have agella DNA sequence data indicate that these three groups of eukaryotes the fungi the animals and their protistan relatives form a clade I members of this clade are called opisthokonts a name that refers to the posterior opistho location of the agellum in these organisms DNA sequence data also indicate that fungi are more closely related to several groups of singlecelled protists than they are to animals suggesting that the ancestor of fungi was unicellu lar One such group of unicellular protists the nucleariids consists of amoebas that feed on algae and bacteria DNA evi dence further indicates that animals are more closely related to a different group of protists the choano agellates than they are to either fungi or nucleariids Together these results sug gest that multicellularity must have evolved in animals and fungi independently from different singlecelled ancestors Based on molecular clock analysis see Chapter 26 scien tists have estimated that the ancestors of animals and fungi diverged into separate lineages about 1 billion years ago However the oldest undisputed fossils of fungi are only about 460 million years old Aquotr39I fl Infquot 7 quotMquot 1 IF31quot x39I39 x YA 391 W1 3939 quot Lmurn um An 0 quot 8 Fl AGEIIIATIFD 394 quot ANCESWOR If 3939r 2 g n I C 3 9 lTquotoi39 1339I39 Are Microsporidia Fungi In addition to animals and protists such as the nucleariids an other group of organisms the microsporidia are closely related to fungi and may in fact be fungi Microsporidia are unicellu lar parasites of animals and protists They are often used to control insect pests While microsporidia do not normally cause illness in humans they do pose a risk to people with AIDS and other immunecompromised conditions In many ways microsporidia are unlike most other eukary otes They do not have conventional mitochondria for exam ple As a result microsporidia have been something of a taxonomic mystery thought by some researchers to be a basal lineage of eukaryotes In recent years however researchers have discovered that microsporidia actually have tiny or ganelles derived from mitochondria In addition most molec ular comparisons indicate that microsporidia are fungi suggesting that they are highly derived parasites One such study a 2006 analysis of DNA sequence data from six genes in nearly 200 fungal species concluded that microsporidia are members of an earlydiverging lineage of fungi Additional ge netic data from species belonging to early diverging lineages of fungi are needed to fully resolve whether microsporidia are fungi or are a closely related but distinct group of organisms The Move to Land Much of the fungal diversity we observe today may have originated during an adaptive radiation that began when multicellular plants and animals colonized land For exam ple fossils of the earliest known vascular plants from the late Silurian period 420 million years ago contain evidence of mycorrhizal relationships between plants and fungi This evi dence includes fossils of hyphae that have penetrated within plant cells and formed structures that closely resemble the haustoria of arbuscular mycorrhizae Indeed plants probably existed in beneficial relationships with fungi from the earli est periods of colonization of land Fungi have radiated into a diverse set of lineages The phylogeny of fungi is currently the subject of much re search In the past decade molecular analyses have helped clarify the evolutionary relationships between fungal groups although there are still areas of uncertainty Figure 3111 on the next page presents a simplified version of one current hypothesis In this section we will survey each of the major fungal groups identified in this phylogenetic tree Chytrids The fungi classified in the phylum Chytridiomycota called chytrids are ubiquitous in lakes and soil Some of the approximately 1000 chytrid species are decomposers while others are parasites of protists other fungi plants or animals as we39ll see later in the chapter one such chytrid parasite has likely contributed to the global decline of amphibian populations Still other chytrids are important mutualists For example anaerobic chytrids that live in the diges tive tracts of sheep and cattle help to break down plant matter thereby contributing significantly to the animal s growth Molecular evidence supports the hypothesis that chytrids diverged early infungal evolution Like other fungi chytrids have cell walls made of chitin and they also share certain key enzymes and metabolic pathways with other fungal groups Some chytrids form colonies with hyphae while others exist as single spherical cells But chytrids are unique among fungi in having agellated spores called zoospores Zygomycetes There are approximately 1000 known species of zygomycetes fungi in the phylum Zygomycota This diverse phy lum includes species of fastgrowing molds responsible for causing foods such as bread peaches strawberries and sweet potatoes to rot during storage Other zygomycetes live as parasites or as com mensal neutral symbionts of animals The life cycle of Rhizopus stolonifer black bread mold is fairly typical of zygomycete species Figure 3113 Its hyphae spread out over the food surface penetrate it and absorb nu trients The hyphae are coenocytic with septa found only where reproductive cells are formed In the asexual phase bulbous black sporangia develop at the tips of upright hy phae Within each sporangium hundreds of haploid spores develop and are dispersed through the air Spores that happen to land on moist food germinate growing into new mycelia If environmental conditions deteriorate for instance if the mold consumes all its food Rhiz0pus may reproduce sexually The parents in a sexual union are mycelia of dif ferent mating types which possess different chemical mark ers but may appear identical Plasmogamy produces a sturdy structure called a zygosporangium in which karyogamy and then meiosis occur Note that while a zygosporangium represents the zygote Zn stage in the life cycle it is not a zy gote in the usual sense that is a cell with one diploid nu cleus Rather a zygosporangium is a multinucleate structure first heterokaryotic with many haploid nuclei from the two parents then with many diploid nuclei after karyogamy Zygosporangia are resistant to freezing and drying and are metabolically inactive When conditions improve the nuclei of the zygosporangium undergo meiosis the zygospo rangium germinates into a sporangium and the sporangium releases genetically diverse haploid spores that may colonize a new substrate Some zygomycetes such as Pilobolus can ac tually aim and then shoot their sporangia toward bright light Glomeromycetes The glomeromycetes fungi as signed to the phylum Glomeromy cota were formerly thought to be zygomycetes But recent molecular studies including a phylogenetic analysis of DNA sequence data from hundreds of fungal species indicate that glomeromycetes form a separate clade monophyletic group Although only 160 species have been identified to date the glomeromycetes are an ecologically sig nificant group in that nearly all of them form arbuscular mycorrhizae Figure 3115 The tips of the hyphae that push into plant root cells branch into tiny treelike arbuscules About 90 of all plant species have such mutualistic partnerships with glomeromycetes Ascomycetes Mycologists have described 65000 species of ascomycetes fungi in the phylum Ascomycota from a wide vari ety of marine freshwater and terres trial habitats The defining feature of ascomycetes is the production of spores in saclike asci singular ascus during sexual reproduction thus they are commonly called sac fungi Unlike zygomycetes during their sexual stage most ascomycetes develop fruiting bodies called ascocarps which range in size from microscopic to macroscopic Figure 3116 The ascocarps contain the sporeforming asci Ascomycetes vary in size and complexity from unicellular yeasts to elaborate cup fungi and morels see Figure 3116 They include some of the most devastating plant pathogens which we will discuss later However many ascomycetes are important decomposers particularly of plant material More than 25 of all ascomycete species live with green algae or cyanobacteria in beneficial symbiotic associations called lichens Some ascomycetes form mycorrhizae with plants Many others live between mesophyll cells in leaves some of these species release toxic compounds that help protect the plant from insects Ascomycetes reproduce asex ually by producing enormous numbers of asexual spores called conidia singular conidium Conidia are not formed inside sporangia as are the asexual spores of most zygomycetes Rather they are produced externally at the tips of specialized hyphae called conidiophores often in clusters or long chains from which they may be dispersed by the wind Conidia may also be involved in sexual reproduction fus ing with hyphae from a mycelium of a different mating type as occurs in Neurospora Fusion of two different mating types is followed by plasmogamy resulting in the formation of dikaryotic cells each with two haploid nuclei representing the two parents The cells at the tips of these dikaryotic hy phae develop into many asci Within each ascus karyogamy combines the two parental genomes and then meiosis forms four genetically different nuclei This is usually followed by a mitotic division forming eight ascospores The ascospores develop in and are eventually discharged from the ascocarp Basidiomycetes Approximately 30000 species includ ing mushrooms puffballs and shelf fungi are called basidiomycetes and are classified in the phylum Ba sidiomycota Figure 3118 This phy lum also includes mutualists that form mycorrhizae and two groups of destructive plant parasites rusts and smuts The name of the phylum derives from the basidium Latin for little pedestal a cell in which karyogamy occurs followed immedi ately by meiosis The clublike shape of the basidium also gives rise to the common name club fungus Basidiomycetes are important decomposers of wood and other plant material Of all the fungi certain basidiomycetes are the best at decomposing the complex polymer lignin an abundant component of wood Many shelf fungi break down the wood of weak or damaged trees and continue to decom pose the wood after the tree dies The life cycle of a basidiomycete usually includes a long lived dikaryotic mycelium Figure 3119 As in ascomycetes this extended dikaryotic stage provides opportunities for many genetic recombination events in effect multiplying the result of a single mating Periodically in response to envi ronmental stimuli the mycelium reproduces sexually by pro ducing elaborate fruiting bodies called basidiocarps The common white mushrooms in the supermarket are familiar examples of a basidiocarp By concentrating growth in the hyphae of mushrooms a ba sidiomycete mycelium can erect its fruiting structures in just a few hours a mushroom pops up as it absorbs water and as cyto plasm streams in from the dikaryotic mycelium By this process a ring of mushrooms popularly called a fairy ring may appear literally overnight Figure 3120 The mycelium below the fairy ring expands outward at a rate of about 30 cm per year decom posing organic matter in the soil as it grows Some giant fairy rings are produced by mycelia that are centuries old The numerous basidia in a basidiocarp are the sources of sexual spores called basidiospores After a mushroom forms its cap supports and protects a large surface area of dikaryotic basidia on gills During karyogamy the two nuclei in each ba sidium fuse producing a diploid nucleus see Figure 3119 This nucleus then undergoes meiosis yielding four hap loid nuclei The basidium then grows four appendages and one haploid nucleus enters each appendage and devel ops into a basidiospore Large numbers of basidiospores are produced The gills of a common white mushroom have a surface area of about 200 cm2 lion basidiospores which drop from the bottom of the cap and are blown away and may release a bil Fungi play key roles in nutrient cycling ecological interactions and human welfare Fungi as Decomposers Fungi are well adapted as decomposers of organic material in cluding the cellulose and lignin of plant cell walls In fact al most any carboncontaining substrate even jet fuel and house paint can be consumed by at least some fungi As you might expect researchers are developing ways to use a variety of fun gal species in bioremediation projects In addition fungi and bacteria are primarily responsible for keeping ecosystems stocked with the inorganic nutrients essential for plant growth Without these decomposers carbon nitrogen and other ele ments would remain tied up in organic matter Plants and the animals that eat them could not exist because elements taken from the soil would not be returned see Chapter 55 Without decomposers life as we know it would cease Fungi as Mutualists Fungi may form mutualistic relationships with plants algae cyanobacteria and animals All of these relationships have profound ecological effects often affecting the growth sur vival or reproduction of many species in a community F ungusPlant Mutualisms We39ve already considered the enormous importance of the mutualistic associations that most vascular plants form with mycorrhizal fungi In addition all plant species studied to date appear to harbor symbiotic endophytes fungi that live in side leaves or other plant parts without causing harm Most endophytes identified to date are ascomycetes Endophytes have been shown to benefit certain grasses and other non woody plants by making toxins that deter herbivores or by in creasing host plant tolerance of heat drought or heavy metals Seeking to discover how endophytes affect a woody plant re searchers tested whether leaf endophytes benefit seedlings of the cacao tree Theobroma cacao Figure 3121 Their findings show that the endophytes of woody owering plants can play an important role in defending against pathogens F ungusAnimal Mutualisms As mentioned earlier some fungi share their digestive services with animals helping break down plant material in the guts of cattle and other grazing mammals Many species of ants take ad vantage of the digestive power of fungi by raising them in farms Leaf cutter ants for example scour tropical forests in search of leaves which they cannot digest on their own but carry back to their nests and feed to the fungi Figure 3122 As the fungi grow their hyphae develop specialized swollen tips that are rich in proteins and carbo hydrates The ants feed primarily on these nutrientrich tips The fungi break down plant leaves into substances the in sects can digest and they also detoxify plant defensive compounds that would otherwise kill or harm the ants In some tropical forests the fungi have helped these insects become the major con sumers of leaves The evolution of such farmer ants and that of their fungal crops have been tightly linked for over 50 million years The fungi have become so de pendent on their caretakers that in many cases they can no longer survive without the ants and vice versa Lichens A lichen is a symbiotic association be tween a photosynthetic microorgan ism and a fungus in which millions of photosynthetic cells are held in a mass of fungal hyphae Lichens grow on the surfaces of rocks rotting logs trees and roofs in various forms Figure 3123 The photosynthetic partners are unicellular or filamentous green algae or cyanobacteria The fungal com ponent is most often an ascomycete but one glomeromycete and 75 basid iomycete lichens are known The fungus usually gives a lichen its overall shape and structure and tissues formed by hyphae account for most of the lichen s mass The algae or cyanobacteria generally oc cupy an inner layer below the lichen surface Figure 3124 The merger of fungus and alga or cyanobacterium is so complete that lichens are given scientific names as though they were single organisms to date 17000 lichen species have been described As might be expected of such dual organ isms asexual reproduction as a symbiotic unit is common This can occur either by fragmentation of the parental lichen or by the formation of soredia small clusters of hyphae with embedded algae see Figure 3124 The fungi of many lichens also reproduce sexually and lichen algae can reproduce inde pendently of the fungus by asexual cell division In most lichens each partner provides something the other could not obtain on its own The algae provide carbon com pounds the cyanobacteria also fix nitrogen see Chapter 27 and provide organic nitrogen compounds The fungi provide their photosynthetic partners with a suitable environment for growth The physical arrangement of hyphae allows for gas exchange protects the photosynthetic partner and retains water and minerals most of which are absorbed either from airborne dust or from rain The fungi also secrete acids which aid in the uptake of minerals Lichens are important pioneers on cleared rock and soil sur faces such as volcanic ows and burned forests They break down the surface by physically penetrating and chemically at tacking it and they trap windblown soil Nitrogenfixing lichens also add organic nitrogen to some ecosystems These processes make it possible for a succession of plants to grow see Chapter 54 Lichens may also have aided the coloniza tion of land by plants Fossils of lichens or lichenlike organ isms date to 550600 million years ago long before plants grew on land Early lichens may have modified rocks and soil much as they do today helping pave the way for plants As tough as lichens are however many do not stand up well to air pollution Their passive mode of mineral uptake from rain and moist air makes them particularly sensitive to sulfur dioxide and other airborne poisons Fungi as Pathogens About 30 of the 100000 known species of fungi make a living as parasites or pathogens mostly of plants Figure 3125 For example Cryphonectria parasitica the ascomycete fungus that causes chestnut blight dramatically changed the landscape of the northeastern United States Accidentally introduced on trees imported from Asia in the early 1900s spores of the fun gus enter cracks in the bark of American chestnut trees and pro duce hyphae killing the tree The oncecommon chestnuts now survive mainly as sprouts from the stumps of former trees Another ascomycete Fusarium circinatum causes pine pitch canker a disease that threatens pines throughout the world Be tween 10 and 50 of the world s fruit harvest is lost annually due to fungi and grain crops also suffer major losses each year Some fungi that attack food crops produce compounds that are toxic to humans Certain species of the ascomycete Aspergillus contaminate grain and peanuts by secreting com pounds called a atoxins Another example is the ascomycete Claviceps purpurea which grows on rye plants forming pur ple structures called ergots If infected rye is milled into our toxins from the ergots can cause ergotism characterized by gangrene nervous spasms burning sensations hallucina tions and temporary insanity An epidemic of ergotism around 944 CE killed more than 40000 people in France One compound that has been isolated from ergots is lysergic acid the raw material from which the hallucinogen LSD is made Although animals are less susceptible to parasitic fungi than are plants about 500 fungi are known to parasitize animals One such parasite the chytrid Batrachochytrium dendrobatidis has been implicated in the recent decline or extinction of about 200 species of frogs and other amphibians Figure 3126 This chytrid can cause severe skin infections leading to massive dieoffs Field observations and studies of museum specimens indicate that B dendrobatidis first appeared in frog populations shortly before their declines in Australia Costa Rica the United States and other countries In addition in regions where it infects frogs this chytrid has very low levels of genetic diversity These findings are consistent with the hypothesis that B dendrobatidis has emerged recently and spread rapidly across the globe deci mating many amphibian populations The general term for an infection caused by a fungal parasite is mycosis In humans skin mycoses include the disease ring worm so named because it appears as circular red areas on the skin The ascomycetes that cause ringworm can infect almost any skin surface Most commonly they grow on the feet caus ing the intense itching and blisters known as athlete s foot Though highly contagious athlete s foot and other ringworm infections can be treated with fungicidal lotions and powders Systemic mycoses by contrast spread through the body and usually cause very serious illnesses They are typically caused by inhaled spores For example coccidioidomycosis is a systemic mycosis that produces tuberculosislike symptoms in the lungs Each year hundreds of cases in North America require treatment with antifungal drugs without which the disease would be fatal Some mycoses are opportunistic occurring only when a change in the body s microorganisms chemical environ ment or immune system allows fungi to grow unchecked Candida albicans for example is one of the normal inhabi tants of moist epithelia such as the vaginal lining Under cer tain circumstances Candida can grow too rapidly and become pathogenic leading to socalled yeast infections Many other opportunistic mycoses in humans have become more common in recent decades due in part to AIDS which compromises the immune system Practical Uses of Fungi We depend on their ecological services as de composers and recyclers of organic matter And without mycorrhizae farming would be far less productive Mushrooms are not the only fungi of interest for human consumption Fungi are used to ripen Roquefort and other blue cheeses A species of Aspergillus produces citric acid used in colas Morels and truf es the edible fruiting bodies of vari ous ascomycetes are highly prized for their complex avors see Figure 3116 These fungi can sell for hundreds to thou sands of dollars a pound Truf es release strong odors that at tract mammals and insects which in nature feed on them and disperse their spores In some cases the odors mimic the pheromones sex attractants of certain mammals For example the odors of several European truf es mimic the pheromones released by male pigs which explains why female pigs are used to help find these delicacies Humans have used yeasts to produce alcoholic beverages and bread for thousands of years Under anaerobic condi tions yeasts ferment sugars to alcohol and CO2 which causes dough to rise Only relatively recently have the yeasts involved been separated into pure cultures for more con trolled use The yeast Saccharomyces cerevisiae is the most im portant of all cultured fungi see Figure 317 It is available as many strains of baker s yeast and breWer s yeast Many fungi have great medical value as Well For example a compound extracted from ergots is used to reduce high blood pressure and to stop maternal bleeding after childbirth Some fungi produce antibiotics that are effective in treating bacterial infections In fact the first antibiotic discovered was penicillin made by the ascomycete mold Penicillium Figure 3127 Other examples of pharmaceuticals derived from fungi include cholesterollowering drugs and cyclosporine a drug used to suppress the immune system after organ transplants Fungi also figure prominently in research For example the yeast Saccharomyces cerevisiae is used to study the molecular ge netics of eukaryotes because its cells are easy to culture and ma nipulate Scientists are gaining insight into the genes involved in Parkinson s disease and other human diseases by examining the functions of homologous genes in S cerevisiae Genetically modified fungi hold much promise Although bacteria such as Escherichia coli can produce some useful pro teins they cannot synthesize glycoproteins because they lack enzymes that can attach carbohydrates to proteins Fungi on the other hand do produce such enzymes In 2003 scientists succeeded in engineering a strain of S cerevisiae that produces human glycoproteins including insulinlike growth factor Such fungusproduced glycoproteins have the potential to treat people with medical conditions that prevent them from producing these compounds Meanwhile other researchers are sequencing the genome of the wood digesting basidiomycete Phanerochaete chrysosporium one of many white rot fungi They hope to decipher the metabolic pathways by which white rot breaks down wood with the goal of harnessing these pathways to produce paper pulp 1 LEVEL 1 KNOWLEDGECOMPREHENSION 1 All fungi share which of the following characteristics 1 symbiotic d pathogenic 2 heterotrophic e act as decomposers 3 agellated 2 Which feature seen in chytrids supports the hypothesis that they diverged earliest in fungal evolution a the absence of chitin within the cell wall b coenocytic hyphae c agellated spores d formation of resistant zygosporangia e parasitic lifestyle 3 Which of the following cells or structures are associated with asexual reproduction in fungi a ascospores d conidiophores b basidiospores e ascocarps c zygosporangia 4 The photosynthetic symbiont of a lichen is often a a moss d an ascomycete b a green alga e a small vascular plant c a brown alga 5 Among the organisms listed here which are thought to be the closest relatives of fungi a animals b vascular plants c mosses d brown algae e slime molds 2 LEVEL 2 APPLICATIONANALYSIS 6 The adaptive advantage associated with the filamentous na ture of fungal mycelia is primarily related to 1 theabilitytoformhaustoriaandparasitizeotherorganisms 2 avoidingsexualrepro ductionuntiltheenvironmentchanges 3 the potential to inhabit almost all terrestrial habitats 4 the increased probability of contact between different mat ing types 5 an extensive surface area well suited for invasive growth and absorptive nutrition Chapter 32 Overviw of Animal Diversity Animals are multicellular heterotrophic eukaryotes with tissues that develop from embryonic layers Nutritional Mode Plants are autotrophic eukaryotes capable of gener ating organic molecules through photosynthesis Fungi are heterotrophs that grow on or near their food and that feed by absorption often after they have released enzymes that di gest the food outside their bodies Unlike plants animals cannot construct all of their own organic molecules and so in most cases they ingest them either by eating other living organisms or by eating nonliving organic material But un like fungi most animals do not feed by absorption instead animals ingest their food and then use enzymes to digest it within their bodies Cell Structure and Specialization Animals are eukaryotes and like plants and most fungi ani mals are multicellular In contrast to plants and fungi how ever animals lack the structural support of cell walls Instead a variety of proteins external to the cell membrane provide structural support to animal cells and connect them to one another see Figure 630 The most abundant of these pro teins is collagen which is found only in animals Many animals have two types of specialized cells not found in other multicellular organisms muscle cells and nerve cells In most animals these cells are organized into tissues groups of cells that have a common structure func tion or both Muscle tissue and nervous tissue are responsi ble for moving the body and conducting nerve impulses respectively The ability to move and conduct nerve impulses underlies many of the adaptations that differentiate animals from plants and fungi For this reason muscle and nerve cells are central to the animal lifestyle lquotquotquotquot quot quot Pnomstome development Eu t examples molluscs quotquot39 quot 39 annelids erieiml Ih hme are E t H E f I m I a Cleavage lmii generdli I itLe ate 2 Ii Le 5 a e rm exwmmm m 9 9 9 9 piopstorrie derelloprr eiiit UeglflihVa39l1il splllldll 39LlEI l39lllll39lllll7 Lll d39u39dgE Devuierosturiie ma Review 4 I uevellvupiiimziit I5 l lsdlldLtEfl eCl 15 As an early by iardidl iintteterimiriate uld more likely I Ll 1 quot1Q3 sable of giving me anquotanmm Spiiral and determinate Fladial and iiiitleterrniiiiiate quotquotel Pquotquotquot quot b oelom formation Coeloiiin 39development Ufl rlJlUll tiegins in he gasiiiula stage llin ylJl Dl39US39I0lIll lE uevellupiimziit the Loizllprri orrris fruit splints M1 the l39l l85UL39l39L flI1 llin deuterrostoiiiiie uew3ll upiiim2ii the Loellprri orrris fruiiv llliquotE 50UEIl l39lrll out Llicetiirn null tliiiz NlE3Jd39El I39l l Blastopoire Blastopoire Mlesuderrn drL wUng5 Solid masses of mesoderrn Fpllds of airchenteron split arid llorm coelom foirm Loell i lll c Fate of the blastopore lri Auius M quot pirotmtorrie iieueIlcapwemt the rrioutlii loiiiiiiis irom the hllastopcxe lri czleiuterosturrie devellJpiiiieii39 the iiiwtlii D9517 quot99 foams fimm 1 sewrmiary Key 39UlJL ll39lTl39lg I Ettommi Mouth Anus Mesoueiini Moutli develops from plastopore Anus develops from Ulld510pJll8 Ericluderir Reproduction and Development Most animals reproduce sexually and the diploid stage usually dominates the life cycle In the haploid stage sperm and egg cells are produced directly by meiotic division unlike what oc curs in plants and fungi see Figure 136 In most animal species a small agellated sperm fertilizes a larger nonmotile quotquot egg forming a diploid zygote The zygote then undergoes 39 4 cleavage a succession of mitotic cell divisions without cell growth between the divisions During the development of 0 most animals cleavage leads to the formation of a multicellu quot I i I lar stage called a blastula which in many animals takes the form of a hollow ball Figure 322 Following the blastula m 1290 stage is the process of gastrulation during which the layers of I embryonic tissues that will develop into adult body parts are 0 39 39 produced The resulting developmental stage is called a gastrula 39 quotr 39 Although some animals including humans develop directly into adults the life cycles of most animals include at least one larval stage A larva is a sexually immature form of an animal 3939Lquot39 I3939quot39 that is morphologically distinct from the adult usually eats dif ferent food and may even have a different habitat than the q 1 adult as in the case ofthe aquatic larva ofa mosquito or drag I U I V on y Animal larvae eventually undergo metamorphosis a j 3 f developmental transformation that turns the animal into a 39 if quot n juvenile that resembles an adult but is not yet sexually mature 39 39 quot3939t I 39 39 Iquot Although adult animals vary widely in morphology the genes 39 quot39 Currlnao39 that control animal development are similar across a broad range of taxa All animals have developmental genes that 39 39 regulate the expression of other genes and many of these 39 quot quot 393 39 regu latory genes contain sets of DNA sequences called homeoboxes see Chapter 21 Most animals share a unique 0 A F I I V homeobox containing family of genes known as Hox genes Hox genes play important roles in the development of animal on an on 39 n39o 0lo embryos controlling the expression of dozens or even quotW 1 W o hundreds of other genes that in uence animal morphology see Chapter 25 Sponges which are among the simplest extant animals lack Hox genes However they have other homeobox genes that in uence their shape such as those that regulate the formation of water channels in the body wall a key feature of sponge morphology see Figure 334 In the ancestors of more com plex animals the Hox gene family arose via the duplication of earlier homeobox genes Over time the Hox gene family under went a series of duplications yielding a versatile toolkit for regulating development In vertebrates insects and most other animals Hox genes regulate the formation of the anterior posterior fronttoback axis as well as other aspects of develop ment Similar sets of conserved genes govern the development of both ies and humans despite their obvious differences and hundreds of millions of years of divergent evolution The history of animals spans more than half a billion years the animal kingdom includes not only a great diversity of living species but an even greater diversity of extinct ones Some paleontologists have estimated that over 99 of all animal species are extinct Various studies suggest that this great diversity originated during the last billion years For ex ample some estimates based on molecular clocks suggest that the ancestors of animals diverged from the ancestors of fungi about a billion years ago Other such studies have esti mated that the common ancestor of living animals lived sometime between 800 and 675 million years ago To learn what this common ancestor may have been like scientists have sought to identify protist groups that are closely related to animals As shown in Figure 323 a combi nation of morphological and molecular evidence indicates that choano agellates are among the closest living relatives of animals Based on such evidence researchers hypothesize that the common ancestor of living animals may have been a sus pension feeder similar to presentday choano agellates We will next survey the fossil evidence for how animals evolved from their distant common ancestor over four geologic eras see Table 251 to review the geologic time scale Each ERA described do we need to learn CONCEPT t The history of animals spans more than half a billion years pp 656658 535 525 mya Origin and Cambrian explosion diversification 365 mya of dinosaurs S65 mia Early land Diversification Ediacaran biota animals of mammals E fa l I F 39 39f41quot U Neoproterozoic I Paleozoic I Mesozoic Cz i cquot 1000 542 251 655 0 Millions of years ago Ijm39afI Animals can be characterized by body plans Animal species vary tremendously in morphology but their great diversity in form can be described by a relatively small number of major body plans A body plan is a particular set of morphological and developmental traits integrated into a functional whole the living animal The term plan here does not imply that animal forms are the result of conscious planning or invention But body plans do provide a succinct way to compare and contrast key animal features They also are of interest in the study of evodevo the interface between evolution and development see Chapters 21 and 25 Like all features of organisms animal body plans have evolved over time Some of the evolutionary changes appear to have occurred early in the history of animal life For exam ple recent research suggests that a key step in the molecular control of gastrulation has remained unchanged for more than 500 million years Figure 326 This early evolutionary inno vation was of fundamental importance Gastrulation helps to explain why most animals are not a hollow ball of cells As we39ll discuss however other aspects of animal body plans have changed multiple times over the course of evolution Thus as we explore the major features of animal body plans bear in mind that similar body forms may have evolved independently in different lineages In addition body features can be lost over the course of evolution causing some closely related species to look very different from one another Symmetry A basic feature of animal bodies is their type of symmetry or absence of symmetry Many sponges for example lack sym metry altogether Some animals exhibit radial symmetry the type of symmetry found in a owerpot Figure 327a Sea anemones for example have a top side where the mouth is located and a bottom side But they have no front and back ends and no left and right sides The twosided symmetry seen in a shovel is an example of bilateral symmetry Figure 327b A bilateral animal has two axes of orientation front to back and top to bottom Such animals have a dorsal top side and a ventral bottom side a left side and a right side and an anterior front end and a posterior back end Many animals with a bilaterally symmet rical body plan such as arthropods and mammals have sen sory equipment concentrated at their anterior end including a central nervous system brain in the head an evolutionary trend called cephalization from the Greek kephale head The symmetry of an animal generally fits its lifestyle Many radial animals are sessile living attached to a substrate or planktonic drifting or weakly swimming such as jellies ommonly called jellyfishes Their symmetry equips them to meet the environment equally well from all sides In contrast bilateral animals typically move actively from place to place Most bilateral animals have a central nervous system that en ables them to coordinate the complex movements involved in crawling burrowing ying or swimming Fossil evidence in dicates that these two fundamentally different kinds of sym metry have been present for at least 550 million years Tissues Animal body plans also vary with regard to tissue organiza tion In animals true tissues are collections of specialized cells isolated from other tissues by membranous layers While sponges and a few other groups lack true tissues in all other animals the embryo becomes layered through the process of gastrulation see Figure 322 As development pro gresses these concentric layers called germ layers form the various tissues and organs of the body Ectoderm the germ layer covering the surface of the embryo gives rise to the outer covering of the animal and in some phyla to the cen tral nervous system Endoderm the innermost germ layer lines the pouch that forms during gastrulation the archen teron and gives rise to the lining of the digestive tract or cavity and organs such as the liver and lungs of vertebrates Animals that have only these two germ layers are said to be diploblastic Diploblasts include the animals called cnidarians jellies and corals for example as well as the comb jellies see Chapter 33 All bilaterally symmetrical animals have a third germ layer called the mesoderm which fills much of the space between the ectoderm and endoderm Thus animals with bilateral symmetry are also said to be triploblastic having three germ layers In triploblasts the mesoderm forms the mus cles and most other organs between the digestive tract and the outer covering of the animal Triploblasts include a broad range of animals from atworms to arthropods to vertebrates Al though some diploblasts actually do have a third germ layer it is not nearly as well developed as the mesoderm of animals con sidered to be triploblastic Body Cavities Most triploblastic animals have a body cavity a uid or air filled space located between the digestive tract and the outer body wall This body cavity is also called a coelom from the Greek koilos hollow A socalled true coelom forms from tissue derived from mesoderm The inner and outer layers of tissue that surround the cavity connect and form structures that suspend the internal organs Animals with a true coelom are known as coelomates Figure 328a Some triploblastic animals have a body cavity that is formed from mesoderm and endoderm Figure 328b Such a cavity is called a pseudocoelom from the Greek pseudo false and the animals that have one are called pseudocoelomates Despite its name however a pseudocoelom is not false it is a fully functional body cavity Finally some triplobastic animals lack a body cavity altogether Figure 328c They are known collec tively as acoelomates from the Greek a without A body cavity has many functions Its uid cushions the suspended organs helping to prevent internal injury In soft bodied coelomates such as earthworms the coelom contains noncompressible uid that acts like a skeleton against which muscles can work The cavity also enables the internal organs to grow and move independently of the outer body wall If it were not for your coelom for example every beat of your heart or ripple of your intestine would warp your body39s surface Terms such as coelomates and pseudocoelomates refer to or ganisms that have a similar body plan and hence belong to the same grade a group whose members share key biological fea tures However phylogenetic studies show that true coeloms and pseudocoeloms have been independently gained or lost multiple times in the course of animal evolution As illustrated by this example a grade is not necessarily equivalent to a clade a group that includes an ancestral species and all of its descen dants Thus while describing an organism as a coelomate or pseudocoelomate can be helpful in describing certain of its features these terms must be interpreted with caution when seeking to understand evolutionary history 39 I I 1 Radial symmolry J ru39I quotr 1 P U xquot 1quot c 39 39 39 39 i 39 p If 2 u 1 1 r39 3939r fv3939 1 rH 1 39quot 39x39 39r M ar r 39iv39 quotquotz394 quot 39239 quottr 39 1 39 1 391quotv quotvquot39l quot3 quot39quotr quotquot J 39J39quot quot1 bl ailmnal symmmry A 39 P8S 1 39vs lt M r 4 12239rv rj wequot 39ar quot39 x39 quot 5 3 Pquot x 39 is 2 3 3 x1 quot 21 fzfoquot If I 54 9 39 39 39 i139quot 39t 39 39 quotquot39l quot9 quotquotquotr quotM139Jquot quot A Hgurc 327 Body symmetry 39 quot3939 ca 3 r I r quotii WiVJquot 31 Iquot39 L 39 J quotquotquot quotYquotquotquot39 2quot39 39d39I39quot L 39i39 d n39 39 iquota Protostome and Deuterostome Development Based on certain aspects of early development many ani mals can be described as having one of two developmental modes protostome development or deuterostome development These modes can generally be distinguished by differences in cleavage coelom formation and fate of the blastopore Cleavage Many animals with protostome development undergo spiral cleavage in which the planes of cell division are diagonal to the vertical axis of the embryo as seen in the eightcell stage of the embryo smaller cells are centered over the grooves be tween larger underlying cells Figure 329a left Furthermore the socalled determinate cleavage of some animals with protostome development rigidly casts determines the developmental fate of each embryonic cell very early A cell isolated from a snail at the fourcell stage for example cannot develop into a whole animal Instead after repeated divisions such a cell will form an inviable embryo that lacks many parts In contrast to the spiral cleavage pattern deutero stome development is predominantly characterized by radial cleavage The cleavage planes are either parallel or perpendicu lar to the vertical axis of the embryo as seen at the eightcell stage the tiers of cells are aligned one directly above the other see Figure 329a right Most animals with deuterostome devel opment also have indeterminate cleavage meaning that each cell produced by early cleavage divisions retains the capacity to develop into a complete embryo For example if the cells of a sea urchin embryo are separated at the fourcell stage each can form a complete larva Similarly it is the indeterminate cleavage of the human zygote that makes identical twins possible Coelom Formation During gastrulation an embryo s developing digestive tube initially forms as a blind pouch the archenteron which becomes the gut Figure 329b As the archenteron forms in protostome development initially solid masses of mesoderm split and form the coelom In contrast in deuterostome de velopment the mesoderm buds from the wall of the archen teron and its cavity becomes the coelom Fate of Blastopore Protostome and deuterostome development often differ in the fate of the blastopore the indentation that during gastrula tion leads to the formation of the archenteron Figure 329c After the archenteron develops in most animals a second opening forms at the opposite end of the gastrula In many species the blastopore and this second opening become the two openings of the digestive tube the mouth and the anus In protostome development the mouth generally develops from the first opening the blastopore and it is for this charac teristic that the term protostome derives from the Greek protos first and stoma mouth In deuterostome development from the Greek deuteros second the mouth is derived from the sec ondary opening and the blastopore usually forms the anus New views of animal phylogeny are emerging from molecular data Researchers have long based their hypotheses about ani mal phylogeny on morphological data Now biologists also reconstruct phylogenies using molecular data Additional clues have come from studies of lesserknown animal phyla along with fossil data that help clarify when key morphologi cal traits arose in various groups Another important change has been the use of cladistics see Chapter 26 Phylogenetic systematists seek to place or ganisms into clades each of which includes an ancestral species and all of its descendants Based on cladistic meth ods a phylogenetic tree takes shape as a hierarchy of clades nested within larger clades the finer and thicker branches of the tree respectively Clades are inferred from shared derived characters that are unique to members of the clade For example a clade might be inferred from key anatomical and em bryological similarities that researchersconclude are homologous Molecular data such as DNA sequences are another source of information for inferring common ancestry But whether the data used are traditional mor phological characters or new mol ecular sequences or a combination the goal is the same to reconstruct evolutionary history Points of Agreement 1 All animals share a common ancestor Both trees indicate that animals are monophyletic forming a clade called Metazoa All extant and extinct animal lineages have descended from a common ancestor 2 Sponges are basal animals Among the extant taxa sponges phylum Porifera branch from the base of both an imal trees Morphological and molecular analyses published in 2009 indicate that sponges are monophyletic as shown here some earlier studies had suggested that sponges are paraphyletic 3 Eumetazoa is a clade of animals with true tissues All animals except for sponges and a few others belong to a clade of eumetazoans true animals True tissues evolved in the common ancestor of living eumetazoans Basal eumetazoans which include the phyla Ctenophora comb jellies and Cnidaria are diploblastic and generally have radial symmetry 4 Most animal phyla belong to the clade Bilateria Bilateral symmetry and the presence of three germ layers are shared derived characters that help define the clade Bilateria This clade contains the majority of animal phyla and its members are known as bilaterians The Cambrian explosion was primarily a rapid diversification of bilaterians 5 Chordates and some other phyla belong to the clade Deuterostomia The term deuterostome refers not only to a mode of animal development but also to the members of a clade that includes vertebrates and other chordates Note however that the traditional and molec ular views of animal phylogeny disagree as to which other phyla are also deuterostomes Progress in Resolving Bilaterian Relationships While evolutionary relationships inferred from morphologi cal data and molecular data are similar in many respects there are some differences For example the morphology based tree in Figure 3210 divides the bilaterians into deuterostomes and protostomes This view assumes that these two modes of development re ect a phylogenetic pat tern Within the protostomes arthropods such as insects and crustaceans are grouped with annelids Both groups have segmented bodies think of the tail of a lobster which is an arthropod and an earthworm which is an annelid A different view has emerged from molecular phylogenies based on ribosomal genes Hox genes and dozens of other proteincoding nuclear genes as well as mitochondrial genes Collectively these studies indicate that there are three major clades of bilaterally sym metrical animals the Deuterostomia Lophotrochozoa and Ecdysozoa see Figure 3211 In contrast to the tradi tional morphological view the molec ular phylogeny holds that the arthropods and annelids are not closely related to one another Note also that Figure 3211 includes a group of acoelomate atworms Acoela not shown in Figure 3210 Traditionally acoelomate atworms were classified with other atworms in the phylum Platyhelminthes However recent re search indicates that acoelomate at worms are basal bilaterians and not members of the phylum Platy helminthes Acoela s basal position suggests that the bilaterians may have descended from a common ancestor that resembled living acoelomate atworms that is from an ancestor that had a simple nervous system a saclike gut with a single opening the mouth and no excretory system As seen in Figure 3211 the molec ular phylogeny assigns the animal phyla that are not in Deuterostomia to two taxa rather than one the ecdysozoans and the lophotrochozoans The clade name Ecdysozoa refers to a characteristic shared by nematodes arthropods and some of the other ecdysozoan phyla that are not included in our survey These animals secrete external skeletons exoskeletons the stiff covering of a cicada or cricket is an example As the animal grows it molts squirm ing out of its old exoskeleton and secreting a larger one The process of shedding the old exoskeleton is called ecdysis Figure 3212 Though named for this characteristic the clade de was proposed mainly on the basis of molecular data that support the common ancestry of its members Further more some taxa excluded from this clade by their molecular data such as certain species of leeches do in fact molt The name Lophotrochozoa refers to two different features observed in some animals belonging to this clade Some lophotrochozoans such as ectoprocts develop a structure called a lophophore from the Greek Iophos crest and pherein to carry a crown of ciliated tentacles that function in feeding Figure 3213a Individuals in other phyla including molluscs and annelids go through a distinctive developmen tal stage called the trochophore larva Figure 3213b hence the name lophotrochozoan Future Directions in Animal Systematics Like any area of scientific inquiry animal systematics is a work in progress At present most systematists think that the tree shown in Figure 3211 is more strongly supported than is the tree shown in Figure 3210 Of course as new informa tion emerges our understanding of the evolutionary rela tionships shown in these trees may change Researchers continue to conduct largescale analyses of multiple genes and morphological traits across a wide sample of animal phyla A better understanding of the relationships between these phyla will give scientists a clearer picture of how the di versity of animal body plans arose In Chapters 33 and 34 we will take a closer look at the diverse phyla of extant animals and their evolutionary history LEVEL 1 KNOWLEDGECOMPREHENSION 1 Among the characteristics unique to animals is a gastrulation d agellated sperm b multicellularity e heterotrophic nutrition c sexual reproduction 2 The distinction between sponges and other animal phyla is based mainly on the absence versus the presence of a a body cavity d true tissues b a complete digestive tract e mesoderm c a circulatory system 3 Acoelomates are characterized by a the absence of a brain b the absence of mesoderm c deuterostome development d a coelom that is not completely lined with mesoderm e a solid body without a cavity surrounding internal organs 4 Which of the following was probably the least important fac tor in bringing about the Cambrian explosion a theemergenceofpredatorpreyrelationshipsamonganimals b the accumulation of diverse adaptations such as shells and different modes of locomotion the movement of animals onto land the origin of Hox genes and other genetic changes affecting the regulation of developmental genes e the accumulation of suf cient atmospheric oxygen to sup port the more active metabolism of mobile animals 0 LEVEL 2 APPLICATION ANALYSIS 5 Which of these is a point of con ict between the phyloge netic analyses presented in Figures 3210 and 3211 1 the monophyly of the animal kingdom 2 the relationship of taxa of segmented animals to taxa of nonsegmented animals 3 that sponges are basal animals 4 that chordates are deuterostomes 5 the monophyly of the bilaterians Chapter 33 Intro to Invertebrates Pornquotrd ANCESTRAL g C11IUxnlIJ 39 quot39 PROTIST 1 1 I 1 9 quots 39LUW 1m can Louquotnu rurhUzoa J U ur39nLesor U 5 amp all ar39urr39al3 2 ELu39y5c zux 1 E g n 3 an Deuterostcxirua gt E Kingdom Animalia encompasses 13 million known species and estimates of total species range as high as 1020 million species Of the 23 phyla surveyed here 12 are discussed more fully in this chapter Chapter 32 or Chapter 34 crossreferences are given at the end of their descriptions Porifera 5500 species Placozoa 1 species Animals in this phylum are informally called sponges Sponges are sessile animals that lack true tissues They live as suspen sion feeders trapping particles that pass through the internal channels of their body see Concept 331 A500099 Cnidaria 10000 species Cnidarians indude corals iellies and hydras These animals have a diploblastic radially symmetrical body plan that includes a gastrovascular cavity with a single opening that serves as both mouth and anus see Concept 332 A jelly Acoela 400 species Acoel flatworms have a simple nervous system and a saclike gut and thus were once placed in phylum Platyhelminthes Molecular analyses however indicate that Aooela is a separate lineage that diverged before the three main bilaterian clades see Concept 324 Acoel atworms LM The single known spedes in this phylum Tridraplax adhaerrns doesn39t even look like an animal It consists of a simple bilayer of a few thousand cells Placomans are thought to be basal animals but it is not yet known how they are related to other earlydiverging animal groups such as Porifera and Cnidaria Trichoplax can repro duce by dividing into two indi viduals or by budding off many multioellular individuals Ctenophora 100 species A placozoan LM Ctenophores comb iellies are diploblastic and radially symmet rical like cnidarians suggesting that both phyla diverged from other animals very early see Fig ure 3211 Comb iellies make up much of the ocean39s plankton They have many distinctive traits including eight combs of cilia that propel the animals through the water When a small animal contacts the tentacles of some comb iellies specialized cells burst open covering the prey with sticky threads A ctenophore or comb jelly Lophotrochozoa Platyhelminthes 20000 species Rotifera 1800 species flatworms including tapeworms planarians and tlukes have bilateral symmetry and a central nervous system that processes information from sensory structures lhey have no body cavity or organs for circulation see Concept 333 A marine atworm Ectoprocta 4500 species Despite their microscopic size rotifers have specialized organ systems including an Q alimentary canal a digestive tract with E both a mouth and an anus 39I11ey feed on 11 microorganisms suspended in water see 8 Concept 333 A rotnfer LM Brachiopoda 335 species lLctoprotts also known as bryozoans a tough exoskeleton see Concept 333 Ectoprocts live as sessile colonies and are covered by Brachiopods or lamp shells may be easily mistaken for clams or other molluscs llowever most brachiopods have a unique stalk that anchors them to their substrate as well as a crown of cilia called a lophophore see Concept 333 A b393h39 0 d tjavmmad on Mr pagr Lophotrochozoa continued Acanthocephala 1100 species Cycliophora 1 species Acanthoeephalans are 1he only known Lydia called spinyheaded worms phoran species Symbiun because of the curved ptmdom was discovered in hooks on the proboscis at 1995 on the mouthparts of the anterior end of their a lobster This tiny vase body All specits are para f3JL39d creature has a unique sites Some acanthoeepha y plan and a particularly lans manipulate the binrre life cyde Males behavior of their inter impregnate females that mediate hosts generally W are still developing in their arthropods in ways that H mothers bodies The fertil increase their chances of ized females then esca reaching their final hosts Aquot quotquot39 quothquotquot39quot um A quotquot quoth quot39quot 39 quot d SEMI settle elsewhere on thtfob generally vertebrates For example acanthocephalans that ster and release their offspring 39lhe offspring apparently leave infect New Zealand mud crabs force their hosts to move to that lobster and search for another one to which they attach more visible areas on the beach where the crabs are more likely to be eaten birds the worms final hosts Some hyl netic analyses plate the acanthoeephalarrs within Rotifefa use Annequotda Mollusca 16500 species 93000 species Nemertea Annelids or segmented worms Molluscs including snails p SPECIES are distinguished from other clams squids and octo worms by their body segmenta puses have a soft body Also called pwbustis Wotms tion IZarthworms are the most that in many species is 01 bbm WOITIIS n39m l39tt al1S familiar annelids but the protected by a hard shell swim through water or bur phylum consists primarily of see Concept 333 13901quot in Sand extending 3 marine and freshwater species unique proboscis to capture sec concept 333 prey Like flatwomis they lack a true coelom However unlike flatworms nemerteans A marine annelid have an alimentary anal and a closed circulatory sys A ribbon worm tem in which the blood is contained in vessels and hence is distinct from fluid in the body cavity Loricifera 10 species Priapula 16 species Loriciferans from the latin Priapulans are worms with lorica corset and font to a large rounded proboscis bear are tiny animals that at the anterior end They inhabit the deepsea bottom are named after Priapos the A loriciferan can telescope Greek god of fertility who its head neck and thorax was symbolized by a giant in and out of the lorica a from pocketformedbysixplates 0Smmto20cminlength surrounding the abdomen most species burrow through Though the natural history seafloor sediments Fossil of loriciferans is mostly a evidence suggests that mystery at least some priapulans were among the species likely eat bacteria maior predators during A loridferan LM A ptiapulan the Cambrian period Ecdysozoa continued Onychophora 110 species Tardigrada 800 species Onychophorans also Tardigrades from the latin called velvet worms lardus slow and xrudus step originated during the are sometimes called water bears Cambrian explosion see for their rounded shape stubby Chapter 32 Originally appendages and lum they thrived in the bearlike gait Most rades ocean but at some are less than 05 mm in point they succeeded in Some live in oceans or fresh colonizing land Today water while others live on plants they live only in humid or animals As many as 2 million forests Onychophorans tardigrades can be found on a have eshy antennae and square meter of moss liarsh several dozen pairs of conditions may cause tardigrades saclike legs to enter a state of dormancy Tardigrades lcobtiled SEM while dormant they can survive temperatures as low as 272 C close to absolute zero Nematoda 25000 species Arthmpoda Also called roundwonns 1 000000 species nematodes are enormously abundant and diverse in line vast majority of known animal the soil and in aquatic species including insects ems habitats many s par taceans and arachnids are arthro asitiaeplantsan animals podsAllarthropodshavea Their most distinctive segmented exoskeleton and iointed feature is a tough cuticle appendages see Concept 334 A roundworm that coats the body see colored SEMI Concept 334 A scorpion an arachnid Deuterostomia Chordata 52000 species Hemichordata 85 species An acorn worm Like echinoderrns and chordates hemichordates are members of the deuterostome clade see Chapter 32 Hemichor dates share some traits with chordates such as gill slits and a dorsal nerve cord The largest group of hemichordates is the enteropneusts or acorn worms Acorn worms are marine and generally live buried in mud or under rocks they may grow to more than 2m in length More than 90 of all known chordate species have backbones and thus are vertebrates However the phylum Ihordata also includes three groups of invertebrates lancelets tuni cates and hagfishes See Chapter 34 for a full discussion of this phylum A tunicate Echinodermata 7000 species Echinoderms such as sand dollars sea stars and sea urchins are marine animals in the deuteros tome clade that are bilaterally symmetrical as larvae but not as adults They move and feed by using a network of intemal canals to pump water to differ ent parts of their body see loncept 335 A sea urchin Sponges are basal animals that lack true tissues Animals in the phylum Porifera are known informally as sponges sponges are sedentary and were mistaken for plants by the ancient Greeks They range in size from a few millimeters to a few meters and most species are ma rine though a few live in fresh water Sponges are suspension feeders They capture food particles suspended in the water that passes through their body which in some species resembles a sac perforated with pores Water is drawn through the pores into a central cavity the spongocoel and then ows out of the sponge through a larger opening called the osculum More complex sponges have folded body walls and many contain branched water canals and several oscula Sponges are basal animals that is they represent a lineage that originates near the root of the phylogenetic tree of animals Unlike nearly all other animals sponges lack true tis sues groups of similar cells that act as a functional unit and are isolated from other tissues by membranous layers However the sponge body does contain several different cell types For example lining the interior of the spongocoel are agellated choanocytes or collar cells named for the fingerlike projec tions that form a collar around the agellum These cells en gulf bacteria and other food particles by phagocytosis The similarity between choanocytes and the cells of choano agel lates supports molecular evidence suggesting that animals evolved from a choano agellatelike ancestor see Figure 323 The body of a sponge consists of two layers of cells sepa rated by a gelatinous region called the mesohyl Because both cell layers are in contact with water processes such as gas exchange and waste removal can occur by diffusion across the membranes of these cells Other tasks are performed by cells called amoebocytes named for their use of pseudopo dia These cells move through the mesohyl and have many functions For example they take up food from the surround ing water and from choanocytes digest it and carry nutrients to other cells Amoebocytes also manufacture tough skeletal fibers within the mesohyl In some sponges these fibers are sharp spicules made from calcium carbonate or silica Other sponges produce more exible fibers composed of a protein called spongin you may have seen these pliant skeletons being sold as brown bath sponges Finally and perhaps most importantly amoebocytes are capable of becoming other types of sponge cells This gives the sponge body remarkable exibil ity enabling it to adjust its shape in response to changes in its physical environment such as the direction of water currents V Figure 334 Anatomy of a sponge 9Choanocytes The spongocoel is lined with flagellated cells called choanocytes By beating flagella the choanocytes create a current that draws water in through the H 99quot39 quotquot F00 quot 39L39E5 Cfugdrngcyie pores and out through the osculum I Collquot m muwf l 3 r Azure vase spurnge ljCalflsporig39a plIcrferaIl Ospongocoel Water I passing through pores enters a cavity called the spongocoel Plhagocyiosns 0 food particles A memcfze O Pores Water enters the sponge through pores formed by doughnut shaped cells that span the body wall OThe movement of a choanocyte39s flagellum also draws water through its collar of fingerlike projections Food particles are trapped in the mucus that coats the projections engulfed by phagocytosis and either digested or 9 Epid quotquotiquot The t 39 transferred to amoebocytes layer consists of tightly packed epidermal cells 0Amoebocytes These cells can transport nutrients to other cells of the sponge body produce materials for skeletal fibers spicules or become any type of sponge cell as needed 0 Mesohyl The wall of this sponge consists of two layers of cells separated by a gelatinous matrix the mesohyl quotmiddle matterquot Most sponges are hermaphrodites meaning that each individual functions as both male and female in sexual repro duction by producing sperm and eggs Almost all sponges ex hibit sequential hermaphroditism They function first as one sex and then as the other Sponge gametes arise from choanocytes or amoebocytes Eggs reside in the mesohyl but sperm are carried out of the sponge by the water current Crossfertilization results from some of the sperm being drawn into neighboring individu als Fertilization occurs in the mesohyl where the zygotes de velop into agellated swimming larvae that disperse from the parent sponge After settling on a suitable substrate a larva develops into a sessile adult Sponges produce a variety of antibiotics and other defen sive compounds Researchers are now isolating these com pounds which hold promise for fighting human diseases For example a compound called cribrostatin isolated from ma rine sponges can kill penicillinresistant strains of the bac terium Streptococcus Other sponge derived compounds are being tested as possible anticancer agents The basic body plan of a cnidarian is a sac with a central digestive compartment the gastrovascular cavity A sin gle opening to this cavity functions as both mouth and anus There are two variations on this body plan the sessile polyp and the motile medusa Figure 335 Polyps are cylindrical forms that adhere to the substrate by the aboral end of their body the end opposite the mouth and extend their tenta cles waiting for prey Examples of the polyp form include hy dras and sea anemones A medusa plural medusae resembles a attened mouth down version of the polyp It moves freely in the water by a combination of passive drifting and contrac tions of its bellshaped body Medusae include freeswimming jellies The tentacles of a jelly dangle from the oral surface which points downward Some cnidarians exist only as polyps or only as medusae others have both a polyp stage and a medusa stage in their life cycle Mouthanus Polyp W u lemade Medusa g w quot A Gastfovascujafkxgig f cavity Gastrodermls I Mesoglea j Body stalk Epidermis gt Tentaclequotquot C outhanus A Figure 335 Polyp and medusa forms of cnidarians The body wall of a cnidarian has two layers of cells an outer layer of epidermis darker blue derived from ectoderm and an inner layer of gastrodermis yellow derived from endoderm Digestion begins in the gastrovascular cavity and is completed inside food vacuoles in the gastroderrnal cells flagella on the gastrodermal cells keep the contents of the gastrovascular cavity agitated and help distribute nutrients Sandwiched between the epidermis and gastrodermis is a gelatinous layer the mesoglea Cnidarians are carnivores that often use tentacles arranged in a ring around their mouth to capture prey and push the food into their gastrovascular cavity where digestion begins Enzymes are secreted into the cavity thus breaking down the prey into a nutrientrich broth Cells lining the cavity then ab sorb these nutrients and complete the digestive process any undigested remains are expelled through the mouthanus The tentacles are armed with batteries of cnidocytes cells unique to cnidarians that function in defense and prey capture Figure 336 Cnidocytes contain cnidae from the Greek cnide nettle capsulelike organelles that are capable of ex ploding outward and that give phylum Cnidaria its name Spe cialized cnidae called nematocysts contain a stinging thread that can penetrate the body wall of the cnidarian s prey Other kinds of cnidae have long threads that stick to or entangle small prey that bump into the cnidarian s tentacles Contractile tissues and nerves occur in their simplest forms in cnidarians Cells of the epidermis outer layer and gastro dermis inner layer have bundles of microfilaments arranged into contractile fibers see Chapter 6 The gastrovascular cavity acts as a hydrostatic skeleton see Concept 506 against which the contractile cells can work When a cnidarian closes its mouth the volume of the cavity is fixed and contraction of selected cells causes the animal to change shape Movements are coordinated by a nerve net Cnidarians have no brain and the noncentralized nerve net is associated with sensory structures that are distributed around the body Thus the animal can detect and respond to stimuli from all directions The phylum Cnidaria is divided into four major clades Hy drozoa Scyphozoa Cubozoa and Anthozoa Hydrozoans Most hydrozoans alternate between the polyp and medusa forms as seen in the life cycle of Obelia Figure 338 The polyp stage a colony of interconnected polyps in the case of Obelia is more conspicuous than the medusa Hydras among the few cnidarians found in fresh water are unusual hydro zoans in that they exist only in polyp form When environ mental conditions are favorable a hydra reproduces asexually by budding forming outgrowths that pinch off from the par ent and live independently see Figure 132 When conditions deteriorate hydras can reproduce sexually forming resistant zygotes that remain dormant until conditions improve Scyphozoans The medusa is the predominant stage in the life cycle of most scyphozoans The medusae of most species live among the plankton as jellies Most coastal scyphozoans go through a stage as small polyps during their life cycle whereas those that live in the open ocean generally lack the polyp stage altogether Cubozoans As their name which means cube animals suggests cubo zoans have a boxshaped medusa stage Cubozoans can be dis tinguished from scyphozoans in other ways such as having complex eyes embedded in the fringe of their medusae They also are comparatively strong swimmers and as a result are less likely to be stranded on shore Most cubozoans live in tropical oceans and are equipped with highly toxic cnidocytes The sea wasp Chironex eckeri a cubozoan that lives off the coast of northern Australia is one of the deadliest organisms known Its sting causes intense pain and can lead to respiratory failure car diac arrest and death within minutes The poison of sea wasps isn t universally fatal however sea turtles have defenses against it allowing them to eat the cubozoan in great quantities Anthozoans Sea anemones see Figure 337d and corals belong to the clade Anthozoa meaning ower animals These cnidarians occur only as polyps Corals live as solitary or colonial forms often forming symbioses with algae see Chapter 28 Many species secrete a hard external skeleton of calcium carbonate Each polyp generation builds on the skeletal remains of earlier gener ations constructing rocks with shapes characteristic of their species These skeletons are what we usually think of as coral Coral reefs are to tropical seas what rain forests are to tropical land areas They provide habitat for many other species Unfor tunately these reefs are being destroyed at an alarming rate Pol lution and overfishing are major threats and global warming may also be contributing to their demise by raising seawater temperatures above the narrow range in which corals thrive bl Scyphozoa Many lellies are C Cubozoa A notorious d Anthozoa Sea anemones bioluminescent Food example is the sea wasp and other anthozoans exist captured by nernatocyst Chironex fJ39ecl39lten39J Its poison only as polyps Many bearing tentacles is trans which can subdue fish and anthozoans torm symbiotic quot ferred to specialized oral arms other large prey is more relationships with 3 HYdf0l0a 50 599095 SW 65 1h i5 that lack nematocysts tor potent than cobra venom photosynthetic algae one live as colonial polyps transport to the mouth A Figure 337 Cnidarians coiled Cnidocyte A Figure 336 A cnldocyte of a hydra This type oil cnidocyte contains a stinging capsule the nematocyst which contains a coiled thread When a quottriggerquot is stimulated by touch or by certain chemicals the thread shoots out puncturing and injecting poison into prey Qotner polyps specialized 0ledusae SWi39n for reproduction lack 0ff 9390 39h and tentacles and produce tiny F9PV0dUCe 59XUaquot rnedusae by asexual pudding quot OSorne of the colony39s polyps equipped with tentacles are specialized for feeding Reproductive I 39 Feeding PR yp polyp pH PJ O A colony of I k interconnected Medusa l polyps inset bud 39 i V LM results Gonad 0 J from asexual I p 1 reproduction rV1edU53 pk LI Dy pudding SEXUAL Egg i sperm REPRODUCTION ASEXUAL REPRODUCTION Portion of BUDDING a colony of polyps ll In Developing polyp Planula larval at Mature Bl polyp j E quot 0 0 5 V quot OTne planula eventually settles OTne zygote develops into a Hapluld r l and develops into a new polyp solid ciliated larva called a planula DpUd igjznjj Lophotrochozoans a clade identified by molecular data have the widest range of animal body forms The vast majority of animal species belong to the clade Bilateria whose members exhibit bilateral symmetry and triploblastic development see Chapter 32 Most bilaterians also have a digestive tract with two openings a mouth and an anus and a coelom While the sequence of bilaterian evolution is a subject of active inves tigation the most recent common ancestor of living bilaterians probably existed in the late Proterozoic eon about 575 million years ago Many of the major groups of bilaterians first ap peared in the fossil record during the Cambrian explosion molecular evidence suggests that there are three major clades of bilaterally symmetrical animals Lophotrochozoa Ecdysozoa and Deuterostomia This section will focus on the first of these clades the lophotrochozoans Although the clade Lophotrochozoa was identified by mo lecular data its name comes from features found in some of its members Some lophotrochozoans develop a structure called a Iophophore a crown of ciliated tentacles that func tions in feeding while others go through a distinctive stage called the trochophore larva see Figure 3213 Other members of the group have neither of these features Few other unique morphological features are widely shared within the group in fact the lophotrochozoans are the most diverse bilaterian clade in terms of body plan This diversity in form is re ected in the number of phyla classified in the group Lophotro chozoa includes about 18 phyla more than twice the num ber in any other clade of bilaterians We39ll now introduce six diverse lophotrochozoan phyla the atworms rotifers ectoprocts brachiopods molluscs and annelids Flatworms Flatworms phylum Platyhelminthes live in marine fresh water and damp terrestrial habitats In addition to free living species atworms include many parasitic species such as ukes and tapeworms Flatworms are so named be cause they have thin bodies that are attened dorsoven trally between the dorsal and ventral surfaces the word platyhelminth means at worm Note that worm is not a formal taxonomic name but rather refers to a grade of ani mals with long thin bodies The smallest atworms are nearly microscopic freeliving species while some tapeworms are more than 20 m long Although atworms undergo triploblastic development they are acoelomates animals that lack a body cavity Their at shape places all their cells close to water in the surround ing environment or in their gut Because of this proximity to water gas exchange and the elimination of nitrogenous waste ammonia can occur by diffusion across the body surface Flatworms have no organs specialized for gas exchange and their relatively simple excretory apparatus functions mainly to maintain osmotic balance with their surroundings This appa ratus consists of protonephridia networks of tubules with ciliated structures called ame bulbs that pull uid through branched ducts opening to the outside see Figure 4411 Most atworms have a gastrovascular cavity with only one opening Though atworms lack a circulatory system the fine branches of the gastrovascular cavity distribute food directly to the animal s cells FreeLiving Species Freeliving rhabditophorans are important as predators and scavengers in a wide range of freshwater and marine habitats The bestknown members of this group are freshwater species in the genus Dugesia commonly called planarians Abun dant in unpolluted ponds and streams planarians prey on smaller animals or feed on dead animals They move by using cilia on their ventral surface gliding along a film of mucus they secrete Some other rhabditophorans also use their mus cles to swim through water with an undulating motion A planarian s head is equipped with a pair of light sensitive eyespots and lateral aps that function mainly to detect specific chemicals The planarian nervous system is more complex and centralized than the nerve nets of cnidar ians Figure 3310 Experiments have shown that planarians can learn to modify their responses to stimuli Some planarians can reproduce asexually through fission The parent constricts roughly in the middle of its body sepa rating into a head end and a tail end each end then regener ates the missing parts Sexual reproduction also occurs Planarians are hermaphrodites and copulating mates typi cally crossfertilize each other Parasitic Species More than half of the known species of rhabditophorans live as parasites in or on other animals Many have suckers that attach to the internal organs or outer surfaces of the host an imal In most species a tough covering helps protect the par asites within their hosts Reproductive organs occupy nearly the entire interior of these worms Trematodes As a group trematodes par asitize a wide range of hosts and most species have complex life cycles with al ternating sexual and asexual stages Many trematodes require an intermedi ate host in which larvae develop before infecting the final host usually a verte brate where the adult worms live For example trematodes that parasitize hu mans spend part of their lives in snail hosts Figure 3311 Around the world some 200 million people are infected with trematodes called blood ukes Schistosoma and suffer from schistoso miasis a disease whose symptoms in clude pain anemia and diarrhea Living within different hosts puts de mands on trematodes that freeliving animals don t face A blood uke for instance must evade the immune sys tems of both snails and humans By mimicking the surface proteins of its hosts the blood uke creates a partial immunological camou age for itself It also releases molecules that manipulate the hosts immune systems into tolerating the parasite s existence These de fenses are so effective that individual blood ukes can survive in humans for more than 40 years Tapeworms The tapeworms are a second large and diverse group of parasitic rhabditophorans Figure 3312 The adults live mostly inside vertebrates including humans In many tapeworms the ante rior end or scolex is armed with suckers and often hooks that the worm uses to at tach itself to the intestinal lining of its host Tapeworms lack a mouth and gas trovascular cavity they simply absorb nu trients released by digestion in the host s intestine Absorption occurs across the Doctors have patients take the drug niclosamide by mouth to kill the adult worms Posterior to the scolex is a long ribbon of units called proglottids which are little more than sacs of sex organs After sexual reproduction proglottids loaded with thou sands of fertilized eggs are released from the posterior end of a tapeworm and leave the host s body in feces In one type of life cycle feces carrying the eggs contaminate the food or water of intermediate hosts such as pigs or cattle and the tapeworm eggs develop into larvae that encyst in mus cles of these animals A human acquires the larvae by eating undercooked meat con taining the cysts and the worms develop into mature adults within the human Large tapeworms can block the intestines and rob enough nutrients from the human host to cause nutritional deficiencies Rotifers Rotifers phylum Rotifera are tiny animals that inhabit fresh water marine and damp soil habitats Ranging in size from about 50 pm to 2 mm rotifers are smaller than many protists but nevertheless are multicellular and have specialized organ systems Figure 3313 In contrast to cnidarians and at worms which have a gastrovascular cavity rotifers have an alimentary canal a digestive tube with two openings a mouth and an anus Internal organs lie within the pseudo coelom a body cavity that is not completely lined by mesoderm see Figure 328b Fluid in the pseudocoelom serves as a hydro static skeleton Movement of a rotifer s body distributes the uid throughout the body circulating nutrients The word rotifer is derived from the Latin meaning wheel bearer a reference to the crown of cilia that draws a vortex of water into the mouth Posterior to the mouth a region of the digestive tract called the pharynx bears jaws called trophi that grind up food mostly microorganisms suspended in the water Digestion is then completed farther along the alimentary canal Most other bilaterians also have an alimentary canal which en ables the stepwise digestion of a wide range of food particles Rotifers exhibit some unusual forms of reproduction Some species consist only of females that produce more fe males from unfertilized eggs a type of asexual reproduction called parthenogenesis Some other invertebrates for ex ample aphids and some bees and even some vertebrates for example some lizards and some fishes can also reproduce in this way In addition to being able to produce females by parthenogeneis some rotifers can also reproduce sexually under certain conditions such as high levels of crowding When this occurs a female produces two types of eggs Eggs of one type develop into females and eggs of the other type develop into males In some cases the males do not feed and survive only long enough to fertilize eggs The fertilized eggs develop into resistant embryos capable of remaining dormant for years Once the embryos break dormancy they develop into a new female generation that reproduces by partheno genesis until conditions once again favor sexual reproduction It is puzzling that many rotifer species survive without males The vast majority of animals and plants reproduce sexu ally at least some of the time and sexual reproduction has cer tain advantages over asexual reproduction see Concept 461 For example species that reproduce asexually tend to accumu late harmful mutations in their genomes faster than sexually reproducing species As a result asexual species should experi ence higher rates of extinction and lower rates of speciation Seeking to understand this unusual group researchers have been studying a clade of asexual rotifers named Bdel loidea Some 360 species of bdelloid rotifers are known and all of them reproduce by parthenogenesis without any males Paleontologists have discovered bdelloid rotifers preserved in 35millionyearold amber and the morphology of these fos sils resembles only the female form with no evidence of males By comparing the DNA of bdelloids with that of their closest sexually reproducing rotifer relatives scientists have concluded that bdelloids have likely been asexual for 100 million years How these animals manage to out the general rule against longlasting asexuality remains a puzzle Lophophorates Ectoprocts and Brachiopods Bilaterians in the phyla Ectoprocta and Brachiopoda are among those known as lophophorates These animals have a Iophophore a crown of ciliated tentacles around their mouth see Figure 3213a As the cilia draw water toward the mouth the tentacles trap suspended food particles Other similarities such as a Ushaped alimentary canal and the ab sence of a distinct head re ect these organisms sessile exis tence In contrast to atworms which lack a body cavity and rotifers which have a pseudocoelom lophophorates have a true coelom that is completely lined by mesoderm see Figure 328a Ectoprocts from the Greek ecto outside and procta anus are colonial animals that superficially resemble clumps of moss In fact their common name bryozoans means moss animals In most species the colony is encased in a hard exoskeleton external skeleton studded with pores through which the lophophores extend Figure 3314a Most ecto proct species live in the sea where they are among the most widespread and numerous sessile animals Several species are important reef builders Ectoprocts also live in lakes and rivers Colonies of the freshwater ectoproct Pectinatella magnifica grow on submerged sticks or rocks and can grow into a gelati nous ballshaped mass more than 10 cm across Brachiopods or lamp shells superficially resemble clams and other hingeshelled molluscs but the two halves of the brachiopod shell are dorsal and ventral rather than lat eral as in clams Figure 3314b All brachiopods are marine Most live attached to the sea oor by a stalk opening their shell slightly to allow water to ow through the lophophore The living brachiopods are remnants of a much richer past that included 30000 species in the Paleozoic and Mesozoic eras Some living brachiopods such as those in the genus Lingula appear nearly identical to fossils of species that lived 400 million years ago Molluscs Snails and slugs oysters and clams and octopuses and squids are all molluscs phylum Mollusca There are 93000 known species making them the second most diverse phylum of ani mals after the arthropods discussed later Although the ma jority of molluscs are marine roughly 8000 species inhabit fresh water and 28000 species of snails and slugs live on land All molluscs are softbodied from the Latin molluscus soft and most secrete a hard protective shell made of calcium car bonate Slugs squids and octopuses have a reduced internal shell or have lost their shell completely during their evolution Despite their apparent differences all molluscs have a similar body plan Figure 3315 on the next page Molluscs are coelo mates and their bodies have three main parts a muscular foot usually used for movement a visceral mass containing most of the internal organs and a mantle a fold of tissue that drapes over the visceral mass and secretes a shell if one is present In many molluscs the mantle extends beyond the visceral mass producing a waterfilled chamber the mantle cavity which houses the gills anus and excretory pores Many molluscs feed by using a straplike organ called a radula to scrape up food Most molluscs have separate sexes and their gonads ovaries or testes are located in the visceral mass Many snails however are hermaphrodites The life cycle of many marine molluscs includes a ciliated larval stage the trochophore see Figure 3213b which is also characteristic of marine annelids segmented worms and some other lophotrochozoans The basic body plan of molluscs has evolved in various ways in the phylum s seven or eight clades experts disagree on the number We39ll examine four of those clades here Polyplacophora chitons Gastropoda snails and slugs Bi valvia clams oysters and other bivalves and Cephalopoda squids octopuses cuttlefishes and chambered nautiluses We will then focus on threats facing some groups of molluscs Heart Most rnolluscs have an open circulatory system The dorsally located neart pumps Radula Tne mouth region in rnany rnollusc species contains a rasplike feeding organ called a radula This pelt of packward curved teetn repeatedly thrusts outward and then retracts into the rnouth scraping and scooping like a packnoe Nephfidiufn Excretory orgaqs Cl39CUatOFy wX Called thl39OUg391 artequotleS caned neomdia remove metaooiic into sinuses pody spaces Tne organs of the wastes from me hemoyrnDq mollusc are thus continually patned in hernolyrnph 3 39 Tne long digestive tract is P 9 T7 W N 9 coiled in tne visceral rnass 9 0 l039Ti 09 Intestine 5 5 quot I Gpnadsquot39 P 7 quot StorTiach Shell I7 Bad ula Mantle cavity Anus The nervous system consists of a nerve 539 39 39 ring around the esopnagus from whicn nerve cords extend Fogt Nerve Esophagus cords A Figure 3315 The basic body plan of a Inollusc Chitons Chitons have an ovalshaped body and a shell composed of eight dorsal plates Figure 3316 The chiton s body itself however is unsegmented You can find these marine animals clinging to rocks along the shore during low tide If you try to dislodge a chiton by hand you will be surprised at how well its foot acting as a suction cup grips the rock A chiton can also use its foot to creep slowly over the rock surface Chitons use their radula to scrape algae off the rock surface Gastropods About threequarters of all living species of molluscs are gas tropods Figure 3317 Most gastropods are marine but there are also freshwater species Still other gastropods have adapted to life on land where snails and slugs thrive in habi tats ranging from deserts to rain forests Gastropods undergo a distinctive developmental process known as torsion As a gastropod embryo develops its vis ceral mass rotates up to 180 causing the animal s anus and mantle cavity to wind up above its head Figure 3318 After torsion some organs that were bilateral may be reduced in size while others may be lost on one side of the body Tor sion should not be confused with the formation of a coiled shell which is a separate developmental process Most gastropods have a single spiraled shell into which the animal can retreat when threatened The shell is often conical but is somewhat attened in abalones and limpets Many gastropods have a distinct head with eyes at the tips of tentacles Gastropods move literally at a snail s pace by a rip pling motion of their foot or by means of cilia often leaving a trail of slime in their wake Most gastropods use their radula to graze on algae or plants Several groups however are pred ators and their radula has become modified for boring holes in the shells of other molluscs or for tearing apart prey In the cone snails the teeth of the radula act as poison darts that are used to subdue prey see the Unit 7 interview with Bal domero Olivera on pp 850851 to learn more about cone snails and their venom Terrestrial snails lack the gills typical of most aquatic gas tropods Instead the lining of their mantle cavity functions as a lung exchanging respiratory gases with the air Bivalves The molluscs of the clade Bivalvia are all aquatic and include many species of clams oysters mussels and scallops Bivalves have a shell divided into two halves Figure 3319 The halves are hinged and powerful adductor muscles draw them tightly together to protect the animal s soft body Bivalves have no distinct head and the radula has been lost Some bi valves have eyes and sensory tentacles along the outer edge of their mantle The mantle cavity of a bivalve contains gills that are used for gas exchange as well as feeding in most species Figure 3320 Most bivalves are suspension feeders They trap small food particles in mucus that coats their gills and cilia then convey those particles to the mouth Water enters the mantle cavity through an incurrent siphon passes over the gills and then exits the mantle cavity through an excurrent siphon Most bivalves lead sedentary lives a characteristic suited to suspension feeding Mussels secrete strong threads that tether them to rocks docks boats and the shells of other an imals However clams can pull themselves into the sand or mud using their muscular foot for an anchor and scallops can skitter along the sea oor by apping their shells rather like the mechanical false teeth sold in novelty shops Coelonn Hinge area 39 Mantle 39 V jut I Heart Adductor muscle ii i one of two Digestwe i gland i quot Anus i Moot T 7 l fs 39 Excurrent 3 siphon HI L I 0 ll 39 1 I38 h h l Water 03 P g V 0 flow Foot 39 39 T 39l incurrent Ca MY 0f393d giphon 7 39 I 39 2 I Y l 39 I 039 I r A Figure 3320 Anatomy of a clam lood particles suspended in water that enters through the incurrent siphon are collected by the gills and passed W3 cilia and the palps to the mouth Cephalopods Cephalopods are active marine predators Figure 3321 They use their tentacles to grasp prey which they then bite with beaklike jaws and immobilize with a poison present in their saliva The foot of a cephalopod has become modified into a muscular excurrent siphon and part of the tentacles Squids dart about by drawing water into their mantle cavity and then firing a jet of water through the excurrent siphon they steer by pointing the siphon in different directions Oc topuses use a similar mechanism to escape predators The mantle covers the visceral mass of cephalopods but the shell is generally reduced and internal in most species or missing altogether in some cuttlefishes and some octo puses One small group of cephalopods with external shells the chambered nautiluses survives today Cephalopods are the only molluscs with a closed circulatory system in which the blood remains separate from uid in the body cavity They also have welldeveloped sense organs and a complex brain The ability to learn and behave in a com plex manner is probably more critical to fastmoving preda tors than to sedentary animals such as clams The ancestors of octopuses and squids were probably shelled molluscs that took up a predatory lifestyle the shell was lost in later evolution Shelled cephalopods called ammonites some of them as large as truck tires were the dominant invertebrate predators of the seas for hundreds of millions of years until their disappearance during the mass extinction at the end of the Cretaceous period 655 million years ago Protecting Fresh water and Terrestrial Molluscs Species extinction rates have increased dramatically in the last 400 years raising concern that a sixth humancaused mass extinction may be under way see Chapter 25 Among the many taxa under threat molluscs have the dubious dis tinction of being the animal group with the largest number of documented extinctions Figure 3322 Threats to molluscs are especially severe in two groups freshwater bivalves and terrestrial gastropods The pearl mus sels a group of freshwater bivalves that can make natural pearls gems that form when a mussel or oyster secretes layers of a lus trous coating around a grain of sand or other small irritant are among the world s most endangered animals Roughly 10 of the 300 pearl mussel species that once lived in North America have become extinct in the last 100 years and over twothirds of those that remain are threatened by extinction Terrestrial gastropods such as the snail in Figure 3322 fare no better Hundreds of Pacific island land snails have disappeared since 1800 Overall more than 50 of the Pacific island land snails are extinct or under imminent threat of extinction Threats faced by freshwater and terrestrial molluscs in clude habitat loss pollution and competition or predation by non native species introduced by people Is it too late to protect these molluscs In some locations reducing water pollution and changing how water is released from dams have led to dramatic rebounds in pearl mussel populations Such results provide hope that with corrective measures other endangered mollusc species can be revived WHY IT MATTERS The extinctions of molluscs represent an irre versible loss of biological diversity and greatly threaten other organ isms too Land snails for example play a key role in nutrient cycling while the ltering activities of freshwater bivalves purify the waters of streams rivers and lakes Annelids Annelida means little rings referring to the annelid body s resemblance to a series of fused rings Annelids are seg mented worms that live in the sea in most freshwater habi tats and in damp soil Annelids are coelomates and they range in length from less than 1 mm to more than 3 m the length of a giant Australian earthworm The phylum Annelida can be divided into two main groups Polychaeta the polychaetes and Oligochaeta the earthworms and their relatives and the leeches Some recent phylogenetic analyses have suggested that the oligochaetes are actually a subgroup of the polychaetes However since this idea continues to be debated we discuss polychaetes and oligochaetes separately Polychaetes Each segment of a polychaete from the Greek poly many and chait39e long hair has a pair of paddlelike or ridgelike struc tures called parapodia beside feet that function in locomo tion Figure 3323 Each parapodium has numerous chaetae bristles made of chitin In many polychaetes the parapodia are richly supplied with blood vessels and also function as gills Polychaetes make up a large and diverse group most of whose members are marine A few species drift and swim among the plankton many crawl on or burrow in the sea oor and many others live in tubes Some tubedwellers such as the fan worms build their tubes by mixing mucus with bits of sand and broken shells Others such as Christmas tree worms see Figure 331 construct tubes using only their own secretions Oligochaetes Oligochaetes oligos few and chaite39 long hair are named for their relatively sparse chaetae far fewer per segment than in polychaetes Molecular data indicate that these segmented worms form a diverse clade that includes the earthworms and their aquatic relatives along with the leeches Earthworms Earthwormseattheirwaythroughthesoilextract ing nutrients as the soil passes through the alimentary canal Undigested material mixed with mucus secreted into the canal is eliminated as fecal castings through the anus Farmers value earthworms because the animals till and aerate the earth and their castings improve the texture of the soil Charles Darwin es timated that a single acre of British farmland contains about 50000 earthworms producing 18 tons of castings per year Each segment is surrounded by longitudinal muscle which in Coelom The coelom Metanephridium Each turn is surrounded by circular muscle Earthworms coordinate of the earthworm is segment of the worm the contraction of these two sets of muscles to move partitioned by septa contains a pair of see Figure 5035 These muscles work against the non excretory tubes Called compressible coelomic fluid which acts as a hydrostatic skeleton metanephridia with ciliated funnelshaped openings called nephrostomes The 5 Pquot39 m39 metanephridia remove Many of the internal structures are repeated lpanltlo wastes from the blood within each segment of between and coelomic fluid the earthworm Se menlsl through exterior pores Longitudinal muscle Chaetae Each segment Domain has four pairs of W5 chaetae bristles that quotquot l39 Tiny blood provide traction for vessels are burrogiing llnitestiine quotquot abundant in the earthworm s T skin which functions as its respiratory or gan The blood Fused 39 nerve vessel Ventral 39 Cords contains oxygen V p carrying Ncphrosmmc hemoglobin C liitcllumi quot Esophagus Metariephridiiunm lntestiine Giant Australian earthworm Cerebral ganglia The earthworm 1 nervous system features a brain quot like pair of cerebral ganglia above and in front of the pharynx A MOW v 39 ring of nerves around the pharynx gubphdryngcaii l connects to a subpharyngeal gangiion I ganglion from which a fused pair of nerve cords runs posteriorly 139 V quotquot3939 quot9quot quotd5 Wm 5 9quotquot 39 339 The circulatory system a network of vessels 9a 9quota The quotd5 9 quot393t h is closed The dorsal and ventral vessels are 5 quotma and 39 the 39 quot9th f he ammaquot linked by segmental pairs of vessels The as d9 th d399 5quotquot Va md dorsal vessel and five pairs of vessels that 39 9quot d39 339 b39 d V9559 circle the esophagus are muscular and pump blood through the circulatory system A guided tour of the anatomy of an earthworm which is representative of annelids is shown in Figure 3324 Earth worms are hermaphrodites but they do crossfertilize Two earthworms mate by aligning themselves in opposite direc tions in such a way that they exchange sperm and then they separate The received sperm are stored temporarily while an organ called the clitellum secretes a cocoon of mucus The cocoon slides along the worm picking up the eggs and then the stored sperm The cocoon then slips off the worm s head and remains in the soil while the embryos develop Some earthworms can also reproduce asexually by fragmentation followed by regeneration Leeches Mostleechesinhabitfreshwaterbuttherearealsoma rine species and terrestrial leeches which live in moist vegeta tion Leeches range in length from 1 to 30 cm Many are predators that feed on other invertebrates but some are para sites that suck blood by attaching temporarily to other animals including humans Figure 3325 Some parasitic species use bladelike jaws to slit the skin of their host whereas others secrete enzymes that digest a hole through the skin The host is usually oblivious to this attack because the leech secretes an anesthetic After making the incision the leech secretes another chemical hirudin which keeps the blood of the host from coagulating near the incision The parasite then sucks as much blood as it can hold often more than ten times its own weight After this gorging a leech can last for months without another meal Until the 20th century leeches were frequently used for bloodletting Today they are used to drain blood that accumu lates in tissues following certain injuries or surgeries Researchers have also investigated the potential use of purified hirudin to dissolve unwanted blood clots that form during surgery or as a result of heart disease Several forms of hirudin have been devel oped using recombinant DNA techniques two of these were re cently approved for clinical use As a group Lophotrochozoa encompasses a remarkable range of body plans as illustrated by members of such phyla as Rotifera Ectoprocta Mollusca and Annelida Next we39ll explore the diversity of Ecdysozoa a dominant presence on Earth in terms of sheer number of species Ecdysozoans are the most speciesrich animal group Although defined primarily by molecular evidence the clade Ecdysozoa includes an imals that shed a tough ex ternal coat cuticle as they grow in fact the group derives its name from this process which is called ecdysis or molting Ecdysozoa consists of about eight animal phyla and contains more known species than all other animal protist fungus and plant groups com bined Here we39ll focus on the two largest ecdysozoan phyla the nematodes and arthropods which are among the most successful and abundant of all animal groups Nematodes Among the most ubiquitous of animals nematodes phylum Nematoda or roundworms are found in most aquatic habi tats in the soil in the moist tissues of plants and in the body uids and tissues of animals In contrast to annelids nema todes do not have segmented bodies The cylindrical bodies of nematodes range from less than 1 mm to more than 1 m long often tapering to a fine tip at the posterior end and to a blunter tip at the anterior end Figure 3326 A nematode s body is covered by a tough cuticle a type of exoskeleton as the worm grows it periodically sheds its old cuticle and se cretes a new larger one Nematodes have an alimentary canal though they lack a circulatory system Nutrients are transported throughout the body via uid in the pseudo coelom The body wall muscles are all longitudinal and their contraction produces a thrashing motion Nematodes usually reproduce sexually by internal fertil ization In most species the sexes are separate and females are larger than males A female may deposit 100000 or more fertilized eggs zygotes per day The zygotes of most species are resistant cells that can survive harsh conditions Multitudes of nematodes live in moist soil and in decom posing organic matter on the bottoms of lakes and oceans While 25000 species are known perhaps 20 times that num ber actually exist It has been said that if nothing of Earth or its organisms remained but nematodes they would still pre serve the outline of the planet and many of its features These freeliving worms play an important role in decomposition and nutrient cycling but little is known about most species One species of soil nematode Caenorhabditis elegans how ever is very well studied and has become a model research organism in biology see Chapter 47 Ongoing studies of C elegans are revealing some of the mechanisms involved in aging in humans among other findings Phylum Nematoda includes many species that parasitize plants and some are major agricultural pests that attack the roots of crops Other nematodes parasitize animals Some of these species benefit humans by attacking insects such as cut worms that feed on the roots of crop plants On the other hand humans are hosts to at least 50 nematode species in cluding various pinworms and hookworms One notorious nematode is Trichinella spiralis the worm that causes trichi nosis Figure 3327 Humans acquire this nematode by eat ing raw or undercooked pork or other meat including wild game such as bear or walrus that has juvenile worms en cysted in the muscle tissue Within the human intestines the juveniles develop into sexually mature adults Females burrow into the intestinal muscles and produce more juveniles which bore through the body or travel in lymphatic vessels to other organs including skeletal muscles where they encyst Parasitic nematodes have an extraordinary molecular toolkit that enables them to redirect some of the cellular functions of their hosts and thus evade their immune sys tems Some species inject their plant hosts with molecules that induce the development of root cells which then supply nutrients to the parasites Trichinella which parasitizes ani mals controls the expression of specific muscle cell genes that code for proteins that make the cell elastic enough to house the nematode Additionally the infected muscle cell releases signals that promote the growth of new blood ves sels which then supply the nematode with nutrients Arthropods Zoologists estimate that there are about a billion billion 1 arthropods living on Earth More than 1 million arthropod species have been described most of which are insects In fact two out of every three known species are arthropods and members of the phylum Arthropoda can be found in nearly all habitats of the biosphere By the criteria of species diver sity distribution and sheer numbers arthropods must be re garded as the most successful of all animal phyla 018 Arthropod Origins Biologists hypothesize that the diversity and success of arthropods are related to their body plan their segmented body hard exoskeleton and jointed appendages arthropod means jointed feet The earliest fossils with this body plan are from the Cambrian explosion 535 525 million years ago indicating that the arthropods are at least that old Along with arthropods the fossil record of the Cambrian explosion contains many species of Iobopods an extinct group from which arthropods may have evolved Lobopods such as Hallucigenia see Figure 254 had segmented bodies but most of their body segments were identical to one an other Early arthropods such as the trilobites also showed lit tle variation from segment to segment Figure 3328 As arthropods continued to evolve the segments tended to fuse and become fewer and the appendages became specialized for a variety of functions These evolutionary changes re sulted not only in great diversification but also in an efficient body plan that permits the division of labor among different body regions What genetic changes led to the increasing complexity of the arthropod body plan Arthropods today have two un usual Hox genes both of which in uence segmentation To test whether these genes could have driven the evolution of increased body segment diversity in arthropods researchers studied Hox genes in onychophorans see Figure 333 close relatives of arthropods Figure 3329 Their results indicate that arthropod body plan diversity did not arise from the ac quisition of new Hox genes Instead the evolution of body segment diversity in arthropods may have been driven by changes in the sequence or regulation of existing Hox genes See Chapter 25 for a discussion of how changes in form can result from changes in the sequence or regulation of develop mental genes such as Hox genes General Characteristics of Arthropods Over the course of evolution the appendages of some arthro pods have become modified specializing in functions such as walking feeding sensory reception reproduction and de fense Like the appendages from which they were derived these modified structures are jointed and come in pairs Figure 3330 illustrates the diverse appendages and other arthropod characteristics of a lobster Cephalothorax Abdomen Yb Antennae Head pQb sen5ory 0m recepnon lIlquot39 Swimming appen dages one pair per abdominal segment Walking legs 3939d1eCr5re392I Moughpans 39 39 feeding The body of an arthropod is completely covered by the cu ticle an exoskeleton constructed from layers of protein and the polysaccharide chitin The cuticle can be thick and hard over some parts of the body and paperthin and exible over others such as the joints The rigid exoskeleton protects the animal and provides points of attachment for the muscles that move the appendages But it also means that an arthro pod cannot grow without occasionally shedding its exoskele ton and producing a larger one This molting process is energetically expensive A molting or recently molted arthro pod is also vulnerable to predation and other dangers until its new soft exoskeleton hardens When the arthropod exoskeleton first evolved in the sea its main functions were probably protection and anchorage for muscles but it later enabled certain arthropods to live on land The exoskeleton s relative impermeability to water helped prevent desiccation and its strength solved the prob lem of support when arthropods left the buoyancy of water Arthropods began to diversify on land following the colo nization of land by plants in the early Paleozoic Evidence in cludes a 428millionyearold fossil of a millipede found in 2004 by an amateur fossil hunter in Scotland Fossilized tracks of other terrestrial arthropods date from about 450 million years ago Arthropods have welldeveloped sensory organs includ ing eyes olfactory smell receptors and antennae that func tion in both touch and smell Most sensory organs are concentrated at the anterior end of the animal although there are interesting exceptions Female butter ies for exam ple taste plants using sensory organs on their feet Like many molluscs arthropods have an open circulatory system in which uid called hemolymph is propelled by a heart through short arteries and then into spaces called sinuses sur rounding the tissues and organs The term blood is generally re served for uid in a closed circulatory system Hemolymph reenters the arthropod heart through pores that are usually equipped with valves The hemolymphfilled body sinuses are collectively called the hemocoel which is not part of the coelom Although arthropods are coelomates in most species the coelom that forms in the embryo becomes much reduced as development progresses and the hemocoel becomes the main body cavity in adults Despite their similarity phyloge netic analyses suggest that the open circulatory systems of mol luscs and arthropods arose independently A variety of specialized gas exchange organs have evolved in arthropods These organs allow the diffusion of respiratory gases in spite of the exoskeleton Most aquatic species have gills with thin feathery extensions that place an extensive surface area in contact with the surrounding water Terres trial arthropods generally have internal surfaces specialized for gas exchange Most insects for instance have tracheal systems branched air ducts leading into the interior from pores in the cuticle Morphological and molecular evidence suggests that liv ing arthropods consist of four major lineages that diverged early in the evolution of the phylum chelicerates sea spi ders horseshoe crabs scorpions ticks mites and spiders myriapods centipedes and millipedes hexapods insects and their wingless sixlegged relatives and crustaceans crabs lobsters shrimps barnacles and many others Chelicerates Chelicerates subphylum Chelicerata from the Greek cheilos lips and cheir arm are named for clawlike feeding ap pendages called chelicerae which serve as pincers or fangs Chelicerates have an anterior cephalothorax and a posterior abdomen They lack antennae and most have simple eyes eyes with a single lens The earliest chelicerates were eurypterids or water scor pions These marine and freshwater predators grew up to 3 m long it is thought that some species could have walked on land much as land crabs do today Most of the marine che licerates including all of the eurypterids are extinct Among the marine chelicerates that survive today are the sea spiders pycnogonids and horseshoe crabs Figure 3331 The bulk of modern chelicerates are arachnids a group that includes scorpions spiders ticks and mites Figure 3332 Ticks and many mites are among a large group of parasitic arthropods Nearly all ticks are bloodsucking parasites that live on the body surfaces of reptiles or mammals Parasitic mites live on or in a wide variety of vertebrates invertebrates and plants Arachnids have a cephalothorax that has six pairs of ap pendages the chelicerae a pair of appendages called pedipalps that function in sensing feeding or reproduction and four pairs of walking legs Figure 3333 Spiders use their fanglike chelicerae which are equipped with poison glands to attack prey As the chelicerae pierce the prey the spider secretes di gestive juices onto the prey s torn tissues The food softens and the spider sucks up the liquid meal In most spiders gas exchange is carried out by book lungs stacked platelike structures contained in an internal chamber see Figure 3333 The extensive surface area of these respiratory organs is a structural adaptation that enhances the exchange of O2 and CO2 between the hemolymph and air A unique adaptation of many spiders is the ability to catch insects by constructing webs of silk a liquid protein produced by specialized abdominal glands The silk is spun by organs called spinnerets into fibers that then solidify Each spider en gineers a web characteristic of its species and builds it perfectly on the first try indicating that this complex behavior is inher ited Various spiders also use silk in other ways as droplines for rapid escape as a cover for eggs and even as gift wrap for food that males offer females during courtship Many small spiders also extrude silk into the air and let themselves be transported by wind a behavior known as ballooning r V Intestine Smmmh 3 Heart Brain u Z I Digestive P ghnd quot O u39ampr3939 P 4 I Arms pq Ifr i o Book Iun g Spirrmcrcts quot39 0J GOVWODOTC C heiccra Pcdi pal p exit for eggsiu Sperm Silk gland mccptaclle A Figure 3333 Anatomy of a splder Myriapods Millipedes and centipedes belong to the sub phylum Myriapoda Figure 3334 All living myriapods are terrestrial The myriapod head has a pair of antennae and three pairs of ap pendages modified as mouthparts including the jawlike mandibles Millipedes have a large number of legs though fewer than the thousand their name implies Each trunk segment is formed from two fused segments and bears two pairs of legs see Figure 3334a Millipedes eat de caying leaves and other plant matter They may have been among the earliest animals on land living on mosses and early vascular plants Unlike millipedes centipedes are carnivores Each seg ment of a centipede s trunk region has one pair of legs see Figure 3334b Centipedes have poison claws on their fore most trunk segment that paralyze prey and aid in defense Insects Insects and their relatives subphylum Hexapoda are more speciesrich than all other forms of life combined They live in almost every terrestrial habitat and in fresh water and ying insects fill the air Insects are rare though not absent in marine habitats where crustaceans are the dominant arthropods The internal anatomy of an insect includes several complex organ systems which are highlighted in Figure 3335 arthropod kin As Cornell University entomologist Thomas Eisner puts it Bugs are not going to inherit the Earth They own it now So we might as well make peace with the landlord Crustaceans While arachnids and insects thrive on land crustaceans for the most part have remained in marine and freshwater envi ronments Crustaceans subphylum Crustacea typically have highly specialized appendages Lobsters and crayfishes for in stance have a toolkit of 19 pairs of appendages see Figure 3330 The anteriormost appendages are antennae crus taceans are the only arthropods with two pairs Three or more pairs of appendages are modified as mouthparts including the hard mandibles Walking legs are present on the thorax and unlike insects crustaceans also have appendages on their ab domen A lost appendage can be regenerated at the next molt Small crustaceans exchange gases across thin areas of the cuticle larger species have gills Nitrogenous wastes also dif fuse through thin areas of the cuticle but a pair of glands reg ulates the salt balance of the hemolymph Sexes are separate in most crustaceans In the case of lob sters and crayfishes the male uses a specialized pair of ab dominal appendages to transfer sperm to the reproductive pore of the female during copulation Most aquatic crus taceans go through one or more swimming larval stages One of the largest groups of crustaceans numbering over 11000 species is the isopods which include terrestrial freshwater and marine species Some isopod species are abundant in habitats at the bottom of the deep ocean Among the terrestrial isopods are the pill bugs or wood lice common on the undersides of moist logs and leaves Lobsters crayfishes crabs and shrimps are all relatively large crustaceans called decapods Figure 3339a The cuticle of decapods is hardened by calcium carbonate the portion that covers the dorsal side of the cephalothorax forms a shield called the carapace Most decapod species are marine Crayfishes how ever live in fresh water and some tropical crabs live on land Many small crustaceans are important members of marine and freshwater plankton communities Planktonic crus taceans include many species of copepods which are among the most numerous of all animals Some copepods are grazers that feed upon algae while others are predators that eat small animals including smaller copepods Copepods are rivaled in abundance by the shrimplike krill which grow to about 5 cm long Figure 3339b A major food source for baleen whales including blue whales humpbacks and right whales krill are now being harvested in great numbers by humans for food and agricultural fertilizer The larvae of many largerbodied crustaceans are also planktonic With the exception of a few parasitic species barnacles are a group of sessile crustaceans whose cuticle is hardened into a shell containing calcium carbonate Figure 3339c Most bar nacles anchor themselves to rocks boat hulls pilings and other submerged surfaces Their natural adhesive is as strong as synthetic glues These barnacles feed by extending appendages from their shell to strain food from the water Barnacles were not recognized as crustaceans until the 1800s when naturalists discovered that barnacle larvae resemble the larvae of other crustaceans The remarkable mix of unique traits and crus tacean homologies found in barnacles was a major inspiration to Charles Darwin as he developed his theory of evolution Echinoderms and chordates are deuterostomes Sea stars sea urchins and other echinoderms phylum Echinodermata may seem to have little in common with vertebrates animals that have a backbone and other members of phylum Chordata Never theless DNA evidence indicates that echinoderms and chor dates are closely related with both phyla belonging to the Deuterostomia clade of bilaterian animals Echinoderms and chordates also share features characteristic of a deuterostome mode of development such as radial cleavage and formation of the anus from the blastopore see Figure 329 As discussed in Chapter 32 however some animal phyla with members that have deuterostome developmental features including ecto procts and brachiopods are not in the deuterostome clade Hence despite its name the clade Deuterostomia is defined pri marily by DNA similarities not developmental similarities Echinoderms Sea stars commonly called starfish and most other echinoderms from the Greek echin spiny and derma skin are slow moving or sessile marine animals A thin epidermis covers an endoskeleton of hard calcareous plates Most echino derms are prickly from skeletal bumps and spines Unique to echinoderms is the water vascular system a network of hy draulic canals branching into extensions called tube feet that function in locomotion and feeding Figure 3340 Sexual re production of echinoderms usually involves separate male and female individuals that release their gametes into the water The internal and external parts of most adult echinoderms radiate from the center often as five spokes However echin oderm larvae have bilateral symmetry Furthermore the sym metry of adult echinoderms is not truly radial For example the opening madreporite of a sea star s water vascular sys tem is not central but shifted to one side Living echinoderms are divided into five clades Asteroidea Sea Stars and Sea Daisies Sea stars have arms radiating from a central disk the undersur faces of the arms bear tube feet By a combination of muscular and chemical actions the tube feet can attach to or detach from a substrate The sea star adheres firmly to rocks or creeps along slowly as its tube feet extend grip release extend and grip again Although the base of the tube foot has a attened disk that resembles a suction cup the gripping action results from adhesive chemicals not suction see Figure 3340 Sea stars also use their tube feet to grasp prey such as clams and oysters The arms of the sea star embrace the closed bi valve clinging tightly with their tube feet The sea star then turns part of its stomach inside out everting it through its mouth and into the narrow opening between the halves of the bivalve s shell Next the digestive system of the sea star se cretes juices that begin digesting the mollusc within its own shell The stomach is then brought back inside the seastar s body where digestion of the mollusc s now liquefied body is completed The ability to begin the digestive process outside of its body allows a sea star to consume bivalves and other prey species that are much larger than its mouth Sea stars and some other echinoderms have considerable powers of regeneration Sea stars can regrow lost arms and members of one genus can even regrow an entire body from a single arm if part of the central disk remains attached The clade Asteroidea to which sea stars belong also in cludes a small group of armless species the sea daisies Discov ered in 1986 only three species of sea daisies are known all of which live on submerged wood A sea daisy s body is typically diskshaped it has a fivesided organization and measures less than a centimeter in diameter Figure 3341 The edge of the body is ringed with small spines Sea daisies absorb nutrients through a membrane that surrounds their body A short digestive mm The surface of a sea star is runs from the mouth covered by spines that help on the bottom of the defend against predators as central disk to the well as by small gills that anus on top of the disk P39 Vid9 935 XCh3quot9 Central disk The central disk has a nerve ring and nerve cords radiating from the ring into the arms Mad reporite Water can flow in or out of the water vascular system into the surrounding water through the d t Digestive glands secrete ma rem e digestive juices and aid in the absorption and storage of nutrients Radial canal The water vascular Each tube foot consists of a bulblike ampulla and a podium foot system consists of a ring canal in the portion When the ampulla squeezes water is forced into the podium central disk and five radial canals which expands and contacts the substrate Adhesive chemicals are then each running in a groove down the secreted from the base of the podium attaching it to the substrate To entire length of an arm Branching detach the tube foot deadhesive chemicals are secreted and muscles from each radial canal are hundreds in the podium contract forcing water back into the ampulla and of hollow muscular tube feet filled shortening the podium As it moves a sea star leaves an observable with fluid footprint of adhesive material on the substrate A Figure 3340 Anatomy of a sea star an echlnoderm Echinoidea Sea Urchins and Sand Dollars Sea urchins and sand dollars have no arms but they do have five rows of tube feet that function in slow movement Sea urchins also have muscles that pivot their long spines which aid in locomotion as well as protection Figure 3343 The mouth of a sea urchin is ringed by highly complex jawlike structures that are well adapted to eating seaweed Sea urchins are roughly spherical whereas sand dollars are at disks Crinoidea Sea Lilies and Feather Stars Sea lilies live attached to the substrate by a stalk feather stars crawl about by using their long exible arms Both use their arms in suspension feeding The arms encircle the mouth which is directed upward away from the substrate Figure 3344 Crinoidea is an ancient group whose mor phology has changed little over the course of evolution fos silized sea lilies some 500 million years old are extremely similar to presentday members of the clade Holothuroidea Sea Cucumbers On casual inspection sea cucumbers do not look much like other echinoderms They lack spines and their endoskeleton is much reduced They are also elongated in their oralaboral axis giving them the shape for which they are named and fur ther disguising their relationship to sea stars and sea urchins Figure 3345 Closer examination however reveals that sea cucumbers have five rows of tube feet Some of the tube feet around the mouth are developed as feeding tentacles Chordates Phylum Chordata consists of two subphyla of invertebrates as well as the hagfishes and the vertebrates Chordates are bilater ally symmetrical coelomates with segmented bodies The close relationship between echinoderms and chordates does not mean that one phylum evolved from the other In fact echino derms and chordates have evolved independently of one an other for over 500 million years We will trace the phylogeny of chordates in Chapter 34 focusing on the history of vertebrates Selected mm Phyla Key Concept Concept 33 Sponges are basal animals that lack true tissues pp 67067 Lacking tissues and organs how do sponges accomplish tasks such as gas exchange nutrient transport and waste removal Concept 332 Cnidarians are an ancient phylum of eumetazoans pp 67l 673 7 Describe the cnidarian body plan and its two major variations Concept 333 Lophotrochozoans a clade identi ed by molecular data have the widest range of animal body forms pp 674683 7 Is the lophotrochozoan clad united by unique morphological features shared by all of its members Explain Concept 334 Ecdysozoans are the most speciesrich animal group pp 683692 7 Describe ecological roles of nematodes and arthropods Concept 335 Echinoderms and chordates are deuterostomes pp 692694 7 You39ve read that echinoderms and chonlates are closely related and have evolved independently for over 500 million years Explain how both of these statements can be correct Metazoa EU N Z08 Bilateria A Lophotrochozoa Ecdysozoa Deu terostom ia Phylum Porifera sponges Cnidaria hydras jellies sea anemones corals Platyhelminths atworms llotifera rotiters Lophophorates Ectoprocta Brachiopoda Mollusca clams snails squids Annelida segmented worms Nematoda roundworrns Arthropoda crustaceans insects spiders Echinodennata sea stars sea urdiins Chordata lancelets tunicates vertebrates ll IQ W W gt 2 9 Desaip on Lack true tissues have choanocytes collar cells flagelated cells that ingest bacteria and tiny food particles Unique stinging structures nematocysts housed in specialized cells cnidocytes diploblastic radialy symmetrical gastrovascular cavity digestive compartment with a single opening Dorsoventrally flattened unsegmented acoelomates gastrovascular cavity or no digestive tract Pseudocoelomates with alimentary canal digestive tube with mouth and anus jaws trophi in pharynx head with ciliated crown Coelomates with lophophores feeding structures bearing ciliated tentades Coelomates with three main body parts muscular foot visceral mass mantle coelom reduced most have hard shell made of calcium carbonate Coelomates with segmented body wall and intemal organs except digestive tract which is unsegmented Cylindrical unsegmented pseudocoelo mates with tapered ends no circulatory system undergo ecdysis Coelomates with segmented body jointed appendages and exoskeleton made of protein and chitin Coelomates with bilaterally symmetrical larvae and fivepart body organization as adults unique water vascular system endoslteleton Coelomates with notochord dorsal hol low nerve cord pharyngeal slits postanal tail see Chapter 34 LEVEL 1 KNOWLEDGECOMPREHENSION 1 A land snail a clam and an octopus all share a mantle b radula c gills d embryonic torsion e distinct cephalization Which phylum is characterized by animals that have a segmented body a Cnidaria b Platyhelminthes c Porifera d Arthropoda e Mollusca 3 The water vascular system of echinoderms 1 functions as a circulatory system that distributes nutrients to body cells 2 functions in locomotion and feeding 3 is bilateral in organization even though the adult animal is not bilaterally symmetrical 4 moves water through the animal39s body during suspension feeding 5 is analogous to the gastrovascular cavity of atworms 4 Which of the following combinations of phylum and descrip tion is incorrect 1 Echinodermata bilateral symmetry as a larva coelom present 2 Nematoda roundwormspseudocoelomate Cnidaria radial symmetry polyp and medusa body forms Platyhelminthes atworms gastrovascular cavity acoelomate Porifera gastrovascular cavity coelom present
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