数量遗传学课件

1 Chapter2 Changesofgenefrequency 2 Changesofgenefrequencyinlargepopulations 3 Migration m proportionofnewimmigrants qm genefrequencyamongtheimmigrants ThefrequencyofA2aftermigration Changeofthegenefrequency q0 genefrequencyintheoriginalpopulation 4 Mutation Mutationrate Changeofgenefrequency whenequilibriumattained q 0 Twobasicfacts themutationratesinmostorganismsaregenerallyverylow about10 5 10 6pergeneration thereversemutationisgenerallymuchlessfrequentthanforwardmutation 5 Selection CompletedominanceofA1 selectionagainstA2 6 Selection s 0 2 s 1 q Effectofselectionongenefrequencyfordifferentinitialfrequencies s 0 2 s 1 q 7 Selection s 0 2 s 1 Changesofgenefrequencyintheselectionprocess 8 Selection Generationsneededforachievingacertaingenefrequency fors 1 9 Balancebetweenmutationandselection Changeduetomutation Changeduetoselection againstcompleterecessiveallele Whenequilibriumattained Whenvandqbothverysmall 10 Polymorphism Definition ifthefrequencyofthemostpopularalleleatalocus 0 99MeasureofgeneticvariationduetopolymorphiclociHeterozygositysinglelocus frequencyofheterozygote Hmultipleloci meanfrequencyofheterozygotesProportionofpolymorphiclociamongthosetestedPolymorphicinformationcontent PIC 11 Polymorphism Reasons Heterozygoteadvantage Frequency dependentselection Heterogeneousenvironment Transition Neutralmutation 12 Changeofgenefrequencyinsmallpopulations Theidealizedpopulation 13 Randomdrift geneticdraft RandomchangeofgenefrequencyfromgenerationtogenerationsOccurringinsmallpopulationsArisingfromtherandomsamplingofgametes GenePool Sample10GametestoCreate5Individuals DoThis20TimesToShowSamplingVariation Number Frequency ofAAlleles 16 Idealizedpopulation DividealargepopulationofHardy Weinbergequilibrium basepopulation intoalargenumberofsub populations lines eachwithsizeNandmeetsthefollowingconditions Nomigrationbetweenlines noselectionandmutationwithineachlinesNooverlapofgenerationsSamenumberofbreedingindividualsinalllinesandallgenerationsSamenumberofbreedingmalesandfemaleswithineachlineRandommating includingself fertilization withineachline 17 Idealizedpopulation Basepopulation N N N N N N N N N N 2N 2N 2N 2N 2N 2N 2N 2N 2N 2N Generation 0 1 2 Gametes Breedingindividuals Gametes Breedingindividuals 18 Changeofgenefrequencies varianceofgenefrequency ConsiderasinglelocuswithtwoallelesA1andA2ThefrequencyofA2inthebasepopulationisq0Ingenerationone the2Ngenesineachlinearearandomsampleofgenesinthebasepopulation ThefrequencyofA2ingenerationonefollowsbinomialdistribution Changeoffrequencyintheithline Expectationoffrequencies Varianceoffrequencies 19 Changeofgenefrequencies variance Generationt Alllinesarefixed A1willbefixedintheproportionp0oflines andA2intheremainingproportionq0oflines Willbeprovedlater 20 Changeofgenefrequencies 2N 20 4isolatedlinesstartedfromoneancestralpopulationwithp 0 5 Generation p 21 Propertiesofrandomdrift HasNoDirectionIsCumulativeStrengthisProportionalto1 2NLeadstoLoss andFixation ofAllelesWithinLinesLeadstoGeneticDifferentiationBetweenIsolatedLinesCreates D 0 22 Changesofgenotypicfrequencies Withineachline Thegenotypicfrequenciesinthepopulationasawhole 23 Inbreeding MatingofindividualsthatarerelatedtoeachotherbyancestryTheoretically anypairofindividualsinanypopulationmustberelatedtoeachother Thesmallerthepopulation themorecloselyrelatedtoeachotherofapairofindividualtakenatrandom OffspringproducedbyinbreedingaresaidtobeinbredindividualsThepropertiesofsmallpopulationscanbetreatedastheconsequencesofinbreeding 24 Inbreeding Coefficientofinbreeding F ProbabilitythatthetwoallelesatanylocusinanindividualareidenticalbydescentIdentitybydescent twogenesthathaveoriginatedfromthereplicationofonesinglegeneinapreviousgenerationInrandommatingpopulation weusuallyusetheaverageofcoefficientofinbreedingasameasureofthedispersiveprocess 25 Inbreeding Example matingoffullsibs 26 Inbreedingintheidealizedpopulation 012t GenerationCoeff inbreedingInbreedingincrement 27 Relationshipofinbreedingcoefficientandgeneandgenotypefrequency Recalltheformulaonslide18 28 MUTATION DRIFTEQUILIBRIUM Randomdrift resultsinthecompletelossofgeneticvariationMutation reintroducevariationatalowrateThenetresultisadynamicequilibrium whereinthepopulationmaintainsacertainamountofvariationTheallelesmakingupthisvariationarechangingovertimeForshorttime thecontributionfrommutationwillbenegligibleForlonger termevolutionaryissues mutationcannotbeignored 29 MUTATION DRIFTEQUILIBRIUM Here allelesaandbareinitiallypresent whileallelescanddarisebymutation Attime1 allelesaandbaresegregating attime2 bandcaresegregating attime3b c anddareallsegregating 30 MUTATION DRIFTEQUILIBRIUM ModelofKimuraandCrow infinite allelesmodelAtypicalgeneconsistsofuptoseveralthousandnucleotidesEachnewmutationlikelygivesadifferentDNAsequence andhenceanewalleleAtthemutation driftequilibriumbetweengeneticdriftandmutation theexpectedheterozygosityis 31 Changeofgenefrequencyinsmallpopulations Thenon idealizedpopulation 32 Effectivepopulationsize Effectivenumberofbreedingindividualsthatwouldgiverisetothesamevarianceofgenefrequencyorrateofinbreedingwhentheybredinthemanneroftheidealizedpopulation Allconclusionsdrawnfortheidealizedpopulationcanbeappliedforanyrealpopulations iftheactualpopulationsizeisreplacedbytheeffectivepopulationsize Theeffectivepopulationsizecanbederivedfromtheactualpopulationsize whenthebreedingstructureisknown 33 Effectivepopulationsize Excludingself fertilization Excludingsib mating Unequalnumberofmalesandfemales twicetheharmonicmean 34 Effectivepopulationsize Unequalnumbersinsuccessivegenerations Non randomvariationoffamilysize whenvarianceoffamilysizesarethesameforbothsexeswhenitisdifferent 35 Effectivepopulationsize EqualnumberofindividualsselectedforbreedingandnovariationinfamilysizeequalnumbersofmalesandfemaleunequalnumbersOverlappinggenerations L generationinterval NT numberofindividualssurvivedinthepopulationE averageageatdeath 36 Pedigreedpopulations Inbreedingcoefficientofanindividual CoefficientofcoancestryorkinshipCoancsetryoftwoindividuals probabilityoftwogametestakenatrandom onefromeach carryingIBDallelesTheinbreedingcoefficientofanindividualisequaltothecoancestryofitstwoparents 37 CalculationofCoefficientofcoancestry Basicrules Generalizedpedigree 38 Coancestryofcloserelatives Self Offspringandparent Fullsibs Halfsibs AandB parentsofPAandC parentsofQ 39 Regularsystemofinbreeding ThesamematingsystemisappliedinallgenerationsAllindividualsinthesamegenerationhavethesameinbreedingcoefficientOftenusedtoproduceinbredlinesTypes CloseinbreedingRepeatedbackcrossIntercrossaftercrossing 40 Closeinbreeding Self fertilization Offspringandparent Fullsibs Halfsibs 41 Repeatedbackcross A BA CA DX Themainuseofrepeatedbackcross totransferaparticulargenefromonestrainintothegeneticbackgroundofanotherstrainTransferofadominantgene successivebackcrossTransferofarecessivegene rotatedbackcrossandintercross 42 Intercrossaftercrossing Inbree