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Biology II Biological Diversity

by: Carlaformoso

Biology II Biological Diversity BSC 2011

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Complete outlines for the material covered in Bio II, following the McGraw Hill textbok for this subject. They are divided in chapters, corresponding to the broader divisions of Evolution (chapters...
Biology II Diversity
Biology, bio II
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This 53 page Bundle was uploaded by Carlaformoso on Sunday March 6, 2016. The Bundle belongs to BSC 2011 at University of South Florida taught by in Spring 2015. Since its upload, it has received 24 views. For similar materials see Biology II Diversity in Biological Sciences at University of South Florida.


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Date Created: 03/06/16
18 - THE ORIGIN AND HISTORY OF LIFE ON EARTH Sunday, April 26, 2015 19:56 18.1. ORIGIN OF LIFE ON EARTH - Chronology ○ 13.8 bya: the Universe began with the Big Bang ○ 4.6 bya: Our solar system began ○ The Earth is 4.55 billion years old ○ 4 bya: Earth had cooled enough for outer layers to solidify and oceans to form ○ Between 4 and 3.5 bya: life emerged - Steps of the origin of life ○ 1: Origin of organic molecules: nucleotides and amino acids were produced prior to the existence of cells  The early conditions of Earth were more conductive to the spontaneous formation of molecules  Abiotic synthesis □ There was an accumulationof the formed moleculesdue to little free oxygen and no living organisms to metabolizethe molecules □ The formation of a prebiotic soup was the result of that accumulation of molecules  Proposedmechanisms for molecule origination □ Reducing atmosphere  Containing water vapor, hydrogen gas, methane, ammonia and little oxygen  The compositionof the atmosphereallowed redox reaction that led to the formationof molecules  The Stanley Miller experimentrecreated this situation and was the first attempt to apply scientific experimentsto understanding the origin of life □ Extraterrestrialhypothesis  Meteoritesbrought organic carbon to Earth, including amino acids and nucleic acid bases  Opponents argue that most of this would be destroyed in the intense het of collision □ Deep-sea vent hypothesis  Moleculeswere formed in the temperaturegradient between hot vent water and the cold water surrounding it  Supported by experiments and ancient fossils  Complex biological communitiesfound in deep-sea vents derive energy from chemicals in the vent, not the sun ○ 2: Organic polymers: (DNA, RNA & proteins) may have formed on the surface of clay or in water  The synthesis of polymerswas thought to be impossible in aqueous solutions due to hydrolysis competing with polymerization  Formationof nucleic acid polymers and polypeptides may have occurred on the negative silicate surface of clay ○ 3: Formationof boundaries: cell-like structures may have originated when polymerswere enclosed by a boundary/ membrane  Protobiont □ An aggregate of prebiotically produced moleculesand macromolecules □ Has a boundary, such as a lipid bilayer, that allows it to maintain an internal □ Has a boundary, such as a lipid bilayer, that allows it to maintain an internal chemical environmentdistinct from that of its surroundings □ Key features  Boundary: separated external environmentfrom the internal contents  Information: contained by polymersinside the protobiont  Enzymatic function: possessed by polymersinside the protobiont  Capability of self-replication  Living cells may have evolved from □ Coacervates  Droplets that form spontaneously from the association of charged polymers  Catalysts trapped inside can perform primitivemetabolic functions □ Liposomes  Vesicles surrounded by a lipid bilayer  Clay can catalyze formationof liposomes that grow and divide  Can enclose RNA ○ 4: RNA world: Cellular characteristics may have evolvedvia chemical selection, beginning with the RNA world  Majorityof scientists favor RNA as the first macromoleculeof protobionts □ Three key RNA functions  Information storage  Self-replication capability  Enzymatic function (ribozymes) □ DNA and proteins cannot perform the three key functions  Chemical selection □ A chemical within a mixture has special properties that cause it to increase in number compared to other chemicals in the mixture □ Hypothetical scenario  One of the RNA moleculesmutates and has enzymatic capability to attach nucleotides together - advantage of faster replication  Second mutation produces enzymaticability to synthesize nucleotides - no reliance on prebiotic synthesis  Modern DNA / RNA / protein world advantages □ Information storage  DNA relieves RNA of informationalrole and allows RNA to do other functions  DNA is less likely to suffer mutations □ Metabolism and other cellular functions  Proteins have greater catalytic potential and efficiency  Proteins can perform other tasks - cytoskeleton,transport, etc. 18.2. THE FOSSIL RECORD - Fossils: preserved remains of life in the past - Paleontologists:scientists who study fossils - Mechanism for the formationof fossils ○ Sediments settle and bury living and dead organisms ○ As moreparticles settle, sediments at the bottom becomecompressed into the rock ○ Over million years, organisms' hard parts are replaced by minerals - Dating of fossils ○ Relative dating: location on sedimentary rock  Older rock is deeper and older organisms are deeper in the rock bed Quantitative dating: radiometric dating ○ Quantitative dating: radiometric dating  Fossils can be dated using elemental isotopes in accompanying rock □ Half-life: length of time required for exactly one half of original isotope to decay □ Quantities measured  Amount of a given isotope  Amount of the decay product  Usually igneous rock is dated  The fossil record is expected to underestimatethe actual date the species came into existence - Factors that affect the fossil record ○ Anatomy: organisms with a harder body are more likely to be preserved ○ Size: fossil remains of larger animals are more likely to be found ○ Number: species that existed over a larger area and / or in greater number are more likely to be found ○ Environment:species that lived in a marine environmentare more likely to be preserved ○ Time: relativelyrecent or that existed for a long time (perduring) are more likely to be preserved ○ Geological processes:due to chemistry of fossilization, certain organisms are more likely to be preserved that others ○ Paleontology: Bias for interest and location (tendency to search for fossils in areas where other fossils have already been found) 18.3 HISTORY OF LIFE ON EARTH - Changes in living organisms are the result of ○ Genetic changes ○ Chance events ○ Environmentalchanges: can allow for new types of organisms; responsible for many extinctions  Major environmentalchanges □ Temperature: the Earth cooled down at the beginning, and in the following billions of years there were fluctuations □ Atmospheric composition: the rise in atmospheric oxygen allowed the origin of many animal body plans, the conquest of arthropods and vertebratesand an increase in body size □ Shifting of landmasses: continental drift □ Floods and glaciations □ Volcanic eruptions caused extinctions,new islands to form and spewing of debris, limiting sunlight □ Meteoriteimpacts - Evolution of the Earth disposition ○ Pre-Paleozoicperiod  Land: Rodinia  Ocean: Panafrican & Panthalassic ○ Paleozoicperiod  Land: Pangaea  Ocean: Panthalassic & Tethys ○ Mesozoicperiod  Land: Laurasia & Gondwana  Ocean: Pacific & Tethys ○ Cenozoic period  Land: America, Africa, Europe, Asia, Antarctica & Australia  Ocean: Pacific, Atlantic & Indic  Ocean: Pacific, Atlantic & Indic - Mass extinctions ○ 5 large mass extinctions ○ Marked the end of some periods (Ordovician, Devonian,Permian, Triassic and Cretaceous) ○ Sixth mass extinction:rapid extinction of many modern species due to human activities - ARCHAEAN EON ○ First prokaryoticcells arose (in this eon all forms of life were prokaryotic) ○ Hardly any free oxygen so all the organisms were Anaerobic. Cyanobacteria allowed the evolutionof aerobic species, since they produce oxygen as a waste product of photosynthesis.I was the doom for many obligate anaerobes ○ The endosymbiosisof bacteria and archaea might have led to the formationof eukaryotic cells  Endosymbiosis:two species live in direct contact, one inside the other  Steps of archaea-bacteria endosymbiosis □ An archaeon species evolvedthe ability to invaginate its plasma membrane □ The invagination process led to the formationof a nuclear envelope □ The invagination process also allowed the archaeon to engulf a bacterium and establish an endosymbiosis  Many bacterial genes were transferred to the nucleus  Formationof mitochondria □ There was a subsequent endosymbioticevent involving the engulfment of cyanobacteria  Formationof chloroplasts - PROTEROZOICEON ○ Multicellular eukaryotesarose  Two possible origins □ Individuals forming a colony □ Single cell divides and the resulting fragments of the division stay stuck together  Multicellular animals emerge toward the end of the eon  First animals were invertebrates - bilateral symmetryfacilitates locomotionand directionality - PHANEROZOIC EON ○ PALEOZOIC ERA  CAMBRIAN PERIOD □ Warm and wet with no ice a poles □ Cambrian explosion: abrupt increase in the diversity of animal species with an unknown cause □ Included all existing major types of marine invertebratesplus many others that are now extinct □ No many reorganizations of body plans □ First vertebrates 19 - INTRO TO EVOLUTION & POPULATION GENETICS Monday, April 27, 2015 04:58 19.1. OVERVIEW OF EVOLUTION - Evolution: heritable change in one or more characteristics of a population or species over generations - Microevolution:at minimum, changes in frequency in a single gene (allele) in a population over generations - Macroevolution:formation of new species or groups of species - Species ○ Group of related organisms that share a distinctive form ○ Among species that reproduce sexually, members of the same species are capable of interbreeding to produce viable and fertile offspring - Population: members of the same species that are likely to encounter each other and thus have the opportunity to interbreed - History of the theory of evolution ○ Empirical thought  Relies on observationto form an idea or hypothesis rather than on a spiritual point of view  Encouraged scholars to look for the basic rationale behind a given process or phenomenon □ Buffon: proposed not too openly that living things changed through time □ Lamarck  Suggested intimate relationship between variation and evolution  Hypothesized that species change over generations by adapting to new environments  Inheritance of acquired characteristics □ Thomas Maltus: only a fraction of population will survive ad reproduce □ Charles Darwin  Voyage of the Beagle, 1831-1836 ◊ Noticed distinctive traits of island species that allowed them to better exploit their environment ◊ Galapagos finches: saw similarities in species yet noted differences that provided them with specialized feeding strategies  Formulated theory of evolution,detailed in "On the Origin of Species"  Evolution is based on ◊ Variation within a given species  Traits heritable, passed from parents to offspring  Genetic basis was not yet known ◊ Natural selection  More offspring produced that can survive  Competitionfor limited resources  Individuals with better traits flourish and reproduce 19.2. EVIDENCE OF BIOLOGICAL EVOLUTION - Type of observation ○ Studies of natural selection:by studying the characteristics of populations over time, researchers have observed how natural selection alters such population in response to researchers have observed how natural selection alters such population in response to environmentalchanges ○ Fossil records  When fossils are compared according to their age, from oldest to youngest, successive evolutionarychanges can be observed □ Fossil analysis in horses for example has revealed adaptive changes in size, foot anatomy,and tooth morphologyin response to large dense forests being replaced with grassland ○ Biogeography: study of the geographical distribution of extinct and modern species  Isolated continents and island groups have evolvedtheir own distinct plant and animal communities(endemic) ○ Convergent evolution  Two different species from different lineages show similar characteristics because the occupy similar environments(homoplasy) □ Examples  Giant anteater and echidna both have long snouts and tongues to feed on ants  Antifreeze proteins in different, very cold water fish ○ Selective breeding / artificial selection: programs and procedures designed to modifytraits on domesticatedspecies  Made possible by genetic variation  Breeders choose desirable phenotypes ○ Homology:fundamental similarity due to descent from a commonancestor  Synapomorphyvs. Symplesiomorphy □ Synapomorphy: shared derived homologouscharacter that originated with the most recent commonancestor  Ex: mammaryglands and hair in mammals □ Symplesiomorphy:shared homologouscharacter originating prior to the most recent commonancestor of a group of species  Ex: vertebral column in mammals  Types of homologies □ Anatomical  Homologousstructures are structures that are anatomicallysimilar to each other because they evolvedfrom a structure in a commonancestor  Vestigial structures: anatomical structures that have no apparent function but resemble structures of presumed ancestors ◊ Ex: tail bone in humans, remnants of hip bones in snakes, remnants of a pelvis in whales, fingernails on the flippers of manatees □ Developmental  An analysis of embryonicdevelopmentoften reveals similar features that point to past evolutionaryrelationships ◊ Ex: presence of gill ridges in human embryosindicated that humans evolvedfrom an aquatic animal with gill slits; human embryoshave long bony tails □ Molecular  Similarities in cells at the molecular level show that living species evolved from a commonancestor ◊ Ex: all living species use DNA to store information;certain biochemical pathways are found in all or nearly all species; the same type of gene is often found on diverse organisms  Types of molecularhomologies ◊ Orthologous: gene loci that are homologousbecause of a lineage- splitting event (speciation) ◊ Paralogous: gene loci that originated by a duplication event within a ◊ Paralogous: gene loci that originated by a duplication event within a lineage 19.3. GENES IN POPULATIONS - Population genetics: study of genes and genotypes in a population ○ Wants to know extent of genetic variation, why it exists, how it is maintained, and how it changes over the course of many generations ○ Helps us understand how genetic variation is related to phenotypic variation - Gene pool: all of the alleles for every gene in a given population - Population: groups of individuals of the same species that occupy the same environmentand can interbreed with one another - Classification of genes according to allele number ○ Polymorphicgene: two or more alleles  Single nucleotide polymorphismsare the smallest type of genetic variation change in a gene; responsible for about 90% of variation in human gene sequences ○ Monomorphic:predominantly single allele - Allele and genotype frequencies Allele frequency = Number of copies of a specific allele in a population Total number of alleles for that gene in a population Genotype frequency = Number of individuals with a particular gene in a population Total number of individuals in a population ○ Hardy-Weinberg equation P +2pq + q = 1 Where: P is the genotype frequency of dominant homozygotes 22 iis the genotype frequency of heterozygotes q s the genotype frequency of recessive homozygotes  Conditions for Hardy-Weinberg equilibrium □ No new mutations occur □ No natural selection occur □ The population is so large that allele frequencies do not change due to random sampling error □ No migration occurs between different populations □ Random mating  In reality, no population meets the conditions - Microevolution:changes in a gene pool from generation to generation ○ Sources of new genetic variation  New mutations within genes that produce new alleles: mutations can be negative, positive or neutral  Gene duplication: caused by abnormal crossoverevents and transposable elements  Horizontal gene transfer: genes from one species may be introduced into another species ○ Evolutionarymechanismsthat alter the frequencies of existing genetic variation  Natural selection  Genetic drift  Migration  Nonrandom mating 19.4. NATURAL SELECTION - Natural selectionis the process in which beneficial traits that are heritable becomemore common in successive generations - Adaptations: result of natural selection;changes in populations of living organisms that promote their survival and reproductions in a particular environment - Reproductivesuccess: likelihood of an individual contributing fertile offspring to the next generation ○ Attributed to two categories of traits  Certain characteristics make organisms better adapted and more likely to survive to reproductive age  Traits directly associated with reproduction, such as ability to find a mate and ability to produce viable gametes and offspring - Modern description of natural selection ○ Within a population, allelic variation arises from random mutationsthat cause differences in DNA sequences ○ Some alleles encode proteins that enhance an individual's survival or reproductive capability compared to other membersof the population ○ Individuals with beneficial alleles are more likely to survive and contribute their alleles to the gene pool of the next generation ○ Over the course of many generations, allele frequencies of many different genes may change through natural selection, thereby significantly altering the characteristics of a population - Fitness: relative likelihood that a genotype will contribute to the gene pool of the next generation as compared to other genotypes ○ Quantitative measure of reproductivesuccess ○ Hypothetical gene with alleles A and a: AA, Aa, aa  Supposed average reproductivesuccesses are: AA produces 5 offspring, Aa produces 4 offspring and aa produces 1 offspring  Fitness is W, maximum is 1 for genotype with highest reproductive ability □ Fitness of AA: WAA = 5/5 = 1 □ Fitness of Aa: Waa = 4/5 = 0.8 □ Fitness of aa: Waa = 1/5 = 0.2 - Natural selectionpatterns ○ Directional selection: individuals at one extremeof a phenotypic range have greater reproductive success in a particular environment  Initiators: new allele with higher fitness introduced; prolonged environmentalchange ○ Stabilizing selection: favors the survival of individual with intermediatephenotypes; extreme values of a trait are selected against ○ Diversifying selection: favors the survival of two or more different genotypes that produce different phenotypes; likely to occur in populations that occupy heterogeneous environments ○ Balancing selection: maintains genetic diversity  Balances polymorphism:two alleles are kept in balance, and therefore are maintained in a population over the course of many generations  Two commonways □ For a single gene, heterozygotefavored □ Negative frequency-dependent selection  Rare individuals have a higher fitness - Sexual selection: directed at certain traits of sexually reproducing species that make it morelikely for individuals to find or choose a mate and / or engage in successful mating In many species, affects male characteristics more intensely than it does female ○ In many species, affects male characteristics more intensely than it does female ○ Explains traits that decrease survival but increase reproductive success ○ Types of sexual selection  Intrasexual selection: between members of the same sex; males directly compete for mating opportunities or territories □ Ex: horns in male sheep, antlers in male moose,male fiddler crap enlarged claws  Intersexual selection: between membersof the opposite sex; involves femaleschoice and often results in showy characteristics for males 19.5. GENETIC DRIFT - Genetic drift changes allelic frequencies due to random chance ○ Characteristics  Random events unrelated to fitness  Favors either loss or fixation of an allele; frequency reaches 0% or 100%  Faster in smaller populations ○ Examples of the phenomenon in nature  Bottleneck □ Populations reduced dramatically and then rebuilds; the new population is likely to have less genetic variation □ Surviving membersmay have allele frequencies different from original population. The frequency can drift substantially when the population is small  Founder effect □ A small group of individuals separates from a larger population and established a new colony □ Allele frequency in founding population may differ from original population; less genetic variation is a small founding population - Neutral theory of evolution ○ Neutral variation: much of the variation seen in natural population is caused by genetic drift and does not preferentially select for any particular allele  Most genetic variation is due to the accumulation of neutral mutations that have attained high frequencies due to genetic drift  Neutral mutations do not affect phenotype: they are not acted upon by natural selection 19.6. MIGRATION AND NONRANDOM MATING - Gene flow occurs when individuals migrate between populations having different allele frequencies - Migration tends to ○ Reduce differences in allele frequencies between two populations ○ Enhance genetic diversity within a population - Nonrandom mating: individuals choose their mates according to their geno/ phenotypes ○ Assortative/ disassortativemating: choice based on phenotype  Assortativemating □ Individuals with similar phenotypes are more likely to mate □ Decreasesthe proportion of homozygotes  Disassortativemating □ Dissimilar phenotypes mate preferentially □ Favors heterozygosity ○ Inbreeding: choice of mate based on genetic history  Does not favor any particular allele  Does not favor any particular allele  Increases the likelihood the individual will be homozygous  May have negative consequenceswith regard to recessivealleles 20 - ORIGIN OF SPECIES AND MACROEVOLUTION Monday, April 27, 2015 02:46 20.1. IDENTIFICATION OF SPECIES - Macroevolution:Evolutionarychanges that create new species and groups of species; concerns the diversity of organisms established over long periods of time through the evolution and extinction of many species - Species: a group of organisms that maintains a distinctive attributes in nature ○ Characteristics used to identified species  Morphologicaltraits: organisms are classified as the same species if their anatomical traits appear to be very similar □ Drawbacks for determining species  How many traits to consider  Traits may vary in a continuous way  What degree of dissimilarity to use  Membersof the same species can look very different  Membersof different species can look very similar  Reproductiveisolation: prevents one species from successfully interbreeding with other species □ Four main problems for determining species  May be difficult to determine in nature  Can interbreed and yet do not  Does not apply to asexual species  Cannot be applied to extinct species  Molecular features: compare features to identify similarities and differences among different populations □ DNA sequences within genes □ Gene order along chromosomes □ Chromosomestructure □ Chromosomenumber  Ecological factors: varietyof factors related to an organism's habitat can be used to distinguish one species from another □ Many bacterial species have been categorized as distinct species based on ecological factors □ Drawback  Different groups of bacteria sometimesdisplay very similar growth characteristics. Even the same species may show great variation in the growth conditions it will tolerate ○ Species concepts: way to define the concept of a species and / or provide an approach to distinguish one species from another  Biological species concept □ Species is a group of individuals whose membershave the potential to interbreed in nature to produce viable, fertile offspring  Evolutionaryconcept □ Lineage is a series of species that forms a line of descent, with each new species the direct result of speciation  Ecological species concept □ Defines each species based on ecologicalniche - ecologicalniche is the unique set of habitat resources that a species requires, as well as the influence on the environmentand other species environmentand other species 20.2. REPRODUCTIVE ISOLATION - Interspecies hybrid: when two species produce offspring - Reproductiveisolation mechanisms: mechanismsthat prevent interbreeding between different species; consequence of genetic changes as species adapts to its environment ○ Prezygoticbarriers: prevent formation of zygote  Habitat isolation: geographic barrier prevents contact  Temporal isolation: species happen to reproduce at different times of the day of year  Behavioral isolation: different mating behavior □ Ex: changes in song  Mechanical isolation: size or incompatiblegenitalia prevents mating  Gametic isolation: gametes fail to unite successfully, important in species that release gametes into the water or air ○ Postzygoticisolating mechanisms: less commonin nature because they are more costly in terms of energy and resources used  Hybrid inviability: an egg of one species is fertilized by sperm of another, but the fertilized egg cannot develop past embryonicstages  Hybrid sterility: an interspecies hybrid might be viable but sterile □ Ex: a horse and a donkey's offspring is a mule, always sterile  Hybrid breakdown: hybrids viable and fertile but subsequent generations have genetic abnormalities 20.3. MECHANISMS OF SPECIATION - Speciation: formationof new species ○ Underlying cause of speciation: accumulation of genetic changes that ultimately promote enough differences so that we judge a population to constitutea unique species - Patterns of speciation ○ Cladogenesis  Division of a species into two or morespecies  Requires gene flow between populations to be interrupted  Allopatric speciation is the most prevalent method for cladogenesis □ Occurs when  some membersof a species become geographically separated  A small population movesto a new location that is geographically separated ◊ Natural selectionmay rapidly alter the genetic compositionof the population, leading to adaption to the new environment ◊ Adaptive radiation: single species evolvesinto array of descendants that differ greatly in habitat, form or behavior ○ Sympatric speciation: membersof a species that are within the same range diverge into two or more different species even though there are no physical barriers to interbreeding  Mechanisms include □ Polyploidy  Organism has two or moresets of chromosomes  Plants more tolerant of polyploidy than animals  Can occur through nondisjunction: completenondisjunction increases the number of chromosomesets in a given species (autopolyploidy) ◊ Ex: tetraploid + diploid = triploid □ Adaptation to local environments □ Adaptation to local environments  Geographic area may have variation so that some membersof a population may diverge and occupy different local environmentsthat are continuous with each other □ Sexual selection  Certain females prefer males with one color pattern, while other females prefer males with a different color pattern 20.4. EVO-DEVO: EVOLUTIONARY DEVELOPMENTAL BIOLOGY - Development:series of changes in the state of a cell, tissue, organ or organism - Evo-Devocompares the developmentof different organisms ○ It attemptsto understand  Ancestral relationships between organisms  Developmentalmechanismsthat bring about evolutionarychange ○ Involves the discoveryof genes that control development,and how their roles vary in different species  Developmentalgenes may influence □ Cell division □ Cell migration □ Cell differentiation □ Cell death (apoptosis)  Interplay produces an organism with a specific body pattern (pattern formation ○ Differences in expression of two cell-signaling proteins defines chicken vs. duck feet  Proteins involved □ BMP4: causes cells to undergo apoptosis and die □ Gremlin: inhibits the function of BMP4 and allows cells to survive  Mutations that change expression of BMP4and Gremlin provide variation □ In terrestrial settings, nonwebbed feet are an advantage □ In terrestrial environments,webbed feet are ad advantage ○ Hox genes  Increases in the number of Hox genes may have led to greater complexity in body structure  Hox gene complexity has been instrumental in the evolution and speciation of animals with different body patterns □ Three lines of evidence support this idea  Hox genes are known to control fate of regions long the anteroposterior axis  General trend for more complex animals to have more Hox genes and Hox clusters  Comparison of Hox gene evolutionand animal evolution bear striking parallels ○ Developmentalgenes that affect growth rate  Genetic variation can influence morphologyby controlling relative growth rates of different parts of the body during development  Heterochrony:evolutionarychanges in the rate or timing of developmentalevents  Compare head growth between human and chimpanzee 21 - TAXONOMY AND SYSTEMATICS Monday, April 27, 2015 04:52 21.1 TAXONOMY - Systematics:study of diversity and evolutionaryrelationships among organisms, both extinct and modern - Taxonomy:science of describing, naming, and classifying extant and extinct organisms ○ Taxonomicgroups are based on hypotheses regarding evolutionaryrelationships derived from systematics ○ Hierarchical system involving successive levels or taxons  Domains are the highest level □ All life belongs to one of three domains, Bacteria, Archaea and Eukarya  Successive divisions are supergroup, kingdom, phylum, class, order, family, genus and species - Binomial nomenclature: genus name and species epithet ○ Rules established and regulated by international associations  Genus name always capitalized  Species epithet never capitalized  Both names either italicized or underlined 21.2. PHYLOGENETIC TREES - Phylogeny:evolutionaryhistory of a species or group of species; to propose a phylogeny, biologists use the tools of systematics - Phylogenetictree: diagram that describes phylogeny based on available information;it's a hypothesis of evolutionaryrelationships among various species New species can be formed by  Anagenesis: single species evolvesinto a different species without lineage splitting  Cladogenesis: a species diverges into two or more species Types of aggrupations that phylogenetic trees represent  Monophyleticgroup or clade: group of species - a taxon - consisting of the most recent commonancestor and all of its descendants  Paraphyletic groups: when taxa are constructed with descendants missing  Polyphyleticgroups: when taxa are constructed with ancestors missing and species from different lineages grouped - Homology:similarities among various species that occur because they are derived from a common ancestor or from the same ancestral gene ○ Some ways to study homology  Morphologicalanalysis □ First systematicsstudies focused on morphologicalfeatures of extinct and modern species □ Convergent evolution(traits arising independently due to adaptation to similar environments)can cause problems  Molecular systematics □ Analysis of genetic data, such as DNA and amino acid sequences, to identify and study genetic homologiesand propose phylogenetic trees □ DNA and amino acid sequences from closely related species are more similar to each other than to sequences from more distantly related species 21.3. CLADISTICS - Cladistics is the study and classification of species based on evolutionaryrelationships ○ Discriminatesamong possible trees by considering the various possible pathways of changes and then choosing the tree that requires the least complicatedexplanation (principle of parsimony)  Principle of parsimony selects the simplest hypothesis as the preferred one  Challenge in a cladistic approach is to determine the correct polarity of events □ It may not always be obvious which traits are primitive or derived □ Fossils may be analyzed to help resolve and determine polarity of character states ○ Makes phylogenetic trees or cladograms ○ Compares homologoustraits, also called characters, which may exist in two or more character states  Shared primitivecharacter - symplesiomorphy □ Shared by two or more different taxa and inherited from ancestors older than their most recent commonancestor  Shared derived character - synapomorphy □ Shared by two or more species or taxa and has originated in their most their most recent commonancestor □ Basis of the cladistic approach is to analyze many shared derived characters to deduce the pathway that gave rise to those species ○ Elements of a cladogram  Branch point: two species differ in shared derived characters  Ingroup: group we are interested in  Outgroup: species or group of species that is assumed to have diverged before the species in the ingroup. It will lack one or more shared derived characters that are found on the ingroup 21.4. MOLECULAR CLOCKS - Most mutations are neutral: favorable mutations are rare, detrimental mutations are quickly eliminated ○ If neutral mutations occur at a constant rate they can be used to measure evolutionarytime ○ Neutral mutations are not perfectly linear over long periods of time  Not all organisms evolve at the same rate  Differences in generation times - Molecular clocks are calibrated using information regarding the date when two species diverged from a commonancestor 21.5. HORIZONTAL GENE TRANSFER - Horizontal gene transfer ○ Characteristics  Any process in which an organism incorporates genetic material from another organism without being the offspring of that organism  The transfer of genes between different species ○ In contrast to vertical evolution  The traditional view of evolution  The traditional view of evolution  Changes in groups due to descendent from a commonancestor 22 - MICROORGANISMS: THE ARCHAEA, BACTERIA, AND PROTISTS Monday, April 27, 2015 06:29 22.1. INTRODUCTION TO MICROORGANISMS - Microorganisms:typically so small in size that they can be seen only with the use of a microscope. Diversityis one of their prominent features. ○ Domain Archaea and domain Bacteria are both prokaryotic,they lack nucleus ○ Protists: multiple phyla within domain Eukarya - Archaea & Bacteria ○ Characteristics  While both Archaea are monophyleticgroups, "prokaryotes"is not  These domains include the smallest known cells and are the most abundant type of organisms  Live nearly in every conceivablehabitat, including extremehabitats such as hot or very salty waters  Extraordinary high metabolic diversityand thus play diverse ecologicalroles  Usually single-celled □ Some aggregate into colonies or filaments □ Some bacteria have true multicellularity(specialized cells) - Protists ○ Characteristics  Earth's first eukaryotes,consist of diverse eukaryotic organisms that do not fit into Fungi, Plantae or Animalia  Most are microscopic □ Example of exception:seaweeds ○ Classification based on functionality  Algae: protists that have chloroplasts  Protozoa:protists that lack chloroplasts - Microbiomes:microbe communitiesassociatedwith a host organism (within bodies of animals, plants, or other organisms ○ Key medical and ecological importance ○ Human microbiome  Skin, digestive and reproductivetracts  Influence digestion and health □ Supply vitamin K □ Fight infectious microbes ○ When both bacteria and host benefit, the associationis a mutualistic symbiosis ○ Microbiomesfoster horizontal gene transfer  Horizontal gene transfer: movementof genes from one species to another  Increases genetic diversity and can result in large genetic changes  Commonamong Archaea and Bacteria 22.2. ARCHAEA 22.2. ARCHAEA - Archaea share a number of features with eukaryotes ○ Histone proteins ○ Ribosomalproteins ○ RNA polymerases - Includes many extremophiles ○ Occupy habitats with extremeconditions  Halophiles: live in high salt content  Acidophiles: live in acidic conditions  Methanogens:live in habitats with high methane levels  Hyperthermophyles - Kingdoms contained in domain Archaea ○ Korarcaeota ○ Nanoarchaeota ○ Thaumarchaeota ○ Eukaryachaeota ○ Crenarchaeota - Distinctivecharacteristics ○ Membranes have ether bonds, not ester bonds ○ Membranes have isoprene, not fatty acid chains ○ Most have cell walls made of protein, not peptidoglycan 22.3. DIVERSITY OF BACTERIAL PHYLA - There are about 50 bacterial phyla ○ Specially important are Cyanobacteria and Proteobacteria ○ Most bacteria favor moderateconditions (although someare extremophiles) ○ Many form symbioticrelationships with eukaryotes ○ Representativebacterial phyla  Cyanobacteria:photosyntheticbacteria abundant in fresh water, oceans and wetlands and soil surface □ Only prokaryotesthat generate oxygen as a product of photosynthesis □ Nitrogen fixators: convertnitrogen into ammonia □ Gave rise to plastids of eukaryoticalgae and plants □ Display the greatest structural diversity found among bacterial phyla  Single cells (unicells) or colonies  Filaments □ Essential ecologicroles in producing organic carbon and fixing nitrogen □ Can also form nuisance blooms that can be toxic  Proteobacteria □ Do not produce oxygen, but play other ecologicallyimportant roles □ Five major classes  Alphaproteobacteria ◊ Related to ancestors of mitochondria ◊ Nitrogen-fixing bacteria like Rhizobium help plants grow  Betaproteobacteria ◊ Nitrosomonas, a soil bacteria ◊ Important for the global nitrogen cycle  Gammaproteobacteria ◊ Includes human pathogens  Neisseria gonorrhoeae: the STD gonorrhea  Neisseria gonorrhoeae: the STD gonorrhea  Vibrio cholera: cholera epidemics  Salmonella and E. coli: food poisoning  Deltaproteobacteria ◊ Colony-formingmyxobacteria ◊ Predatorybdellovibrios can drill into cell walls of other bacteria  Epsilonproteobacteria ◊ Helicobacter pylori: increases risk of peptic ulcers and stomach cancer 22.4. DIVERSITY IN BACTERIAL CELL STRUCTURE - Bacteria and archaea share small size, rapid growth and simple cellular structure - Species have different adaptations that increase their complexity ○ Specialized organelle-like structures: complex intracellular structures similar to the organelles of eukaryotes  Thylakoids: make it possible for cyanobacteriato use light energy □ Ingrowths of the plasma membranethat increase surface area and contain chlorophyll for photosynthesis  Magnetostomes:organelles that respond to the Earth's magnetic fields in Magnetospirillum □ Tiny crystals of magnetite □ They orient the cells, helping them to stay submerged in a low-oxygenhabitat  Nucleus-like structures: possessed by Planctomycetes □ It lacks pores but encloses the bacterial cell's DNA ○ Differences in cell shape  Five major shapes □ Cocci: spheres □ Bacilli: rods □ Vibrio: comma-shaped □ Spiral shaped  Spirochete: flexible  Spirilli: rigid  Arrangements: cocci and bacilli may be grouped in characteristicways, indicated by terms or prefixes □ Diplo-: pairs □ Staphylo-: clusters like grapes □ Stepto-: chains □ Tetrads: sets of four □ Sarcina: sets of eight set as to the corners of a cube □ Palisades: bacilli aligned along their long axes ○ Differences in cell-wall structures  Most have a rigid cell wall outside the plasma membrane  Maintains cell shape and helps protect against attack; also helps avoid lysis in hypotonic solutions  Most bacteria use peptidoglycan □ Gram stain: differentiates cells in terms of the percentage and disposition of peptidoglycan  Gram positivebacteria ◊ Relativelythick peptidoglycan layer ◊ Purple dye is held in the thick layer ◊ Cells are stained purple ◊ Vulnerable to penicillin that interferes in cell wall synthesis ◊ Vulnerable to penicillin that interferes in cell wall synthesis  Gram negative bacteria ◊ Less peptidoglycan and a thin outer envelope of lipopolysaccharides ◊ Lose the purple stain but retain final pink stain ◊ Cells are stained pink ◊ Resists penicillin and requires other antibiotics ○ Specialized cell coating: mucilage coats some cells  Mucilage is sometimescalled a capsule, glycocalyx,or extracellular polymeric substance; it’s a slimy coating secreted from cells and composedof polysaccharides  Functions □ Evade host defenses □ Protectfrom UV damage □ Hold colony together: biofilms, like dental plaque ○ Structures for motility  Motility allows cells to respond to chemical signals and move to favorable conditions  Cells can swim, twitch, glide or adjust flotation □ Internal buoyancy vesicles help cyanobacteria float □ Pili: threadlike cell surface structures allow some species to twitch or glide across surfaces □ Flagella allows cells to movequickly in liquid  Cells with flagella can spread infection through the body  Flagella in bacteria lack an outboard motor,differ in number and location of flagella 22.5. ECOLOGICAL AND MEDICAL IMPORTANCE OF BACTERIA - Small size and genome allow fast reproduction - Generate large populations that affect other organisms and the entire planet - Understanding bacterial reproduction is key to understanding how microbes play major ecological and medical roles ○ Breaking down organic carbon ○ Processing minerals ○ Symbionts ○ Disease agents - Bacterial reproduction ○ Binary fission: divide by splitting in two ○ Basis for widely used methods of detecting and counting bacteria in samples  Place measured volumeof sample into plastic dishes of agar  Each single cell will form a visible colony  Can also use fluorescent dye that binds bacterial DNA to directly count bacteria - Surviving harsh conditions ○ Akinetes  Found in aquatic filamentous cyanobacteria  Developwhen winter approaches  Survive winter and produce new filaments in spring ○ Endospores  Tough protein coat  Amazingly long dormant span  Found in someGram-positivebacteria - Bacterial energy & carbon source requirements ○ Autotrophs: able to produce all or most of their organic compoundsfrom inorganic sources  Photoautotrophs use light as a source of energy  Chemoautotrophs get energy from compounds in the environment  Chemoautotrophs get energy from compounds in the environment □ Chemolithoautotrophsget energy from compounds in the environmentby nitrification or oxidation □ Chemoorganoautotrophs get energy from organic compounds ○ Heterotrophs: require one or more organic compounds from the environmentas a source of carbon  Photoheterotrophs use light energy to generate ATP, but must take in organic compounds as a source of carbon  Chemoheterotrophsmust use organic moleculesfor both energy and a carbon source - Bacterial oxygen needs ○ Obligate aerobes: require oxygen in order to survive ○ Obligate anaerobes: are poisoned by oxygen ○ Aerotolerantanaerobes: do not use oxygen, but not poisoned by it either  Obtain energy by fermentation or anaerobic respiration, using electronacceptors other than oxygen ○ Facultative anaerobes: can shift between modes depending on conditions ○ Microaerophiles:grow best in low oxygen concentrations ○ Capnophiles: require enrichment with carbon dioxide - Pathogenic bacteria ○ Pathogens: microorganismsthat cause disease ○ Examples of human diseases caused by bacterial pathogens:  Cholera, leprosy, tetanus, pneumonia, whooping cough, diphtheria, etc. ○ Bacteria also cause many plant diseases  Blights, soft roots, and wilts ○ Ceratin bacteria also attack other bacteria, protists, and fungi ○ Koch's postulates 1. The presence of the suspected pathogens must correlatewith occurrenceof symptomsin the host 2. The pathogen must be isolated from an infected host and grown in pure culture if possible 3. Cells from the pure culture should cause disease when inoculated into a healthy host 4. One should be able to isolate the same pathogen from the second infected host 22.6. PROTIST CLASSIFICATION BY HABITAT, SIZE, AND MOTILITY - Protists are eukaryotesthat are not classifies in the plant, animal or fungal kingdoms. Some protists are howeverclosely related to those kingdoms ○ Two commoncharacteristics  Abundant in moist habitats  Microscopicin size ○ Classification by ecologicalrole  Three major groups (although they lack taxonomicor evolutionarymeaning) □ Algae: generally photoautotrophic □ Protozoa:heterotrophic □ Fungus-like protists: like fungi in form and nutrition ○ Classification by motility  Flagellates: swim using eukaryoticflagella; sometimesjust reproductivecells are flagellated  Ciliates: have cilia, which are shorter and more abundant than flagella  Amoebae: amoeboid movementusing pseudopodia ○ Classified by habitat  Plankton: swimmingof floating □ Phytoplanktonis photosyntheticplankton □ Phytoplanktonis photosyntheticplankton  Periphyton: attached to underwater surfaces, produce large multicellular bodies  Seaweed: photosyntheticprotists large enough to see with the unaided eye □ Ex: kelp 22.7. EUKARYOTIC SUPERGROUPS: ECOLOGICAL AND MEDICAL IMPORTANCE OF PROTISTS - "Protists" is not a monophyleticgroup - Prokaryoticsupergroups ○ Excavata  Related to some of Earth's earliest eukaryotes  Named for a feeding groove"excavated"into the cells of many representatives  Food particles are taken into cells by phagocytosis:evolutionarybasis for endosymbiosis  Possesshighly modified mitochondria  Some are parasites that cause disease □ Trichomonas vaginalis □ Giardia intestinalis  Euglena is a commonexcavate protist that has green plastids ○ Plants and relatives ○ Alveolata  Named for saclike membranous vesicles (alveoli)present in cell periphery  Includes three important phyla □ Ciliophora (ciliates) □ Dinozoa (dinoflagellates)  Some are photosynthetic,others not  Red tide and mutualistic relationship with coral □ Apicomplexa  Medically important parasites  Plasmodium: causes malaria ○ Stramenopila  Wide range of algae, protozoa,and fungus-like protists; usually produce flagellate cells  Named for distinctive straw-like hairs on the surface of flagella  Heterotrophicor photosynthetic □ Plastids from secondary endosymbiosiswith red algae ○ Rhizaria  Have thin, hair-like extensionsof the cytoplasmcalled filose pseudopodia  Include ocean plankton with fine mineral shells □ Phylum Radiolaria □ Phylum Foraminifera ○ Amoebozoa  Moveusing pseudopodia  Ex: Dictyostelium discoideum, slime mold □ Model organism for understanding movement,cell communication,and development □ In response to starvation, single amoebae aggregate into a multicellular "slug" that develops into a stalked structure containing spores □ Spores pop out and produce amoebae ○ Opisthokonta - Plastids and endosymbiosis Primary endosymbiosis:occurs when a heterotrophic host cells captures cyanobacterial cells ○ Primary endosymbiosis:occurs when a heterotrophic host cells captures cyanobacterial cells via phagocytosis but do not digest them  Endosymbioticcyanobacteriaprovided host cells with photosyntheticcapacity and other useful biochemical pathways; eventually evolvedinto primary plastids ○ Secondary endosymbiosis: occurs when a eukaryotichost cells ingests and retains another type of eukaryoticcell that already has one or more primary plastids, such as a red or a green alga  Typically more than two envelopes  Over half of the dinoflagellates possess photosyntheticplastids of diverse types that originated by secondary or even tertiary endosymbiosis - Protist characteristics ○ Basic types of nutrition  Phagotrophy: heterotrophsthat ingest particles  Osmotrophy:heterotrophsthat rely on uptake of small organic molecules  Photoautotrophy:photosynthetic  Mixotrophy:able to use autotrophy and heterotrophydepending on conditions ○ Algal protists have a varietyof pigments  Photosystemsadapted to capture more light  Accessorypigments absorb light and transfer it to chlorophyll a ○ Protists have varied defenses  Slimy mucilage  Cell walls: calcium carbonate, silica, iron, manganese  Bioluminescence:startle herbivores / predators  Toxins: inhibits animal physiology ○ Reproductivebehavior  All protists can reproduce asexually □ Allows for rapid population growth in favorable conditions  Eukaryoticsexual reproduction arose among protists □ Generally adaptive: increased genetic diversity □ Gametic, sporic & zygotic life cycles  Zygotic life cycle: zygote is the only diploid cell ◊ Unicellular diploid zygotes is often tough ◊ Most unicellular protists with sexual reproduction  Sporic life cycle: alternation of generations ◊ Many multicellular green and brown seaweeds ◊ Two types of multicellular organisms  Gametic life cycle: all cells except the gametes are diploid ◊ Gametesproduced in meiosis ◊ Diatoms:one of the few protists with this life cycle  Asexual reproduction reduces the size of the daughter cells  Sexual reproduction restores maximal size 22.8. TECHNOLOGICAL APPLICATIONS OF BACTERIA AND PROTISTS - Mi


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