Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model 英文参考文献.docVIP

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Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model 英文参考文献.doc

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Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model 英文参考文献

EstimatingDivergenceTimeandAncestralEffective PopulationSizeofBorneanandSumatranOrangutan SubspeciesUsingaCoalescentHiddenMarkovModel ThomasMailund1*,JulienY.Dutheil1,AsgerHobolth1,2,GertonLunter3,MikkelH.Schierup1,4 1Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark, 2Department of Mathematical Sciences, Aarhus University, Aarhus, Denmark, 3The Wellcome TrustCentreforHumanGenetics,Oxford,UnitedKingdom,4DepartmentofBiology,AarhusUniversity,Aarhus,Denmark Abstract Duetogeneticvariationintheancestoroftwopopulationsortwospecies,thedivergencetimeforDNAsequencesfrom two populations is variable along the genome. Within genomic segments all bases will share the same divergence— becausetheyshareamostrecentcommonancestor—whennorecombinationeventhasoccurredtosplitthemapart.The sizeofthesesegmentsofconstantdivergencedependsontherecombinationrate,butalsoonthespeciationtime,the effectivepopulationsizeoftheancestralpopulation,aswellasdemographiceffectsandselection.Thus,inferenceofthese parametersmaybepossibleifwecandecodethedivergencetimesalongagenomicalignment.Here,wepresentanew hidden Markov model that infers the changing divergence (coalescence) times along the genome alignment using a coalescent framework, in order to estimate the speciation time, the recombination rate, and the ancestral effective population size. The model is efficient enough to allow inference on whole-genome data sets. We first investigate the powerandconsistencyofthemodelwithcoalescentsimulationsandthenapplyittothewhole-genomesequencesofthe twoorangutansub-species,Bornean(P.p.pygmaeus)andSumatran(P.p.abelii)orangutansfromtheOrangutanGenome Project.Weestimatethespeciationtimebetweenthetwosub-speciestobe334+145thousandyearsagoandtheeffective populationsizeoftheancestralorangutanspeciestobe26,800+6,700,consistentwithrecentresultsbasedonsmallerdata sets. We also report a negative correlation between chromosome size and ancestral effective population size, which we interpretasasignatureofre