BIOL FOR SCI MAJ II
BIOL FOR SCI MAJ II BIOL 1202
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Chapter 27 Prokaryotes Goals Know differences between three domains Archaea Bacteria and Eukaryotes Know 3 main bacterial cell shapes differences in cell walls Understand the basics of bacterial sex nutrition and why photosynthesis evolved early Know an example of each major bacterial clade Know why prokaryotes are important to ecosystems Prokaryotes 39 Diverse 5000 species but up to four million possible 39 Some deleterious but most are Beneficial 39 Symbionts in eukaryotes origin of mitochondria and chloroplasts 39 Two main domains Archaea Bacteria Basic Cell Structure Unicellular or colonial Three main shapesspheres rods and helices Cell wall of peptidoglycan outside cell membrane Double cell wall ofgram bacteria more resistant and pathogenic Penicillin breaks down bacterial cell walls does not affect eukaryotic cells Figure 272 The most common shapes of prokaryotes Figure 273 Grampositive and gramnegative bacteria Prokaryote Anatomy May have protective sticky capsule that attaches to host cells Have small hair like appendages mbriae or pill to attach to host cells Have a smaller simpler agellum a small motor below cell wall turns rigid shaft Fig 274 Fig 275 Fig 276 Differences from Eukaryotes 39 Lacks nucleus 39 fewer simpler organelles 39 Much smaller genomes in circular DNA chromosomes 39 Small circular DNA plasmids induce enzymes or resistance to antibiotics 39 Plasmids replicate independently and are transmitted during conjugation Prokaryote Reproduction Asexual binary fission three types of genetic transfer Transformation DNA from environment Conjugation DNA from another bacterium Transduction DNA from viruses Mutations spread rapidly with short generation times and geometric growth Endospores withstand environmental extremes Fig 279 Fig 2712 Nutrition of Prokaryotes Table 271 39 Based on energy and carbon sources Photo sun or chemo oxidize compounds Know the differencell Auto only need 002 or hetero other organic compounds needed Know the Differencell Nutrition of Prokaryotes 39 saprobes decompose parasites feed on cell uids 39 Prokaryotes x atmospheric N2 as NH4 and make available for other organisms 39 Obligate aerobes facultative anaerobes can still use 02 or obligate anaerobes use fermentation or anaerobic respiration Prokaryotes can be colonial or form mats called biofilms Fig 2714 Fig 2715 Fig 2716 Table 272 Look at this table to determine differences between Bacteria Archea and Eukarya The first three are the most important Domain Archaea o Halophiles thermophiles and other extremophiles Major Bacterial Clades Fig 2718 0 Proteobacten39a symbionts on plant roots that x N2 to ammonia 0 Others oxidize ammonia to nitrate 0 responsible for Legionnaire s disease salmonella cholera spotted fevers includes E coli 0 bacterium that causes ulcers Chlamydias KNOW THIS 9gram negative bacteria causing sexually transmitted diseases Spirochaetes internal agella causes spiral motion cause syphilus lyme disease Fig 271821 Gram bacteria produce antibiotics but also cause leprosy tuberculosis botulism and anthrax Cyanobacteria photosynthetic many nitrogen xers may have evolved into chloroplasts Ecological Importance of Prokaryotes Important in decompostion Convert inorganic to organic molecules usable by other organisms Important symbionts Cause numerous diseases produce exotoxins botulism cholera or endotoxins cell wall toxic as in salmonella which causes typhoid fever Important in sewage and oil spill treatment Biosynthesis of drugs like insulin Goals for Chapter 23 Population Genetics Use Hardy Weinberg law to calculate gene and genotypic frequencies Understand how population size gene flow and mutation affect gene frequencies Explain 3 ways genetic variation is maintained in populations Differentiate between 3 modes of selection directional stabilizing and disruptive Understand why sex evolved and how sexual dimorphism evolved Know some factors that limit selection 0 Natural Selection and Genetic Variation Biologists initially rejected natural selection because of lack of genetics mechanism How do variants arise and how are they conserved Blending theory predicted loss of variation Rediscovery of Mendel s work explained conservation of discrete traits either or like eye color Still studying continuous traits like height or weight 0 The Modern Synthesis Populations are units of evolution Small differences in fitness gradually change populations Population is group of interbreeding individuals same area and time Gene pool is number of genes in diploid organisms per locus 2 x no of individuals 0 Genotypes AA aa homozygote Aa heterozygote 2 alleles genes at locus location determine genotypes which determines phenotype Microevolution is change in gene allele frequencies through time HardyWeinberg Law Meiosis does not change gene frequencies Consider wild ower example in text 500 individuals so there will be 1000 genes or alleles in population Example of HW Law 0 R and W are codominant o All owers are pink heterozygotes in G2 But in subsequent generations a 1 2 1 ratio of genotypes Notice how variation is preserved all owers don t become pink Also notice how gamete allele frequencies don t change because of meiosis c Figure 237 The HardyWeinberg theorem 0 Assume that one minus gamete frequencies equal allele frequencies p08andqorfW02 0 Then fRR in next generation p2 and fWW q2 and fRW 2 pq fR or p in next generation p2 and f 2 o 0 Notice that enot IC frequencies obey l i r 1 0 Also notice allele freque ncies do not change Calculating allele and genotypic frequencies 0 lfthe recessive genotypic frequency is known the HW equation can be used to calculate all other frequencies 0 Suppose that 9 ofa population exhibits the recessive phenotype q2 009 q 009 03 p 1 q 07 p2 049 2pq 042 Conditions for HW equilibrium Large Population No migration with respect to the genes No mutation Random mating No selection for alleles at the locus lf frequencies not at HW equilibrium one ofthese may be occurring Genetic Drift When few individuals reproduce rare alleles lost to sampling error or chance 0 Differences within the population decrease o Alleles become fixed at F 100 or 0 o Populations become more homozygous Bottleneck is one example Founder s effect is another 0 More differences between populations 0 Fig 238 Loss ofalleles due to genetic drift 0 Assume only highlighted plants reproduce Since only a few plants reproduce eg population size is low none ofthe white owers reproduce in generation 2 o The white allele is xed at f 0 in generation 3 0 Fig 239 0 Fit 2310 Gene Flow Migration among populations 0 Increases differences within a population 0 Selective with respect to allele 0 Reduces differences between populations and opposes genetic drift 0 Ex Marine organisms with planktonic larvae thought to be panmictic or well mixed Fig 2312 Mutation Low rates 105 not important unless organisms have short life cycles HIV Or mutant allele has higher fitness resistance to pesticides etc Most mutations are deleterious hidden in heterozygotes or redundant DNA or are neutral and don t effect tness Source of new alleles Non random mating Mate selected by phenotype 0 Like marrying like is assortitative mating o Mating with a relative or inbreeding may expose recessive deleterious alleles Increases frequency of homozygotes but does not alter allele frequencies Modes of natural selection Fig 2313 Directional selection favors one extreme of population Stabilizing selection extremes of a population are selected against 0 Small or large lizards are selected against stabilizing selection Diversifying disruptive selection extremes ofa population are favored 0 Seed eating birds have bills selected for small or large disruptive selection Genetic Variation the Substrate for Natural Selection Variation within populations 0 Discrete either or caused by just a few genes 0 Polymorphism multiple phenotypes in population Such as snail shells Variation between populations 0 Geographic variation Clines 0 Fig 234 Discrete characteristics Fig 233 Fig 234 What preserves genetic variation That is why doesn t natural selection remove all genetic variation 0 Diploid genotype can t remove recessive lethal because at low frequencies its only in heterozygotes Because the allele is hidden in the heterozygotes so it is hard for selection to act again 0 o What preserves genetic variation Balanced polymorphism sickle cell anemia 0 SS Dominant homozygote not anemic but susceptible to malaria o Ss Resistant to malaria but produces some normal hemoglobin Ss favored over SS in tropics where malaria common even though ss is lethal 14 of offspring of heterozygote cross are recessive homozygotes o q may be 02 in Africa since q2 only 004 Often called heterozygote advantage Fig 2317 Frequency dependent selection also maintains variation Phenotype is favored during mating green dots Maintains the rare phenotype in the population May explain how hosts can escape parasites by producing rare antigens that are hard to mimic Fig 2318 Neutral variation can also maintain variation Alleles with no effect on fitness are neutral so they are not affected by selection Could explain considerable genetic variation in many populations Much of polymorphism in electrophoresis gels or fingerprints may be neutral ls Sex Maladaptive Asexual clones produce carbon copies Sexual females pass half their genome to offspring 0 Sexual species have to produce twice as many offspring But sex by recombination of genes each generation produces genetic variation in offspring lf genetic variation important to resist diseases sex is maintained Figure 2316 The twofold disadvantage of sex Sexual Selection Sexual dimorphism polymorphism in size or color between sexes Males usually showier in order to stand out to the females lntrasexual selection completion between males between males favors evolution of secondary characters based on lntersexual selection of bestquot males by provider 0 The idea is that showy male is best provider Females invest more in reproduction are choosy males invest less and are promiscuous How do I pick my Man Fig 2316 Female frogs favor males with longer calls The longer calls are a sign of superior genes Experiments where eggs were arti cially fertilized indicate long call genes produce larvae that mature faster at a bigger size Limits to selection Phylogenetic historical and physiological constraints limit evolution Adaptations are lash ups because selection acts on existing variation Trade offs between traits are important can t select for many and large offspring at the same time Not all evolution is adaptive drift is an example Goals for Chapters 29 30 Know the major advances oftrue plants over green algae and what changes occurred with a terrestrial existence Understand the major differences in the life cycles of mosses ferns and seed plants Know a representative of each major group not responsible for Phylum names Know the anatomy of owers and fruits and how flowering plants have coevolved with animals Origin of Land Plants 280000 species in 4 main groups 1 Bryophytes mosses non vascular 2 Pteridophytes vascular but seedless ferns 3 Gymnosperms conifers with naked seeds 4 Angiosperms owering plants Figure 296 297 Table 291don t worry about Phylum Names Evidence for Origin from Charophyceans green algae Homologies between land plants and Charophyceans Roseshaped cellulosesynthesizing complexes in cell wall Peroxisome enzymes homology Homologous sperm structure Cell division similar Molecular homologies Advances over Algae Apical meristems growth areas on shoot and root 0 Areas of rapid mitotic growth at the tip of the shoot and root Multicellular dependent embryos with maternal nutritive cells Alternation of generations Sporangia produce spores 0 Produce spores by meiosis Multicellular gametangia O Pluses and Minuses of Terrestrial Existence First land plants 500 million years ago Increased sunlight and C02 levels Nutrient rich soil Water becomes limited Structural support necessary o In orderto ght gravity Fig 295 Terrestrial Adaptations of Plants Waxy cuticle limits evaporative water loss Evolution of specialized water and nutrient transport 0 Phloem o Xylem Evolution of secondary chemicals to deter herbivores Evolution of Land Plants Fig 294 Bryophytes All lack any type ofvasculartissue and form ground hugging carpets Gametophyte is dominant generation 3 phyla o Liverworts hornworts and mosses Good at surviving desiccation often in extreme environments peat moss is good example Fig 298 11 0 Male gametophyte antheridium produces sperm 0 Female gametophyte archegonium produces egg 0 Fertilized zygotes develops into dependent o Sphagnum or peat moss is an important energy source and its acidic soil preserves decaying bodies 0 Nitrogen is often limiting o Mosses cover sandy soil 0 When mosses removed nitrogen lose increase Pteridophytes o Sporophyte dominant independent reduced gametophyte 0 Vascular but seedless o Evolved from mosses with evolution of branching sporophytes o P Lycophyta club moss were rst trees now mostly epiphytes o P Pterophyta o Horsetails o Whisk ferns o Ferns Fig 2913 16 Dominant sporophyte sporangia produce spores Spores develop into gametophytes First forests lowered 002 levels and caused the ice age Chapter 30 Advantages of Seed Plants Gametophytes microscopic nourished by dominant sporophytes Haploid gametophytes screen deleterious alleles nourish sporophyte embryo Seed replaces spore in dispersal Two main clades 1 Gymnosperms naked seeds 2 Angiosperms owering plants Fig 302 Some de nitions Pollen grain like sperm male gametophyte Ovule like egg female gametophyte and supporting tissues Fertilization 2 pollen grains fertilize ovule 1 combines with egg Second forms 3N endosperm nutrient reserve Seed embryo food supply protective coat Seed allows dormancy Protection during dispersal Fruit mature ovary that protects dormant seeds and aids in dispersal Cotyledon seed leaf that nourishes seedling after germination Seed Plants 0 Gymnosperms have seeds exposed or naked on modi ed leaves 0 3 fairly common phyla 1 Ginkgo trees 3 Conifers by far most diverse group grow well in poor soils or areas with short growing season or with dry season because they have leaves all year long Also do well with fire Fig 306 Simplified gymnosperm life cycle Fig 306 Gymnosperm life cycle simplified h Male cone Pollen Female cone Spompnyle tree Formation of Seedling pollen lube and lerlilizalion Seed Dvu e zygale load and coal Fig 305 P Ginkgophyta unique leaves P Cycadophyta palm like outside LSA P Coniferphyta conifers Important Conifers Douglas Fir most common timber Bristlecone Pine one of oldest living organisms at 4000 years Sequoia World s largest plant at 2500 tons 2000 years old P Anthophyta o Angiosperms Flowering Plants Two major clades monocots have parallel veins monophyletic grasses and grains Dicots have netlike veins polyphyletic trees Dicots divided into eudicots and magnolias n iosperm reproduction Flowers are specialized shoots with four groups of leaves Sepals protect immature flower Petals attract insect pollinators Stamen produces male gametophytes pollen Carpel produces female gametophytes Fruits are mature ovaries with fertilized seeds Fruits adapted for dispersal Fig 307 8 know structure of a ower and reasons for different seeds Fig 3010 simplified Fig 3010 Angiosperm life cycle simplified Pollen Anther Sporophyte with flower 1 Ovule in carpel Pollen tube Stigma Seedling with cotyledons Fertilization one sperm for egg seed zygote P an sperm for en nsperm endosperm coat Flowers and coevolution with pollinators Bee owers are white or yellow because insects cannot see red Bird owers are red and have greater nectar rewards Flowers have coevolved to attract seci c ollinators Seed Plant evolution Gymnosperms evolved 350 million years ago replaced lycophytes and horsetails in forests as climate dried Angiosperms evolved in early Cenozoic 130 mya Amborella and water lilies basal rst evolved in Angiosperms Herbivory caused evolution of secondary compounds used for defense increase in size of trees coevolved with insect and bird pollinators Figure 3012 Figure 3013 6 KNOWTHE DIFFERENCE BETWEEN MONOCOTS AND DICOTS Humans and Angiosperms Six seed crops provide 80 of our calories Arti cial selection for increased seed fruit size 13000 YA Tea coffee cocoa also domesticated Spices from flowers cloves fruits vanilla and pepper leaves mint and bark cinnamon Produce wood for fuel building and paper production Medicinal value willow original source of aspirin Plant biodiversity at risk in rain forests Table 301 Only angiosperms have ovaries and owers 6 might be one test Chapter 22 Principles of Evolution Goals for Lecture 1 Learn historical context for theory of natural selection Understand how Darwin developed the theory and his observations and predictions Understand how artificial selection biogeography homologies and fossil record all support the theory Theory is a general explanation of important natural phenomena developed through extensive and reproducible observations Hypothesis is a tentative explanation of observations Evolution Changes through time in populations Darwin s contributed the mechanism natural selection Putting the theory in historical context 0 Plato and Aristotle believed that species were immutable 0 Species never changed Cuvier recognized fossils and that they were extinct and older fossils were in deeper rocks but still thought species immutable In the early 1800 s Lyell realized geological formations were due to long term Lamarck developed the first theory for evolution that structures evolved as they were used more Giraffe s neck is the classic example Fig 222 Fig 223 DanNin s contributions Darwin noticed different geographic faunae during his voyage on the Beagle Darwin s finches colonized the Galapagos evolved different beak shapes to use different food types He realized that species slowly accumulated adaptations to new environments Published Origin of Species in 1859 0 Viewed Evolution as a tree with ancestors at the base and the descendant species as branches Fig 226 example of adaptive radiation Danvin s theory of evolution by natural selection Based on five observed facts All populations can overreproduce and grow rapidly Malthus But most populations are stable through time Natural resources are limited Individuals vary in their characteristics 2210 Variation is heritable Allows several inferences Only a fraction of the offspring will survive Those best adapted to the environment survive and leave more offspring Favorable adaptations gradually increase in frequency in populations EVIdence of natural selection Artificial selection man is the agent ofthis selection but it is the same as any other type of selection Evolution of resistance to insecticides Initial spraying kills most bugs But a few resistant bugs survive and increase rapidly in number New pesticides must now be developed Super Bugs antibiotic resistant bacteria are another example Fig 229 artificial selection from a wild plant species Fig 2214 evolution of resistance to drugs by HIV is yet another example An Example of Natural Selection from the Field John Endler observed following effects of predators on tropical guppy populations 0 Brightly colored males more attractive to females 0 Brightly colored males vulnerable to predation o Guppies in pools with few predators had more brightly colored males 0 Fig 2213 Endler transferred drab guppies with many predators to a pool with few predators As predicted the population became more brightly colored Coloration a tradeoff between mating advantage and increased risk of predation Example of natural selection in field Other evidence for evolution Biogeography Ancestors migrated to new areas and evolved differences This explains regional variation in faunas that Darwin observed Fig 2220 this is really an example of convergent evolution Comparative anatomy Analogous structures have similar functions in unrelated organisms convergent evolution eg sugar glider and flying squirrel Homologous structures different environments cause changes in common structures of related organisms divergent evolution 0 Comparative anatomy Homologous structures may have different uses but are derived from common ancestor have similar internal anatomy Fig 2217 0 Fossil record Prokaryotes ancestral based on molecular and anatomical data Also see chronological appearance of the vertebrates 0 Fish gt amphibians gt reptiles gt birds gt mammals Adults may have vestigial structures no longer useful Fig 2216 Fig 2219 Percent of Amino Acids That Are memicai lo the Amino Acids in a Species a Human Hemoglobin Polypeptide 4 l Human quot Molecular homologies include fact that 100 Cytochrome C is present in all species that are aerobic the common genetic code and greater genetic relatedness of recently evolved Species Evolutionary trees are hypotheses 1 4 Lamprey Summary of Darwin s Ideas Natural Selection is differential success in reproduction Natural selection occurs through interaction of environment and variability inherent in populations The product of natural selection is the adaptation of organisms to their environment Important pomts regarding evolution Natural selection works at individual level evolution at population level ONLY affects heritable characteristics The variation on which natural selection works is produced by random mutations Evolution by natural selection selects for organisms that are best adapted to a particular environment Adaptations are not perfect but lashups of available variation Goals for Chapter 24 2556 Understand differences between Biological and phylogenetic species concept Micro and macroevolution Allopatric and sympatric speciation Know examples of each type of isolating mechanism both pre and postzygotic Understand what is meant by the punctuated equilibrium model Understand 3 ways developmental genes can cause rapid evolution Macroevolution Macroevolution is generation ofa new species by Anagenesis slow accumulation ofdifferences Cladogenesis rapid splitting or branching oftwo new species What is a species Biological species concept Interbreeding populations reproductively isolated from others Based on fertility not similarity Phylogenetic species concept Differences in DNA Different alleles xed at same locus indicate genetic isolation AA Species 1 BB Species 2 Subunit of biological species often can t tell apart morphology Isolating Mechanisms Prezygotic isolate species before fertilization 7 Ecological separation habitat or temporal 7 Behavioral sympatric but differences in mating behavior 7 Anatomicalphysiological barriers 7 Gametic isolation Figure 244 A summary of reproductive barriers between closely related species Figure 242a Eastern and Western meadowlarks look similar and overlap geographically but are behaviorally isolated by differences in the male s courtship song Fig 244F Mechanical isolation Isolating Mechanisms Postygotic Reduced hybrid survival amphibians Reduced hybrid fertility horse and donkey produce sterile mule fig 244 Hybrid breakdown Loss of vigor in F2 rice Fig 244 Mechanisms of Speciation Allopatric speciation geographic isolation of populations 0 Sympatric speciation loss of gene ow without geographic separation Figure 245 Two modes of speciation Figure 246 Allopatric speciation of squirrels in the Grand Canyon Figure 247 Fig 249 Mechanisms of Sympatric speciation Ecological or behavioral isolation Changes in ploidy chromosome number can create a species in one generation Figure 2410 Sympatric speciation by autopolyploidy in plants An example of ecologicalbehavioral sympatric speciation Cichlids are a sh in African lakes Females select males by color this is another example of sexual selection Females cannot discriminate in monochromatic light or in murky water in the polluted lakes Fig 2412 Punctuated Equilibrium 39 Evolution slow accumulation of mutations 39 Rapid because of polyploidy or adaptive radiation lt Punctuated Evolution 39 Speciation lasts 5000 yrs but species exist over 5 million yrs 39 Stabilizing selection breaks down during adaptive radiation Fig 241718 Fig 2413 14 16 19 Evolution and Development Fig 2519 0 Evodevo slight alterations in development have profound effects on adults 0 An example is allometric growth Evolution and Developmental Timing Figs 252021 0 Heterochrony change in the rate ortiming of development 0 Paedomorphosis juveniles reproduce 0 Duplication of Hox genes allowed evolution of vertebrates from invertebrates The Evolution of Development Fig 2522 Fig 2525 Evolution is not goal oriented Lineage of horse was not a simple progression from small to large Fig 2524 Complex structures can evolve in steps over time Goals for Chapter 26 39 Know the difference between systematics and taxonomy 39 Know higher taxonomic levels 39 Be able to set up a phylogenetic tree 39 Understand what a parsimonious tree is and the basic steps in using molecular data in phylogenies and molecular clocks Systematics 39 lncludes taxonomy classi cation of organisms by homologies 39 Binomial of genus and species 39 Also includes higher levels in hierarchical classi cation know levels Figure 263 Hierarchical classification Phylogenies 39 Evolutionary history ofa group 39 Cladogram is a tree and each branch a clade 39 Clades can be monophyletic have a common ancestor paraphyletic evolve in parallel or polyphyletic have different ancestors see Fig 2610 Figure 2610 Monophyletic versus paraphyletic and polyphyletic groups Constructing a Phylogeny 39 Closely related taxa have more homologous 39 Must beware of analogies 39 Shared derived characters are most important 39 Select out group closely related but outside taxa ofinterest 39 Consider vertebrates Fig 2611 Two types of phylogenetic trees branches of unequal length that represent the degree of evolutionary change that has occurred Fig 2612 branch lengths that approximate the divergence times of lineages based on fossil record Fig 2613 arsimony and Maximum Likelihood Most parsimonious trees require fewest changes to explain phylogeny Fig 2615 Maximum Likelihood techniques select tree out of all possible that have the most uniform evolutionary rates in lineages Fig 2614 But there are exceptions 7 C5 F 39 quot This most parsimonious leard Mammal phylogeny assumes 4 chambered hearts evolved once and is homologous between mammals and birds Fourchambered hean a WWW Glade This phylogeny says the 4 chambered heart evolved more than once in the lineage its analogous in the two groups and is probably the better tree based on other evidence Fourchambered head I Pamchambered hean b Lizardhim clade Fig 2614 A simple example of nding the most likely tree Note that humans have diverged from tulips by 40 in DNA sequence The tree on the le is more likely because divergences are more similar The tree on the right is less likely because it argues that mushrooms have evolved slowly 5 and tulips much faster 25 Molecular Clocks If you assume that genes evolve at a more or less constant rate then you can determine when events occurred by how genetically similar two organisms are For example assuming HIV genes have evolved at a constant rate we estimate from samples of HIV collected in 1959 that HIV first infected humans in the 1930s Fig 2619 20 Molecular Phylogenies DNA coding for mRNA evolves slowly is conservative and is used for higher taxa 39 mT DNA evolves rapidly and is used for recent species For example mRNA has been used to assemble the universal tree of life Fig 2622