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Department
Organismic and Evolutionary Biology
Course
Organismic and Evolutionary Biology OEB 53
Professor
Andrew Berry
Semester
Spring

Description
 ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES 02.04.2013 [Lecture 3: Genetic Variation & Hardy­Weinberg] The Theory Descent with Modification Sharedhardware:all organismsusethesamebasicbiochemicalandmoleculargeneticpathways, implyingthatthesewereacquiredfromanancientcommonancestor. Evolutionisdisinclinedtoalter somethingthatworks,sooncethesefundamentalprocesseshadevolved,theybecameafeatureofall livingorganisms. Thus,despitetheapparentdiversityoflifeonearth,biologicalsystemsareinfact remarkablyuniform. >>Homology:i.e.derivedfromacommonancestor Sharedsoftware:1)about1.2%ofthehumangenomeencodesproteins;2)99%ofall humangenes arepresentinthemouse,fromwhichwedivergedabout75millionyearsago;3)61%offruitflyand 43%ofnematodewormproteinshaveaclearhumanhomologsdespiteanevolutionaryseparationof half abillionyears >>pax­6 = eyeless (differentnamesforthesameancestralgeneindifferentspecies) >>Deephomology:theexchangeabilityofthepax­6 (mouse)and(mouse)andeyeless (Drosophila)genesbetweeninsectsandvertebrates,implyingconservationofancientancestral function Complexity’sdirectionality: evidencefordescentwithmodification=anincreaseincomplexityover time Historicalcongruence:congruenceoftwodifferentapproachestomappingthehistoryofli>e> fossils& phylogenyaretwodifferentapproachestomappingthehistoryoflife Intermediateforms:reptile-fishintermediate(Archaeopteryx),fish-amphibianintermediate (Tiktaalik),greatape-humanintermediate(Australopithecus) N. B.: intermediateformsdoesnotimplyhalfwayforms,descent from a common ancestor does notimplythatthecommonancestorofwhalesandhipposwasahybridbetweenmodernwhales andhippos Vestiges:rudimentaryhindlegsonsnakes,blindeyesofcavefish,kiwis(flightlessfromflighted birds),whalepelvis Atavism:geneticinformationremains,butisunexpressedexceptincasesofmutation(whalewith poorlyformedhindlimbs,tailsinhumans) Lousydesign:thepanda’s“thumb”isn’tatruethumbbutratheramodifiedwristbone,serratedridges insteadofteethinsomebirds;inotherwords,you’reonlyworkingwithwhatyou’vealreadygot  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES Embryology:all theearlyembryologicalstagesofvertebratesaresimilar.Humanembryospass throughaphasewhentheyhavefish-likegills.Again,thisisafunctionoftheirhavingbeen ultimatelyderivedfromfishancestors. Biogeography:Analysisofthegeographicaldistributionofanimalsandplantsshowsthatclosely relatedspeciestendtobefoundincontiguous(oroverlapping)regions.Thisisbecauseofevolution: speciesA livinginlocationX givesrise– throughdescentwithmodification– tospeciesB. Necessarily,B mustbelocatedsomewhereclosetoX, though,ofcourse,itmaysubsequentlymigrate toadifferentregion. Natural Selection Axioms:Naturalselectionisalogicalresultof1)superfecundity,2)variation,3)heritability Mutations:Themutationsfuellingnaturalselectionmustbe:1)undirectedwithrespecttothevector ofchange,2)small ineffect,3)plentiful Role:Naturalselectionisthecreativeforceinevolution,occursattheleveloftheindividual,explains macroevolutionofthebasisofextrapolationfrommicroevolution >>An adaptation isaphenotypicvariantthatresultsinthehighestfitnessamongaspecifiedset ofvariantsinagivenenvironment >>Selectioningeneraloperatesonindividuals TheDarwin-WallaceRevolution: 1. TheDarwin-Wallacetheoryisadeparturefromthetraditionalessentialist (i.e.typological) viewsofnature. Insteadofseeingvariation asmeredeviationfromanideal,Darwin elevatedittoanewstatusastherawmaterialofevolutionarychange.Thefocushasshifted fromtheideal(i.e.themeanofadistribution)tothepopulation(i.e.thevarianceofthe distribution) 2. Naturalselectionisavariational theoryofchange,asopposedtoatransformational one. Transformational(anensembleofindividualschangesbecausetheindividualswithinit change)versusvariational(differentmaintenanceofkinds) For/Of: “Selectionof redballs,selectionfor small size”Difficulttodeterminewhatisbeingselected versuswhatisacorrelate. Darwin Meets Mendel Blending inheritance criticizedbyFleemingJenkin(red/white>pink) Pangenesis, aLamarckiantheoryof inheritance:“gemules”in blood(disprovedbyexperimentswith blackandwhiterabbits,bloodtransfusions,JohnGalton) Mendeliancharacters:discrete,discontinuous  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES Polygenetic Inheritance WiththerediscoveryofMendel’sworkin1900cametheMendeliansvs.BiometriciansControversy, biometricalcharacters:continuous >>R.A. Fisher:if youtakeacharacter,suchasheight,andassumethatistheproductofnotone Mendelianlocus,butofmultipleloci,andyouaddtothatalittleofenvironmentalvariation,you couldhavetwoindividualswithsamegenotypebutdifferentphenotype…leadingtobell curve distributionasobservedinnature >>Polygenicinheritance:thereconciliationoftheMendeliansandtheBiometricians Hardy­Weinberg ThepopulationconsequencesofMendeliantransmission:pandqaretheallelefrequenciesinthe populationoftwoalleles;if thereareonlytwoalleles,p+q=1 2 2 p +2pq+q =1 1) Thefrequencyoftheheterozygoteisgreatestwhenallelicfrequenciesareequal(p=q=0.5) 2) Whenthefrequencyofonealleleishigh,mostoftheindividualsarehomozygotes. AssumptionsofHardy-WeinbergRelation: Statistical:largepopulationsize PopulationGenetic:randommating,noselection,nomigration,nomutation H-WisanequilibriumbecausethefrequencyofA, p’,inthenextgenerationisthesameastheold frequencyofA, p.UnderH-W,allele& genotypefrequenciesremainthesame. H-Wequilibriumisthepopulation-levelconsequenceofMendeliansegregation:permitstranslation betweenalleleandgenotypefrequencies,providesevidenceof“evolutionaryaction”(e.g.selection, migration)whengenotypefrequenciesdepartfromHW,evolutionisachangeinalleleorgenotype frequencies(i.e.departuresfromHW) >>similartoanull hypothesisforevolution  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES 02.06.2013 [Lecture 4: Genetics of Natural Selection] Evolutionarybranching:evolutionofthediversityoflife What is evolution?  Darwin:“descentwithmodification”  A changeinmorphology,ecology,behavior,physiology  Evolutionarychangemustbehereditary,genetic  Modern,geneticdefinition:Evolution is change in allele frequencies, p, whAre pa + P  – 1  Evolutionarybiology:history,andmechanisms  Science:understanding,predictions Hardy­Weinberg ‘Equilibrium’ (HWE)  Note that the “Hardy Weinberg law” refers to the ratio of genotype , freq,uen)cies (p not the fact that they add to 1 (which is only because p + q = 1)  Assumptions: infinitely large population (no random drift), random mating, no selection, no migration or gene flow, no mutation  Therefore, evolutionary biologists are most interested in deviations from HWE What is natural selection?  “A consistentbiasinsurvivalorfertilitybetweengenotypes”  Naturalselectioncancauseevolution,butmayalsopreventevolution(e.g.stablepolymorphism)  Evolutiondoesnotrequirenaturalselection(e.g.randomdriftisimportant:>95%ofthehuman genomemaybe“junk”!”  However,manyinterestingtypesofevolutiondoinvolvenaturalselection. Selection and the Single Gene  “Quantitativetraits”:e.g.behavior,IQ, beaksize(usuallymultipleloci +environmentaleffects) versussingle-geneorsingle-locustraits  Examplesofsingle-genetraits Industrial melanisminmoths(resistancetourbanpollution)  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES Heavymetaltoleranceinplantsgrowinginminetailings Malariaresistanceinhumans(sickle-cell hemoglobin,etc.) Drug/antibioticresistanceinbacteria,protozoanparasites Humangeneticdiseases:cysticfibrosis,Huntington’sdisease,etc.(cysticfibrosisasa recessivegeneticdisease,causedbyalargediversityof“loss-of-function”alleles,morethan 300differentmutationsidentified,massivegene~2000aa,27exons,250kbtotal) Pesticideresistance:createsincreasingproblemsinagricultureanddiseasecontrol (cyclodieneresistance,GABA-gatedchloridechannelinsensitivitythroughAla302> >serine, occursinmanyinsectspecies) How does evolution by natural selection work? Evolutionbynaturalselectionisaninevitable,mathematicalprocess.Thefrequencyofanallelewill change,anditsrateofchangedependsonrelativefitness Mathematicalevolutionarytheoryhelpsusunderstand.Forexample,giveninformationaboutfitness,how fastisevolution?Usefultounderstandantibioticresistance,pestresistance,eradicatedeleteriousgenes, predictoutbreaksofinfluenza,improvecrops.Evolutionisapredictivescience. Ecology versus Evolution Ecologists:dynamicsofnumbersofindividuals(orspecies),generallyignoresgeneticvariation, concernedwithnumbersofindividuals. Evolutionists:changeswithinpopulations,canleadtospeciation,macroevolution,ignorenumbersof individuals What is “fitness”? Fitnessandpopulationgrowth:inecology,absolute fitness(populationgrowthrate)matters,whilein evolution,onlyrelative fitnessmatters. Selection against Recessive Allele (i.e. selection FOR Dominant Allele) Forgivenfitnesses,howfastisevolutionbynaturalselection? Relativefitness,W: 1(AA), 1(Aa),1– s (aa),wheres isthe“selectioncoefficient”(approx.thefraction dying) 2 2 Relativefrequenciesafterselection(multiplyfrequenciesbyfitnesses): p 1 +2pq 1 +q (1−s) Selection Against Recessive Allele  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES Whathappensinapopulationunderselection: Genotypefrequenciesbefore(H-W) Genotypefrequenciesafterselection Whatisthechangeingenefrequenciesduetothischangeingenotypefrequencies?Evolution. Thenrandommatingandnewgenotypefrequencies 2 2 Frequenciesshouldalwayssumto1,therefore,itisnecessarytodivide p 1 +2pq 1 +q 1−s ) by 2 2 2 the“meanfitness,” W=p +2pq+q 1−s =1−sq) 2 ( ) p + 2pq +q 1−s =1 1−sq 2 1−sq 2 1−sq 2 >>Whatisthenewgenefrequency(p’)? >>p’=newfrequencyofAA +½newfrequencyofAa p +pq p p= 2= 2 1−sq 1−sq >>Whatistherateofevolutionpergeneration?Weneedtoknowthechangeofgenefrequency, Δp 2 ' spq ∆ p=p −p= 2 1−sq >>Thisisthesimplestversionofthefundamentalequationofall Darwinianevolution! >>Doesnotneedtobememorized The Basic Analytical Equation for Evolution Naturalselectionatadominantgene: 2 ∆ p= spq ≈spq ,if sis small 1−sq 2 2 >>Thechangeinfrequencypergenerationforadominantalleleisproportionalto sp q Dominants versus Recessives  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES  Howfastdopopulationsrespondtonaturalselection? 2  ∆ p≈spq ∆ p≈sp  If p issmall, q isapproximatelyequalto1, ,i.e.RAPID > >selectionfor/againsta dominantallelewhenrareisrapid 2  If p islarge,sothatq isapprox.0.01orless,p approaches1, ∆ p≈sq ,i.e.SLOW > > selectionfor/againstarecessiveallelewhenrareisslow Forevolutionbynaturalselection,onlyrelativefitnessesmatter!Effectsof“selectioncoefficients” dependontheexactmodelused. Estimating Selection 1. Changeofgenefrequenciespergeneration th  e.g. peppered moth ince 1n9tury, rapid spread  Melanismduetoasingledominantgene, C (carbonaria)  JBS Haldane(1924)estimateds ~0.3 2. DeviationfromHardy-Weinbergratios 3. Directcomparisonofreproductiveorsurvivalrates(perhapsthebestmethod)  Kettlewell, survivalinfieldexperimentsonthepepperedmothinthe1950s  Typica(cc)vs.Carbonaria(Cc& CC)  CentralBirmingham:typical0.43 fitness Manycomplications,butthebasicprincipleofevolutionbynaturalselectionremainsthesame!  Manydifferentkindsofselection(fertilityselection,sexualselection)  Overlappinggenerations  Non-randommating(inbreeding,matechoice)  Quantitativetraitsaffectedbymultiplegenes Quantitative Traits  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES  Selectiononmultiplegenes,suchasinhumanheight:themore“additive”genesthereare,the closertoa“normaldistribution”isthepopulation. Whenthephenotypeisunderselection,the allelesofeachgenewill change.  FrancisGalton:“theprogenyofall exceptionalindividualstendstoreverttowardsmediocrity,” demonstratingthiswithhumanadultstature.Doeshis“regression”preventevolution?  Galtonatfirstdidn’trealizethatparentsofexceptionaloffspringalsotendstobemoremediocre, or“regress”towardstheaverage. Explanation is actually simple >> heritability V +V =V  G E P  Notethatonlyadditive geneticvariationcanbeselected >>Regressiontowardsthemeanisduetoenvironment The Speed of Evolution by Natural Selection 2  Responsetoselection R≈h S ,whereS istheselectiondifferential 2 2 V G  Inonegeneration, R≈h S ,where h = V P  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES 02.11.2013 [Lecture 5: Drift and Inbreeding (And Other Mating Habits)] Lecture Outline 1. AssortativeMating.Matechoice.Importantinsexualselectionandinspeciation. 2. Inbreeding:does not cause genetic evolution alone.Instead,affectsarrangementofgenesin populations;mayaffectfitness 3. Finitepopulationsize>>bothinbreedingandrandomevolutionarychange(or“randomgenetic drift”) 4. Mutation,randomgeneticchange.Usuallydeleterious,butevenif adaptive,doesn’talwaysget fixed Types of Non­Random Mating  Assortativemating(likexlike):>>sexualselection,speciation  Disassortativemating(likexunlike)>>sexualselection Non­Random Mating in Humans  Assortativemating:tall femalesprefertall males  Disassortativemating:“smellyT-shirthypothesis”– womenprefermen’sT-shirtswithdissimilar genotypesattheMHC loci involvedindiseaseresistance Regular Systems of Inbreeding  Inbreeding:whenanindividualmateswitharelative(orwithitself)  Offspring:homozygousforallelewhichisidenticalbydescentfromasingleancestor Inbreeding Coefficient >>usedtogaugethestrengthofinbreeding  F = probabilitythattwoallelesinindividualare“identicalbydescent”  Beinghomozygous(identicalinstate)doesnot necessarilyimplyrecentidentitybydescent  F forfixationindex:homozygosity,or“fixation,”resultsfrominbreeding Sewall Wright’s “Path” Method to Calculate F N n 1 i th F= ∑ ()2 ,whereN=¿paths∧n=¿linis∈i path i=1  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES Effect of Interbreeding on Populations >>Inbredoffspringhavereducedheterozygosity. >>F measuresreductionofheterozygosity,orheterozygotedeficitcomparedtoH-W,aswell asthe probabilityofidentitybydescent Problems of Inbreeding >>Manyrecessivedeleteriousalleles,or“lethalequivalents,”innaturalpopulations >>Whenmadehomozygous,resultsin“inbreedingdepression,”thereducedfitnessinoffspringproduced byincestuousmatings,mostlyduetorecessivedeleteriousloci Inbreeding Not All Bad >>Advantages:ecological(asinglefemalecancolonize),mayalsousefullypreventrecombination, deleteriousrecessivesininbreedingspeciescanbepurgedbyselection >>Inbreedinginhumans:mildinbreedingisnotsodangerous Inbreeding and Pre­Adult Mortality in Human Populations Conclusions:inbreedingispotentiallyaproblem,butenvironmentismuchmoreimportant Random Genetic Drift  If thereisH-Wequilibrium,thereisnogenefrequencychange.Thisistrueonlyinaninfinitely largepopulation;evolutionisdeterministic  Onlyapproximatelytrueinpopulationsoffinitesize.Stochastic orrandomchangesbecomemore importantinsmall populations Drift in a Small Population Refertop.14foridentityinstateandcoalescence Genetic Drift as a Cause of Inbreeding >>InbreedingresultsfromdriftbecauseallelesbecomeIBD. Effective Population Size >> Every allele does not usually have the same probability of being transmitted. An effective population size (e) that differs from the actual population size can be calculated. >> 1) unequal sex ratio, 2) some individuals more likely to reproduce than others, 3) population fluctuations, founder events N e N (often):  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES  Variation in number of progeny  Unequal sex ratio  Natural selection  Overlapping generations  Fluctuation in population size 02.13.2013 [Lecture 6: Evolution of Genetic Diversity] Mutation: The Source of Variation Mutation Rates & Genome Size >>Biggergenomesmoremutationpronepernucleotide,perhapsbecausemutationratesareselectedto minimal> >organismswithlargegenomeshavesmallerpopulationsizes,respondtoselectionless efficiently(drift)  Mutations are Mostly Deleterious >>Manyrecessivedeleteriousallelesinnaturalpopulations,withonlyapprox.1/1000beingbeneficial >>Mostadvantageousmutationsarelostsoonaftertheyarrive “Polymorphism”:whentherarerformismorecommonthanabout1% How Can Genetic Variation Be Maintained?  Selectionbyitself – “balancingselection” Heterozygoteadvantage Diversifyingfrequency-dependentselection  A balanceofdifferentforces Mutation/selectionbalance Migration/selectionbalance Mutation/geneticdrift A combination What is heterozygote advantage? (a.k.a. overdominance) >>Heterozygotemorefitthaneitherhomozygote> >Polymorphismisstable  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES >>Heterozygote disadvantage (underdominan>polymorphismisunstable Example:sickle-cell anemia,AS heterozygotesfavored Message:analleleisnot“dominant”or“recessive”– onlythephenotype(s)itcausesare Frequency­Dependent Selection Examples:yellow/purpleorchids,butterflymimicry Types of Selection for Quantitative Traits >>1)directional,2)stabilizing,3)diversi>canfavordiversityorleadtolossofvariability Directional Selection Ratesofevolutionhavebeenmeasuredin1)Darwins,unitsofe­folds(i.e.2.718x)permillionyears2) Haldanes:unitsofstandarddeviationspergenerations Stabilizing Selection Example:humanbirthweight Disruptive Selection >>Oftenresultsinphenotypicplasticity Mutation­Selection Balance in Humans >>A numberofhighlydeleteriousmutationsknockoutimportantgenes.Typicallythesemutationsare recessive,andvirtuallylethal,sos ~1. >>Notonlycanyounotpurgedeleteriousrecessivemutationsfromyourgenomeverywell, butalso, evenif youhaveabeneficialdominantmutation,youarelikelytoloseitfromthepopulationsoonafterit arose. Migration­Selection Balance in Peppered Moth >>Polymorphismsareoftenduetoabalancebetweenmigrationandselection CONCLUSIONS: Polymorphismsarecommon—why? Naturalselectioncanitself directlyfavorpolymorphism:  Heterozygoteadvantage  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES  Diversifyingfrequency-dependentselection  Disruptiveselectiononaquantitativetrait A balanceofdifferentforces:  Equilibriumbetweenmutation,selection,randomgeneticdrift(neutralevolution),migration  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES February 20, 2013 [Lecture 7: Finding Darwin in DNA –Testing Neutrality] Population Genetics Processes:  Hardy-Weinbergequilibrium:Noevolutionoccurring  Selectioninfavorofarecessiveallele:takessometimetogetgoing,thenstreaksforwardathigh frequency  Selectioninfavorofdominantallele:increasesquickly,takestimetoreachfixationbecause heterozygotesmustbeeliminated  Balancedpolymorphism:whenfitnessofheterozygoteexceedsthoseofhomozygotes,maintained atintermediatefrequenciesbynaturalselection  Nofitnessdifferencesamonggenotypes:drift-driven,influencedbypopulationsize What drives evolution: selection or drift? >> The Neutralism Controversy Too much genetic variation? Cost of selection [J. S. Haldane] If naturalselectionistoostrong…all organismswouldbeselectedagainst.Haldane’shypothesisthat ofselectionagainst10allelesonpepperedmoths. > >Wecanexplainthepresenceofmultipleselectedloci inapopulationwiththreshold selection wherebyindividualsselectedagainstexceedathresholdnumberof“bad”alleles Kimura & the Neutral Theory If µ isthemutationrate,therateoffixationofanunselectedmutationpergenerationpergeneis½N (theprobabilityoffixationofanewmutation)×2Nµ (thenumberofnewmutationsenteringthe populationpergeneration)=µ,whereµ isthemutationrate.NotethatthisisNOT population-size dependent. > >Therateofneutralmutationisconstantrelatedtothemutationrate. > >“Polymorphismismerelyatransientphaseofmolecularevolution.” Are new fixed differences the product of neutral evolution or of adaptive evolution (i.e. of natural  selection?) The Molecular Clock > >Differentproteins’clockstickatdifferentratesbecauseofselectiveconstraintondifferentgenes– i.e.differencesintheintensitiesofpurifyingselection > >Ex.slowratesofmutationsincytochromec versusproteinsthatarelessconstrained,suchas fibrinopeptides  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES However,themolecularclockdoesnothelpusdifferentiatebetweenthetwomodels. Neutrality & Selection Compared  Bothmodelsagreethatthevastproportionofall mutationsaredeleterious(nodisagreement onnegative/purifyingselection).  However,selectionplacesimportanceontheraremutationsthatarebeneficial… Purifying selection > >Nonsynonymousevolutionisslowerthansynonymousevolution(whichislargelyneutral evolution) Codon bias > >But“silent”positionsdosometimesmatter…codonusagebiasincreaseswithlevelofgene expressionyeast. > >In agenethatishighlyexpressed,evennonsynonymousmutationscanexperiencepurifying selection. Testing the Neutral Theory  DirectTests: Demonstratethatthekeymutation(s)haveadaptivevalue Blowfly: inpopulationsfacingstrongorganophosphatepesticideselection,asingle aminoacidchangeinanesteraseenzymegeneresultedinanewenzymethatcoulddetoxify thepesticide Onesingleaminoacidchangegrantspesticideresistance  EcologicalTests Clinestoindicatevariancethroughoutageographicdistribution,ratherthanhomegeneity  ConvergenceTests(acrossandwithinspecies) Cow,colobusmonkey,hoatzin:sameindependentmutationsfound> >mustbepowerful selection,evenatthemolecularlevel ConvergentadaptationofhumanlactasepersistenceinAfricaandEurope> >dueto differenceinmoleculardetails,cantell thattheyevolvedindependently  FootprintTests  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES Excessofnonsynonymousmutations:normallyexpecttoseeexcessiveofsynonymous evolutionrelativetononsynonymousmutationsothatmostgeneshavevaluesforthe nonsyn/synsubst.rateunder1.If over1,suggestionistherehasbeenselectioninfavorof newaminoacids. Within/BetweenCorrelation:relatedtoKimura’stheory>>Underneutralitythealleles thatgotofixationarearandomsampleofthetotalsetofallelessegregatinginapopulation. It isthesefixedallelesthatultimatelyaccountfordifferencesbetweenspecies.Thereisthus anexpectedcorrespondencebetweenthepatternofvariationseenwithin aspeciesandthe patternofdivergenceseenbetween species.  TheNeutralExpectation:correlationbetweenlevelsofpolymorphismandlevels ofdivergence  Purifyingselectioncandecouplethecorrelation…  Directionalselectionresultsinalossofgeneticvariatio>thiscanbe especially markedinareasofthegenomeofreducedrecombination(“hitchhiking”)> > selectivesweep LinkageDisequilibrium  Underneutrality,acommonalleleisbydefinitionanoldallele,meaningthat recombinationhashadplentyofopportunitytoerodelinkagedisequilibrium.A testfor selection,then,isbasedonthehuntforrelativelyhighfrequencyallelesthatexhibit extensivelinkagedisequilibrium.  Ex.Lactasepersistencealleleispresentinabout77%ofEuropeans,butliesona longhaplotype,suggestingthatitisofrecentoriginascomparedtothecommonAfrican haplotype  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES February 25, 2013 [Lecture 8 – Sex and Sexual Selection] What is Sex?  Recombination– all oflife  Meiosis– eukaryotes  Anisogamy– multicellulareukaryotesonly  Dioecy– separatesexes(vs.hermaphroditesandmonoecy) The Evolution of Sex Costsofsex:recombinationandsexiscomplicated,costly,predation-prone Two-foldcostofsex:populationsgrowfasterif parthenogenetic Advantages of Sex a. Recombinationincreasesevolutionaryrate(groupselection):allowsadvantageousmutationsto combineinthesameindividuals b. Individualselection:environmentofoffspringmaybeverydifferentfromthatoftheirparent, parent’sadaptationsmaynotbesufficient Advantages for species to be asexual? Higherevolutionaryratecanbeadaptiveforaspecies.Mayworkagainstindividualdisadvantagesforsex withinpopulations:sogroupselection.Asexual“cheats”gainindividualadvantage,spreadtofixation withinspecies,nottootherspecies.Asexualspeciesdoexist—whydotheynottakeover? If otherspeciesevolving/adaptingfaster,competitionmaycauseextinctionofasexualspecies> >Oneof thefewcaseswheregroupselectionmayactuallybeoperating. Evolution of Sexual Dimorphism – Sexual Selection Darwin:secondarysexualcharacteristicsduetoastruggleforgeneticrepresentationbetweenmembersof thesamesex Sexualselection(struggleformatingsuccess)vs.naturalselection(struggleforsurvivalandreproduction aftermating) Nowadays,sexualselectionaspecialformofnaturalselection Males: cheapgametes,canproducelots,littleparentalinvestment> >potentiallyfathermanyoffspring Females:expensivegametes,producefew,oftenshowmoreparentalcare,morelimited#  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES March 4, 2013 [Lecture 9 – Evolution in Space and Time] Phylogenetic Tree with Anagenesis and Cladogenesis Anagenesis isevolutionwithinlineages(microevolution),whilecladogenesis issplittingoflineages (speciation>macroevolution) Cancladogenesis,speciation,andmacroevolutionbeexplainedbythesameprinciplesasAnagenesisand microevolution?Darwinarguedthatitcouldbe,throughhis“PrincipleofDivergence,”whicharguedthat disruptive selection,orecologicalcompetitionbetweenincipientspecies,wasinvolved. Speciation is Difficult to Study Morphologicalevolutionisslowinthefossil record(thoughpotentiallyfastundernaturalorartificial selection)…speciationisevenslower! >>A.R. Wallace:By studyinggeneticvariationandspeciesinspace,wemaybeabletounderstanda littlemoreaboutgeneticdivergenceandspeciationin time >>A.R. Wallace,1855:“Onthelawwhichhasregulatedtheintroductionofnewspecies.… The followinglawmaybededuced:- Everyspecieshascomeintoexistencecoincidentbothinspaceandtime withapre-existingcloselyalliedspecies.” Geographic Proximity of Populations Geographicrelationscanbeclassifiedintotwomajormodes: 1. Localoverlap,sympatry:Populationsaresaidtobesympatricorinsympatryif theyareinthe sameneighborhood population,becausetheyoverlapwithin“cruising range,” ordispersal  range (bluejaysandcardinals) 2. Geographicseparation:a)parapatry(populationsincontactatedges,ex.beachmiceoftheGulf Coast),b)allopatry(populationsnotincontact,ex.islandpopulations) Why does geography matter? Becausedispersalislimited!Dispersalandgeneflowisgreatlymisunderstoodbyevensomeexperts. Populationgeneticistsoftencall dispersalmigration,butdonotmeanthekindwherebirdsreturnafter migrationtoneartheirparents’nest!Dispersalbyindividualsleadstogene flow (thoughweusuallymean genotype flow).Gene flow can prevent divergence duetoselection,drift. Migration/Drift Balance in Sewall Wright’s “Island Model” of Population Structure  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES Migration (measured as a frm actieachpopulation)froma“mainland”canbalancedriftonislands withsmall populationsizes(Ne) >> With no selection, very approximately,divergenceispreventedbyN m = ene migrant enters each population per generation, whatever the N e ABO blood groups in native human populations: although selection may be involved in maintaining the polymorphism, most of similarities and difference are due to migration (or lack of) Migration/Selection Balance in Haldane’s Model of Population Structure ̂ ≈́ If m> >sthenequilibrium – “swamping” ̂ ≈m ́ If m< > 1/(2N ),ethen migration “wins,” populations are swamped Selection:  If m << s, then selection “wins,” maintains divergence  If m >> s, then migration “wins,” populations are swamped However,becauseN eis often a large number (so 1/(2N ) ie small), we usually expect  more divergence due to selection Dispersal incontinuous populations:if dispersalbetweenbirthplaceandbreedingsiteis~random, equivalenttothe“drunkard’swalk.”Sameaspassivediffusion:atwo­dimensional normal distribution. Standarddeviation, σ ,ofthedispersaldistributionisausefulmeasure of migration distance.Sewall Wrightdevelopedthisasadifferentmodelhecalledthe“isolationbydistance”modelofpopulation structure.A “neighborhood”populationconsistsofindividualswhocomefromanarea 2σ wide.  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES Genetic Variation across a Geographic Area: Clines A consistent changeingenefrequencyheritablephenotype,acrossageographicalrangeisknownasa cline.Clinesoccurbecausedispersal islimited;thewholeregiondoesnotformasinglepanmictic  population (inwhichall individualsarepotentialpartners). Causesofclines: a. Clinesproducedbymigration/driftbalance:randomgeneticdrift(noconsistentdirectional changes),expectpatchypolymorphicdivergence b. Clinesduetomigration/selectionbalance  Extrinsicselection(dependsonenvironment):selectionfavorsdifferentallelesin differentareas;dispersallimited;frequenciesmaydiverge>>cline  Intrinsicselection:includesthekindsofselectioninvolvedinincompatibilitiesamong species,suchashybridinviabilityorsterility i. Heterozygousdisadvantageorfrequency-dependentselection(singlelocus): heterozygousdisadvantagecreatesakindofdisruptiveselection.Equilibrium genefrequencyisunstable,selectionpreventspolymorphism> >narrowhybrid zonesmaintainedbyselectionagainstchromosomalheterozygotes ii. Selectionduetoepistasis(twoormoreloci): epistasisleadingtohybrid inviabilityorsterility,impliesselectionfor“coadapted”combinationsofgenes, A, B. Forexample,AB orabfavored,butAb and/oraBdisfavored Hybrid zones: narrow zones of contact between divergent forms or even species, “multiple narrow clines.” Few hybrids or many hybrids themselves may con,so 1 isrofnl1,F2,and every kind of backcross. Many species and/or races are distributed in parapatry, and have narrow hybrid zones between them. Ex. chromosomal races of mammals, warningly colored butterflies, sexually selected birds Hybrid zones, then, are places where narrow gene frequency clines at multiple loci occur together. Held together by a mix of extrinsic and intrinsic selection. Hybrid zones offer a direct approach to the study of divergence in time via divergence in space. Hybrid zones separate forms that are “almost species,” giving us some idea of the sorts of traits that may be involved in the evolution of new species.  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES How did hybrid zones, clines originate? Via allopatry then secondary contact? Or via divergence in parapatry? Controversy in the understanding of speciation: did species evolve in allopatry, parapatry, or sympatry? Do hybrid zones between divergent races represent a first step? Theory tells us that genetic differentiation can occur in parapatry, over short distances.  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES March 6, 2013 [Lecture 10 – Hybridization between Species] Species “Concepts” – What Do We Mean by Species? Darwinprovedthatspeciesevolved,butthisleadstoadifficulty: speciesweren’tcreatedkinds,withan essence.Theygraduallyevolvedfromeachother.Speciesaren’t“real”anymore,andtheypresumably evolvegradually. Darwinpointedoutthatthismeanshumanshavetodrawthelinebetweenspeciesand varieties. >>“Hereafter,weshall becompelledtoacknowledgedthattheonlydistinctionbetweenspeciesandwell- markedvarietiesis,thatthelaterareknown,orbelieved,tobeconnectedatthepresentdayby intermediategradations,whereasspecieswereformerlythusconnected.” >>“Independentlyofblendingformintercrossing,thecompleteabsence,inawell-investigatedregion,of varietieslinkingtogetheranytwoclosely–alliedforms,isprobablythemostimportantofall the criterionsoftheirspecificdistinctness.” Species Concepts To understandtheoriginofspecies,wemustknowwhatspeciesare.Today,thereismuchdebateandasa result,many“speciesconcepts.” Sowhereisthedividinglinebetweenspeciesand“varieties”? 1. Darwin’s “Morphological Species Concept” :speciesaredelimitedbygapsinmorphology, drawalinebetweenspeciesandvarietiesusingmorphologicaldifferences  Ex.primrosevs.oxslipvs.cowslip> >separatespecies,eventhoughmanyintermediates (all rare, somesterility)  Incontrast,Darwinarguedthatracesofhumanswereall thesamespecies.Inthiscase, no good dividing lines betweenraces.  LouisAgassiz,acreationist,arguedtheopposite:“…Thedifferencesbetweendistinct [human]racesareoftengreaterthanthosedistinguishingspeciesofanimalsfromtheother.”  PheneticSpeciesConcept:multivariatestatisticalrestatementofDarwin’sideas,phonetic differencescanapplytogeneticvariationaswell asmorphologicalvariation,suchasenzyme differences,chromosomenumber,immunologicaldifferences,DNA divergence,anyother “geneticmarkers”  ArgumentsagainstDarwin’sspeciesconcepts: i. Plentyofmorphologicalgapsbetweenspecies:e.g.majoreffectsofMendelianalleles, ex.pepperedmoths,mimeticbutterflies(suchastheAfricanPapilio dardanus) ii. Fewornomorphologicaldifferencesbetweensomespecies:“siblingspecies”whichare 1)morphologicallysimilar,2)evolvemoreorlessseparately,3)littleorno  ORGANISMIC AND EVOLUTIONARY BIOLOGY 53, LECTURE NOTES hybridization/geneflow,e.g.Drosophila pseudoobscura vs.D. persimili> > chromosomaldifferences& sterilityofhybrids/Anopheles mosquitos:habitat,biting, malaria/somebirds 2. The Biological Species Concept:speciesdefinedbyinterbreeding,1)geneflowhomogenizes variationwithineachspecies,2)lackofhybridizationorgeneflowbetweenspecies,whichcan divergeindefinitely>lackofgeneflowisdueto“reproductiveisolatingmechanisms,”today called“barriers” i. Pre-zygoticbarriers(“pre-mating”):1)ecological/seasonalbarriers(matesdonotmeet), 2)behavioralbarriers(meetbutdonotattemptmating),3)barriers(attemptsatmatingdo notwork) ii. Post-zygoticbarriers(“post-mating”):1)gameticincompatibility(gametesdonotfuse duetoincompatibilities:N.B. post-matingbutpre-zygotic), 2)hybridinviability(hybrid zygoteshavereducedfitness:i) genomicfactors,selectionagainsthybrids(intrinsic selection),ii) hybridsarenotsuitedecologically(extrinsicselection),iii) reducedmating propensityofhybrids(sexualselection),3)hybridsterility(eventhoughmaysurviveand mateasnormal),4)sexualselectionagainsthybrids(disfavoredduringmating)  Aricia agestis / Aricia artaxerxes: mtDNA studiessuggestedtwospeciesin Britain,N. England& N.Walesunivoltine (single-brooded)pops.Wereinterpretedas pureA. agestis becauseofmtDNA haplotypes  Hybridinviabilityandhybridsterility: geneticincompatibility,e.g.mules, chromosomalheterozygotes(otherhybridsbetweenspecieshavenosterilityor viabilityproblems:e.g.Darwin’sfinches,ducks)  Darwindiscussedhybridsterilityatlength,however,hecouldcertainlynot “explain”it.Becausesterilityandinviabilitywereseenbymanyasimportant characteristicsofspecies,manyfelthedidnotexplain“TheOriginofSpecies” properly.  However,Darwindidarguethathybridsterilitywasnotanadaptation(oraGod- given“isolatingmechanism”):“Nowdothesecomplexandsingularrulesindicatethat specieshavebeenendowedwithsterilitysimplytopreventtheirbecoming confoundedinnature?I thinknot…”“Theforegoingrulesandfacts,ontheother hand,appeartomeclearlytoindicatethatthesterility,bothofthefirstcrossesandof hybridsissimplyincidentalordependentonunknowndifferences,chieflyinthe reproductivesystems,ofthespecieswhicharecrossed.”Today,we’dtendtoagree withthis,andwearenowbeginningtounderstandhowhybridincompatibilitiesdo evolve.
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