Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model 英文参考文献.docVIP

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Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model 英文参考文献.doc

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Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model 英文参考文献

GenomicRelationshipsandSpeciationTimes ofHuman,Chimpanzee,andGorillaInferred fromaCoalescentHiddenMarkovModel Asger Hobolth1*,Ole F.Christensen2,Thomas Mailund2,3,Mikkel H.Schierup2 1BioinformaticsResearchCenter,NorthCarolinaStateUniversity,Raleigh,NorthCarolina,UnitedStatesofAmerica,2BioinformaticsResearchCenter,UniversityofAarhus, Aarhus,Denmark,3DepartmentofStatistics,UniversityofOxford,Oxford,UnitedKingdom Thegenealogicalrelationshipofhuman,chimpanzee,andgorillavariesalongthegenome.WedevelopahiddenMarkov model(HMM)thatincorporatesthisvariationandrelatethemodelparameterstopopulationgeneticsquantitiessuchas speciationtimesandancestralpopulationsizes.OurHMMisananalyticallytractableapproximationtothecoalescent processwithrecombination,andinsimulationsweseenoapparentbiasintheHMMestimates.WeapplytheHMMto fourautosomalcontiguoushuman–chimp–gorilla–orangutanalignmentscomprisingatotalof1.9millionbasepairs.We find a very recent speciation time of human–chimp (4.1 6 0.4 million years), and fairly large ancestral effective populationsizes(65,000630,000forthehuman–chimpancestorand45,000610,000forthehuman–chimp–gorilla ancestor).Furthermore,around50%ofthehumangenomecoalesceswithchimpanzeeafterspeciationwithgorilla.We alsoconsider250,000basepairsofX-chromosomealignmentsandfindaneffectivepopulationsizemuchsmallerthan 75% of the autosomal effective population sizes. Finally, we find that the rate of transitions between different genealogiescorrelateswellwiththeregion-widepresent-dayhumanrecombinationrate,butdoesnotcorrelatewith thefine-scalerecombinationratesandrecombinationhotspots,suggestingthatthelatterareevolutionarilytransient. Citation: Hobolth A, Christensen OF, Mailund T, Schierup MH (2007) Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescenthiddenMarkovmodel.PLoSGenet3(2):e7.doi:10.1371/journal.pgen.0030007 HCancestraleffectivepopulationsizeNHCof2–10timesthe human present-day effective population size NH ? 10,000 I