Evolutionary Biology PCB 4683
University of Central Florida
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Popular in Biology Molecular Cell & Dev
This 16 page Class Notes was uploaded by Mrs. Carol Pagac on Thursday October 22, 2015. The Class Notes belongs to PCB 4683 at University of Central Florida taught by Parkinson in Fall. Since its upload, it has received 39 views. For similar materials see /class/227681/pcb-4683-university-of-central-florida in Biology Molecular Cell & Dev at University of Central Florida.
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Date Created: 10/22/15
svstematics Phylogenetics 39 t39 39 39 39 e iuellLe cladograw shows relationships no data in branch lengths nL I s o Apomorphy derived char Autapomorohve not shared and derived svnapomorphv shared derived Define Evolutionary Branching Points Plesiomorphy ancestral char svmplesiomorphv shared ancestral Convergence same traits individuallv derived Reversal revert to ancestral character u i 439 r A HY r Homologous a similar charfrom a common ancestor Monophvletic a all members from a point up Paraphyletic a Mono out exclude onesome decendents Polyphyletic unrelated have dih common ancestors Polvtomv Apommplvy Pluiomarphy Au pnmorvhy Synapumorphy Humoplasy manual Polyuhylezi39z W E Anteslral mil lo Devived trait ll Munuphyieh39z llNothing in biology makes sense except in light of evolutionquotT Dobzhansky 1973 Speciation Process 1 2 3 NATURAL SELECTION o Acts on individuals and phenotype o Nonrandom o 4 Postulates 1 Variation 2 Heritable 3 BorngtSurvive 4 Variable Fitness Macroevolution speciation Microevolution changes in gene frequencies within a population Evolution o 2 Basic Tenets o Decent with modification from common ancestor 0 Chief agent natural selection on variation 0 Acts on Populations and Allele Frequencies o Mutation is the raw material of evolution 3 Types of Variation 0 Genetic 391 39U 39 histone quotquot 39 via chemical signals 0 Genotype by environment ex depression gene Transitional form is not an ancestor but shows a mix of novel and ancestral traits Law of Succession the general pattern of correspondence bt fossil and living forms Methodological Naturalism no hocus pokus Assumes nothing else exists Ontological Naturalism Believes nothing else exists ModernNew SynthesisNeoDarwinian comb of Genetics Math and evo into Population Genetics Darwinian Fitness ability of an individual to survive and reproduce Adaptation traitcharacteristic that increases its fitness relative to those wo it Preadaptation trait that is used in a novel way and eventually elaborated on Exaptation Preadaptation Cooption Heritability proportion of variation due to genes Over estimated Increased by Under estimated Reduced by 1 Maternal Effects Misidentified Paternity 2 Shared Enviroment Conspecific nest Parasitism Processed Pseudeogenes lack introns and promoters PHYLOGENIC METHODS Distance Based Neighbor Joining UPGMA NOT CLADISTIC fastest method homoplasy I Errors Maximum Likelihood Best Method COMPUTATIONALLY INTENSE uses all data even autapomorphs o Pdatatree Probability of data given tree Bayesian Markov Chain Monte Carlo BMCMC new LH method wstats and alogorhythms o Ptreeldata Probability of tree given data Bootstrapping evaluates confidence in nodes quickly shown as Phylogeography Biogeography Phylogeny Historical Geography Vicarence Rafting Epigenetics 1 What types of mutations create new alleles New Genes Alleles Point mutationsalters single point in base sequence of a gene transition A for G purine or T for C pyrimidine MORE COMMON transversion a purine for a pyrimidine frame shift are added or deleted nucleotides cause a change in the reading frame of the protein for a gene Genes Gene duplications retro transportation reverse transcribed from mRNA template and reincorporated into genome gt retro gene hybrid of original gene unequal crossovereXtra copy is free to accumulate mutations MORE COMMON Mutations effect on proteins and selection Point Mutations Effect of proteins point mutations in the l or 2 are more likely to change the amino acid while those in the 3 rarely change the amino acid point mutations that do change the amino acid produced are called replacement or non synonymous substitutions point mutations that cause no change in the amino acid produced are called silent site or synonymous substitutions Selection individuals that are adapted to their environment then most mutations will be deleterious lower fitness individuals with high mutation rates appear to be favored when a populations is in a novel or rapidly changing environment 3 what mutations are responsible for gene duplication and the evolution of multigene families retrotransposition unequa1 cross over 4 What are some modern techniques for examining genetic vaariation in populations and species Protien electrophoresis DNA sequences Microsatellites determining Genotypes calculating allele frequencies 5 calculatealleleic genotype and migration rates m number of migrants number of migrantsresident population 6 The two principals of HW and how they can be broken 1 the allele frequencies in a population will not change generation after generation 2 if the allele frequencies in a population are given by p and q the genotype frequencies will be given by 10 2m and q2 migration violates l and 2 gt after random mating 2 will be reestablished Genetic drift violates l and 2 Nonrandom mating violates 2 inbreeding 7 HW assumptions 1 N0 selection equal survival and reproduction rate if violated allelic frequencies change 2 N0 mutation no copies of exsisting alleles will be converted to new or other existing alleles if violated allelic frequencies change 3 N0 migration gene ow no individuals move into or out of the model population if violated allelic frequencies change 4 No chance events indefinitely large no events will occur that allow an individuals to pass more more of their gametes into the gene pool 5 Random mating panmiXia gametes find each other at random If violated genotype frequencies will change generation after generation but not allelic frequencies 6 discrete generations offspring do not mate with previous generations if assumptions are violated evolution occurs How can selection violate HW selection decreases variation in a population allele frequencies change from one generation to the next evolution CCRS delta 32 will the frequency of the allele increase in response to the HIV epidemic model 1 20 fre after generation 100 with delta 32 model 2 20 frefor delta 32 and 1 HIV selection is too weak to cause a large change in allele frequencies and stay 20 fre for delta 32 model 3 1 fre after generations pass the frequency remains 1 because the delta 32 is hidden in the heterozygotes and hidden from selection Patterns of Selection Disruptive individuals with extreme values of a trait have the highest fitness down slope homo increases variation Stabilizing individuals with intermediate values of a trait have highest fitness upward slope homo reduces variation Directional fitness consistently increases or decreases with the value of the trait reduces variation in a population 10 Selection relative to fitness Overdominance favors heterozygotes lethal recessive heterozygotes have higher tness maintains genetic diversity underdominance favors homozygotes homozygotes are more fit usually one homozygote will go toward xation while the other will be lost if not in equilibrium 1 1 Prairie chickens mutational melt downgt extinction vortex population size decreased lead to no gene ow causing genetic drift powerful genetic drift caused decline in heterozygosity which could move toward fixation of deleterious recessive the reduction off1tness due to genetic drift and interbreeding leads to interbreeding depression fixed by gene owSEX 12 Genetic drift vs population size Sampling error founder effect smaller populations leads genetic drift to be more powerful larger effect because more chance events occur no adaptation causes allele frequencies to change decreases variation can also increase Inbreeding effect on allele and genotype frequencies decreases the frequency of heterozygotes and increases the frequency of homozygotes allele frequencies stay the same but genotype frequencies can not be calculated inbreeding depression occurs when inbreeding leads to reduced mean fitness if it generates offspring homozygous for deleterious alleles l4 Linkage disequilibrium when there is nonrandom association between a chromosome s genotype at one locus and its genotype at the other locus dependent product of allele frequencies do not equal the genotype frequency D does not equal 0 reduced by sexual reproduction recombination 15 Adaptation a trait that allows an individual to leave more offspring than it would if it lack the trait adaptationist program determines if traits are adaptations l6 Adaptation study methods experiments y wings observational studies giraffe comparative method gt remove effects of evolutionary history from an analysis 17 sexual selection form of natural selection in which individuals with certain inherited characteristics are more likely than other individuals to obtain mates and reproduce Intra vs Inter sexual selection Intra between same sex sperm competition males fighting for females Inter between opposite sex females choosing males 19 Runaway selection stalk eyed ies With longer stalks win more ghts assortative mating of long eye stalk males and long eye stalk preferring females gt lead to females and males with long eye stalks from father gene and the preference of long eye stalk from mothers gene gt xation of long eye stalks 20 Kin Selection characteristics are favored due to their beneficial effects on the survival of close relatives including offspring and nondescendent kin Inclusive fitness direct fitness due to personal reproduction or indirect fitness due to additional reproduction by relatives 22 Altruism ones actions the cost the actor but benefit the receiver does not occur in natures lkin selection 2reciprocity 3mutualism 4manipulation Molecular Clock Method for estimating the time required for a given amount of evolutionary change based on the observation that some regions of genomes appear to evolve at constant rates 24 species concepts def1nes different species groups 1 morphological differences in characters especially morphology 2 biological interbreeding potential to breed individuals 3 phylogenetic smallest monophyletic group 4 evolutionary a single lineage of ancestor descendent populations 25 speciation Formation of new species lpopulation isolation 2divergence of phenotypes and genotypes 3reproductive isolation 26 Allopatric most common mode phisicalissolation population is homogenized and gene ow stops gtvicariance a new barrier to gene ow arises gt Dispersal peripatric individuals migrate to new area 27 Modes of Speciation Allopatric physical ba1rier sympatric complete panmictic mating and a reproductive isolating mech evolves peripatric drift effects initial changes then selection diverges it parapatric reproductive isolation between populations phylogeny cladogram does not show change Phylogram do show change Mono all from one ancestor Para all from one ancestor but some removed Poly unrelated lineages outgroups produce polarity Practice Questions 1 A notable feature of HIV s life cycle is that the viruse uses the host cell s own A Polymerases B Ribosomes C tRNA s D Both A and B 2 Several antiretroviral drugs have been invented but when used alone they eventually fail This is an example of A evolution by mutation B evolution by random gentic drift C Linnean evolution E Lamarckian evolution 3 in determining heritability ofa trait one uses a regression analysis If the slope of the bestfit line is zero this would indicate A You do not use a regression analysis to determine heritabilities C No relationships between traits thus it is genetically controlled D All variation is due to genotype E both B and C 4 OntheOrigin of speciesbymeans of natural selectionwaswrittenby A Wallace B Lamark DVonKalm E None of theabove 5 In theacute or initial phase of HIV infection the number and concentration of virons in one s body increases explosively You would expect A CD4 Tcell counts to increase over time C CD4 Tcell counts to decrease over time D CD4 T cell counts to increase initially then slowly decrease over time until the chronic phase stars 6 To identify a trait as a synapomorphy a researcher must first establish that it IS with traits found is closely related taxa A homoplasious B convergent C analogous D synonomous 7 Despite 25 years of research the mechanism whereby HIV leads to immune deficiency remains incompletely understood however we believe B HIV uses killtase an enzyme to kill helper tcells CHIV parasites the immune system cellsespecially the red blood cells DHIV parasites the immune system cells especially the nerve cells E Both B and D 8 Gene duplication is probably the most important source for new genes what are the potential fates of the quotnewquot gene copy A becomes a psuedogene B becomes a transposable element C gains a new function D both A and C E both A and B 9 Mutations in the gp120 protein conform the ability to use CXCR4 instead of CCR5 as the coreceptor use of CXCR4 is unfavorable to the virus initially because choose all correct answers go get credit A T cells utilizing CXCR4 divide much more slowly than T cells with CCRS C T cells displaying CXCR4 divide much more quicly than T cells with CCRS D HIV infected cells displaying CXCR4 replicate quicker than those with CCRS I39 I39ylv c m m I 10 One hypothesis why humans have not evolved a resistance to HIV as certain monkeys have evolved resistance to SIV is A HIV is too sneaky due to natural selection thus humans will not evolve resistance ii iu rldll Jr L1 IJ L39II m lu III Uquot mil ml l r39i I39 H In I r yii umbi I39eiil Mil TIN quotuquot39i39i IN fulfill l i Iw39i I W C HIV is not affected by natural selection thus its free to change D HIV is too variable humans will never evolve resistance to HIV 11 General correspondence between fossil and living forms coming from the same locale is known as A Berman s rule B Law uniformities and succession 11 Law all M D none of the above E both A and B 12 Which isare true concerning evolution A It is testable B it is proven C It can generate predictions E No correct answer 13 The graph on your right indicates that Note the line ending with the black dot corresponds to the axis label ending with the back dot the plain linde corresponds to the plain axis lable A deaths have increased over time and patient days has decreased C deaths have decreased over time due to AIDS D deaths have decreased due to HAARTS 14 in phylogentic analyses using morphology fossils are used to polarize the character transformation series however in molecular studies there are no fossils therefore one must use aan A Novel taxon C ngroup D Both A and D E All of the above 15 Phylogenetic trees can be choose all correct answers to get credit A Estimates of common descent B evolutionary history of gene sequences C cladograms D factes E Phylogramsi 16 Raxworthy et al constructed an area cladogram to tet the Gondwanaland Hypothesis for chameleon evolution They were trying to determine the of the group lll l39iquotill392ll 7 y B Homology C Phylogeny Dboth A and B 17 Which of the following statements is NOT true regarding natural selection A It requires variation but does not need mutation B It is not forward looking C it acts on phenotype but evolution is change in allele frequencies D it acts on existing traits but novel traits can emerge 18 Natural selection is the that Darwin used to explain evolution A Pattern B Fact C Theory iii iv 23 um E Holy grail 19 According to the HIVT 39 39 Rate 39 39 39 if 39 39 is rare the virus should be A highly virulent and kill the host slowly B less virulent and kill the host quickly Chighly virulent and kill the host quickly D less virulent and kill the host slowly a E Resistan to AZT 20 The theory of special creation tries to explain life on earth The main assertions are A species are immutable created independently from each other and the earths very old B species are immutable were created independently of one another and earth is young Cspecies can mutate were created independently from each other and the earth is very old Dspecies can mutate they come from a single form and the earth is very young 21 In 2011 you catch 20 males of the lizard species measure their tails and find 12 with 2quot tails 5 with 25 tails and 3 with 3quottails in 2012 you return and repeat the procedure and find 10 with 2quot tails 8 with 25quot tails and 2 with 3quot tails Which of these evolutionary tenets have you confirmed A there is variation amoung individuals in a population a B variation is heritable Cindividuals vary in their success at surviving and reproducing D Evolution has occurred E A and D 22 why did peter amp rosemary grant estimate the heritability of beak size in Galapagos finches A heritability of a trait influences its response to evolution by natural selection a B heritability values determine if speciation can occur C heritability values indicate the amount of genetic polymorphism in a population D if the beak size were not heritable the species would likely go extinct E The high heritability of traits reduces negative effects of gene flow 23 when individuals in a population exhibit variation inheritance excess reproduction and the population will evolve A random genetic drift B recombination C altruism D iu liiii ll39l l y in w x2 5 E E sexual group selection 24 Analyses of lossof function mutations underestimate actual mutation rates One reason this is the case is A all nonsynonymous mutations have effects too subtle for researchers to detect B phenotype changes cant be caused by point mutations 3 my yin mii gjiu D All are correct 25 Bootstrapping is A An exhaustive method to determine a phylogenetic tree B A method for determining anagenesis D both A and C E both A and B 26 the human coccyx is an example of A autopomorphy B homoplasy D convergence E All of the above 27 When patterns of speciation are congruent among ants and the fungi they farm is taking place A Convergence l2 Scu mgl 07 0 C Cladistics D Polyphyly E A B and C 28 It ends up many students have bad breath and this is controlled by an autosomal locus BBbad breath Bb cinnamon breath and bb mint breath Dr Parkinson surveyed this class and determined that 13 student are BB 2Bb and 98 have mint breath What is the allele frequency fro the bad breath allele A 01150 C 08755 D 02300 29 A nucleotide substitution at the second position in the amino acid coding rippled using the universal genetic code will result in A frameshift B nonsynonymous substitution C synonymoussubstition D a wobble event E A B and possibly D 30 This node represents the common ancester of all venomous lineages Aa Bb Dd Ee 31 True or False The monophyletic group that has the common ancestor labeled B is the sister group to the monophyletic group with the common ancestor labeled E A True 32 Using the principle of parsimony and the lizard diagrams to the right limblessness is thought to have evolved how many timesinthephylogeny A1 D4 E Evolved 3 times lost 10 times 33 PLAZ type III in gold on screen quot 39 39 Iaan for the group containing helodermatidae anguidae and varanidae A pleiseomorphy Bautapomophy C homoplasy E Primitive character A paraphyletic group B homologous group D pleiseomorphic group E autapomophic group 35 Using an evolutionary classification the above phylogenetic history indicates lizarda are with respect to snakes serpents AMonophyleti T r Cpolyphyletic Dhomologous
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