Download Lab 8 - Population Genetics and Evolution

Name:_____________________________________________ Lab8–PopulationGenetics
INTRODUCTION
Date:________________________
In1908,G.H.HardyandW.Weinbergindependentlysuggestedaschemewherebyevolutioncouldbe
viewedaschangesinthefrequencyofallelesinapopulationoforganisms.Inthisscheme,ifAandaare
allelesforaparticulargenelocusandeachdiploidindividualhastwosuchloci,thenpcanbedesignatedas
thefrequencyoftheAalleleandqasthefrequencyoftheaallele.Thus,inapopulationof100individuals
(eachwithtwoloci)inwhich40%oftheallelesareA,pwouldbe0.40.Therestofthealleles(60%)would
bea,andqwouldequal0.60(i.e.,p+q=1.0).Thesearereferredtoasallelefrequencies.Thefrequencyof
thepossiblediploidcombinationsofthesealleles(AA,Aa,aa)isexpressedasp2+2pq+q2=1.0.Hardyand
Weinbergalsoarguedthatiffiveconditionsaremet,thepopulation'salleleandgenotypefrequencieswill
remainconstantfromgenerationtogeneration.Theseconditionsareasfollows:
1. Thebreedingpopulationislarge.(Theeffectofchanceonchangesinallelefrequenciesisthereby
greatlyreduced.)
2. Matingisrandom.(Individualsshownomatingpreferenceforaparticularphenotype.)
3. Thereisnomutationofthealleles.(NoalterationintheDNAsequenceofalleles.)
4. Nodifferentialmigrationoccurs.(Noimmigrationoremigration.)
5. Thereisnoselection.(Allgenotypeshaveanequalchanceofsurvivingandreproducing.)
TheHardy-Weinbergequationdescribesanexistingsituation.Ifthefiveconditionsaremet,then
nochangewilloccurineitheralleleorgenotypefrequenciesinthepopulation.Ofwhatvalueissucha
rule?Itprovidesayardstickbywhichchangesinallelefrequency,andthereforeevolution,canbe
measured.Onecanlookatapopulationandask:isevolutionoccurringwithrespecttoaparticular
genelocus?Sinceevolutionisdifficult(ifnotimpossible)toobserveinmostnaturalpopulations,we
willmodeltheevolutionaryprocessusingtheclassasasimulatedpopulation.Thepurposeofthis
simulationistoprovideanopportunitytotestsomeofthebasictenetsofpopulationgeneticsand
evolutionarybiology.
EXERCISE8A:EstimatingAlleleFrequenciesforaSpecificTraitwithinaSample
Population
Usingtheclassasasamplepopulation,theallelefrequencyofagenecontrollingtheabilitytotaste
thechemicalPTC(phenylthiocarbamide)couldbeestimated.Abitter-tastereactiontoPTCisevidenceof
thepresenceofadominantalleleineitherthehomozygouscondition(AA)ortheheterozygouscondition
(Aa).Theinabilitytotastethechemicalatalldependsonthepresenceofhomozygousrecessivealleles
(aa).
ToestimatethefrequencyofthePTC-tastingalleleinthepopulation,onemustfindp.Tofindp,one
mustfirstdetermineq(thefrequencyofthenon-tastingPTCallele),becauseonlythegenotypeofthe
homozygousrecessiveindividualsisknownforsure(thosewiththedominanttraitcouldbeAAorAa).
Procedure
1. UsingthePTCtaste-testpapersprovided,tearoffashortstripandpressittoyourtonguetip.PTC
tasterswillsenseabittertaste.Forthepurposesofthisexercisetheseindividualsareconsideredtobe
tasters.
2. Adecimalnumberrepresentingthefrequencyoftasters(p2+2pq)shouldbecalculatedbydividingthe
numberoftastersintheclassbythetotalnumberofstudentsintheclass.Adecimalnumber
representingthefrequencyofnon-tasters(q2)canbeobtainedbydividingthenumberofnon-tasters
bythetotalnumberofstudents.YoushouldthenrecordthesenumbersinTable8.1.
3. UsetheHardy-Weinbergequationtodeterminethefrequencies(pandq)ofthetwoalleles.The
frequencyqcanbecalculatedbytakingthesquarerootofq2.Onceqhasbeendetermined,pcanbe
determinedbecause1–q=p.RecordthesevaluesinTable8.1fortheclassandalsocalculateand
recordvaluesofpandqfortheNorthAmericanpopulation.
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Name:_____________________________________________ Lab8–PopulationGenetics
Date:________________________
Table8.1:PhenotypicProportionsofTastersandNon-tastersandFrequenciesoftheDetermining
Alleles
Class
Population
North
American
Population
Allelefrequencybasedon
HardyWeinbergequilibrium
Phenotypes
Tasters
(p2+2pq)
#
%
Non-tasters
(q2)
#
%
0.45
p
q
TopicsforDiscussion
1. Whatisthepercentageofheterozygoustasters(2pq)inyourclass?__________________
2. WhatpercentageoftheNorthAmericanpopulationisheterozygousforthetastertrait?__________________
EXERCISE8B:CaseStudies
CASEI–ATestofanIdealHardy-WeinbergPopulation
Theentireclasswillrepresentabreedingpopulation,sofindalargeopenspaceforthis
simulation.Inordertoensurerandommating,chooseanotherstudentatrandom.Inthis
simulation,wewillassumethatgenderandgenotypeareirrelevanttomateselection.
Theclasswillsimulateapopulationofrandomlymatingheterozygousindividualswithaninitial
genefrequencyof0.5forthedominantalleleAandtherecessivealleleaandgenotypefrequenciesof0.25
AA,0.50Aa,and0.25aa.YourinitialgenotypeisAa.RecordthisontheDataPage.Eachmemberofthe
classwillreceivefourcards.TwocardswillhaveAwrittenonthemandtwocardswillhavea.Thefour
cardsrepresenttheproductsofmeiosis.Each"parent"contributesahaploidsetofchromosomestothe
nextgeneration.
Procedure
1. Tumthefourcardsoversothatthelettersdonotshow,shufflethem,andtakethecardontopto
contributetotheproductionofthefirstoffspring.Yourpartnershoulddothesame.Putthetwocards
together.Thetwocardsrepresenttheallelesofthefirstoffspring.Oneofyoushouldrecordthe
genotypeofthisoffspringintheCaseIsectionontheDataPage.Eachstudentpairmustproducetwo
offspring,soallfourcardsmustbereshuffledandtheprocessrepeatedtoproduceasecondoffspring.
2. TheotherpartnershouldthenrecordthegenotypeofthesecondoffspringontheDataPage.Thevery
shortreproductivecareerofthisgenerationisover.Youandyourpartnernowbecomethenext
generationbyassumingthegenotypesofthetwooffspring.Thatis,Student1assumesthegenotypeof
thefirstoffspringandStudent2assumesthegenotypeofthesecondoffspring.
3. Eachstudentshouldobtain,ifnecessary,newcardsrepresentingtheallelesinhisorherrespective
gametesaftertheprocessofmeiosis.Forexample,Student1becomesgenotypeAaandobtainscards
A,A,a,a;Student2becomesaaandobtainscardsa,a,a,a.Eachparticipantshouldrandomlyseekout
anotherpersonwithwhomtomateinordertoproducetheoffspringofthenextgeneration.
Remember,thesexofyourmatedoesnotmatter,nordoesthegenotype.Youshouldfollowthesame
matingproceduresasyoudidforthefirstgeneration,beingsuretorecordyournewgenotypeafter
eachgeneration.Classdatashouldbecollectedaftereachgenerationforfivegenerations.Attheendof
eachgeneration,remembertorecordthegenotypethatyouhaveassumed.Yourteacherwillcollect
classdataaftereachgenerationbyaskingyoutoraiseyourhandtoreportyourgenotype.
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Name:_____________________________________________ Lab8–PopulationGenetics
Date:________________________
4. AlleleFrequency:Theallelefrequencies,pandq,shouldbecalculatedforthepopulationafterfive
generationsofsimulatedrandommating.
NumberofAallelespresentatthefifthgeneration
NumberofoffspringwithgenotypeAA_________x2=_________Aalleles
NumberofoffspringwithgenotypeAa_________x1=_________Aalleles
Total=_________Aalleles
p=TOTALnumberofAalleles
TOTALnumberofallelesinthepopulation(numberofstudentsx2)
Inthiscase,thetotalnumberofallelesinthepopulationisequaltothenumberofstudentsintheclassx2.
Numberofaallelespresentatthefifthgeneration
Numberofoffspringwithgenotypeaa_________x2=_________aalleles
NumberofoffspringwithgenotypeAa_________x1=_________aalleles
Total=_________aalleles
q=TOTALnumberofaalleles
TOTALnumberofallelesinthepopulation(numberofstudentsx2)
Questions
1. WhatdoestheHardy-Weinbergequationpredictforthenewpandq?
2. Dotheresultsyouobtainedinthissimulationagree?
3. Basedonyouranswerto#2,whatmajorassumption(s)werenotstrictlyfollowedinthissimulation?
CASEII–Selection
InthisCaseyouwillmodifythesimulationtomakeitmorerealistic.Inthenaturalenvironment,notall
genotypeshavethesamerateofsurvival;thatis,theenvironmentmightfavorsomegenotypeswhile
selectingagainstothers.Anexampleisthehumanconditionofsickle-cellanemia.Thisisadiseasecaused
byamutationononeallele,andindividualswhoarehomozygousrecessiveoftendonotsurvivetoreach
reproductivematurity.Forthissimulationyouwillassumethatthehomozygousrecessiveindividuals
neversurvive(100%selectionagainst),andthatheterozygousandhomozygousdominantindividuals
survive100%ofthetime.
Procedure
TheprocedureissimilartothatforCaseI.
1. Startagainwithyourinitialgenotypeandproduceyour"offspring"asyoudidforCaseI.Thistime,
however,thereisoneimportantdifference.Everytimeyour"offspring"isaa,itdoesnotreproduce.
Sincewewanttomaintainaconstantpopulationsize,thesametwoparentsmusttryagainuntilthey
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Name:_____________________________________________ Lab8–PopulationGenetics
Date:________________________
producetwosurvivingoffspring.Youmayneedtogetnew"allele"cardsfromthepool,allowingeach
individualtocompletetheactivity.
2. Proceedthroughfivegenerations,selectingagainstthehomozygousrecessiveoffspring100%ofthe
time.Thenaddupthegenotypefrequenciesthatexistinthepopulationandcalculatethenewpandq
frequenciesinthesamewayyoudidforCaseI.
Questions
1. HowdothenewfrequenciesofpandqcomparetotheinitialfrequenciesinCaseI?
2. Whatmajorassumption(s)werenotstrictlyfollowedinthissimulation?
3. Predictwhatwouldhappentothefrequenciesofpandqifyousimulatedanotherfivegenerations.
4. Inalargepopulationwoulditbepossibletocompletelyeliminateadeleteriousrecessiveallele?
Explain.
CASEIII–HeterozygoteAdvantage
FromCaseIIitiseasytoseewhathappenstothelethalrecessivealleleinthepopulation.However,data
frommanyhumanpopulationsshowanunexpectedlyhighfrequencyofthesickle-cellalleleinsome
populations.Thus,oursimulationdoesnotaccuratelyreflecttherealsituation;thisisbecauseindividuals
whoareheterozygousareslightlymoreresistanttoadeadlyformofmalariathanhomozygousdominant
individuals.Inotherwords,thereisaslightselectionagainsthomozygousdominantindividualsas
comparedtoheterozygotes.Thisfactiseasilyincorporatedintooursimulation.
Procedure
1. InthisroundkeepeverythingthesameasitwasinCaseII,exceptthatifyouroffspringisAA,flipacoin.
Ifthecoinlandsheadsup,theindividualdoesnotsurvive;iftails,theindividualdoessurvive.
2. Simulatefivegenerations,startingagainwiththeinitialgenotypefromCaseI.Thegenotypeaanever
survives,andhomozygousdominantindividualsonlysurviveifthecointosscomesuptails.Sincewe
wanttomaintainaconstantpopulationsize,thesametwoparentsmusttryagainuntiltheyproduce
twosurvivingoffspring.Getnew"allele"cardsfromthepoolasneeded.Totaltheclassgenotypesand
calculatethepandqfrequencies.
3. StartingwiththeF5genotype,gothroughfivemoregenerations,andagaintotalthegenotypesand
calculatethefrequenciesofpandqasdoneinCaseI.
4. Iftimepermits,theresultsfromanotherfivegenerationswouldbeextremelyinformative.
Questions
1. HowdothechangesinpandqfrequenciesinCaseIIcomparewithCaseIandCaseIII?
2. DoyouthinktherecessiveallelewillbecompletelyeliminatedineitherCaseIIorCaseIII?
3. Whatistheimportanceofheterozygotes(theheterozygoteadvantage)inmaintaininggeneticvariation
inpopulations?
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Name:_____________________________________________ Lab8–PopulationGenetics
CASEIV–GeneticDrift
Date:________________________
Itispossibletouseoursimulationtolookatthephenomenonofgeneticdriftindetail.
Procedure
1. Dividethelabintoseveralsmaller"populations"(forexample,aclassof30couldbedividedintothree
populationsofteneach)sothatindividualsfromoneisolated"population"donotinteractwith
individualsfromanotherpopulation.
2. NowgothroughfivegenerationsasyoudidforCaseI.Recordthenewgenotypicfrequenciesand
calculatethenewfrequenciesofpandqforeachpopulation.
Questions
1. Explainhowtheinitialgenotypicfrequenciesofthepopulationscompare.
2. Whatdoyourresultsindicateabouttheimportanceofpopulationsizeasanevolutionaryforce?
Hardy-WeinbergProblems
1. InDrosophila,theallelefornormal-lengthwingsisdominantoverthealleleforvestigialwings
(vestigialwingsarestubbylittlecurlsthatcannotbeusedforflight).Inapopulationof1,200
individuals,360showtherecessivephenotype.Howmanyindividualswouldyouexpecttobe
homozygousdominant?Howmanywouldbeheterozygousforthistrait?
2. Thealleleforunattachedearlobesisdominantoverthealleleforattachedearlobes.Inapopulationof
700individuals,15%showtherecessivephenotype.Howmanyindividualswouldyouexpecttobe
homozygousdominant?Howmanywouldbeheterozygousforthistrait?
3. Thealleleforthehairpatterncalled"widow'speak"isdominantoverthealleleforno"widow'speak."
Inapopulationof3,000individuals,720showthedominantphenotype.Howmanyindividualswould
youexpectforeachofthepossiblethreegenotypesforthistrait?
4. IntheUnitedStatesabout15%ofthepopulationisRhnegative.ThealleleforRhnegativeisrecessive
tothealleleforRhpositive.IfthestudentpopulationofSouthis1,900,howmanystudentswouldyou
expectforeachofthethreepossiblegenotypes?
5. IncertainAfricancountries3%ofthenewbornbabieshavesickle-cellanemia,whichisarecessive
trait.Outofarandompopulationof1,000newbornbabies,howmanywouldyouexpectforeachofthe
threepossiblegenotypes?
6. Inacertainpopulation,thedominantphenotypeofacertaintraitoccurs89%ofthetime.Whatisthe
frequencyofthedominantallele?
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Name:_____________________________________________ Lab8–PopulationGenetics
DATAPAGE
CASEI
Hardy-WeinbergEquilibrium
InitialClassFrequencies:
AA_____
Aa_____
aa_____
p_____
q_____
MyInitialGenotype:_____
F1Genotype_____
F2_____
F3_____
F4_____
F5_____
FinalClassNumbers:
AA_____
Aa_____
aa_____
FinalClassFrequencies:
AA_____
Aa_____
aa_____
p_____←SeePage3→ q_____
CASEII
Selection
InitialClassFrequencies:
AA_____
Aa_____
aa_____
p_____
q_____
MyInitialGenotype:_____
F1Genotype_____
F2_____
F3_____
F4_____
F5_____
FinalClassNumbers:
AA_____
Aa_____
aa_____
FinalClassFrequencies:
AA_____
Aa_____
aa_____
p_____←SeePage3→ q_____
Date:________________________
CASEIII
HeterozygoteAdvantage
InitialClassFrequencies:
AA_____
Aa_____
aa_____
p_____
q_____
MyInitialGenotype:_____
F1Genotype_____
F6Genotype_____
F2Genotype_____
F7Genotype_____
F3Genotype_____
F5Genotype_____
F4Genotype_____
F9Genotype_____
F5Genotype_____
FlOGenotype_____
AfterFiveGenerations
FinalClassNumbers:
AA_____
Aa_____
aa_____
FinalClassFrequencies:
AA_____
Aa_____
aa_____
p_____←SeePage3→ q_____
AfterTenGenerations
FinalClassNumbers:
AA_____
Aa_____
FinalClassFrequencies:
AA_____
Aa_____
p_____←SeePage3→
aa_____
aa_____
q_____
CASEIV
GeneticDrift
InitialClassFrequencies:
AA_____
Aa_____
aa_____
p_____
q_____
MyInitialGenotype:_____
F1Genotype_____
F2_____ F3_____
F4_____ F5_____
FinalClassNumbers:
AA_____
Aa_____
aa_____
FinalClassFrequencies:
AA_____
Aa_____
aa_____
p_____←SeePage3→ q_____
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