Pervasive Adaptive Protein Evolution Apparent in Diversity Patterns around Amino Acid Substitutions in Drosophila simulans 英文参考文献.docVIP

PervasiveAdaptiveProteinEvolutionApparentin DiversityPatternsaroundAminoAcidSubstitutionsin Drosophilasimulans ShmuelSattath1,EyalElyashiv1,OrenKolodny1,YosefRinott2,GuySella1* 1Department of Ecology, Evolution, and Behavior, Hebrew University of Jerusalem, Jerusalem, Israel, 2Department of Statistics, Hebrew University of Jerusalem, Jerusalem,Israel Abstract In Drosophila, multiple lines of evidence converge in suggesting that beneficial substitutions to the genome may be common. All suffer from confounding factors, however, such that the interpretation of the evidence—in particular, conclusions about the rate and strength of beneficial substitutions—remains tentative. Here, we use genome-wide polymorphism data in D. simulans and sequenced genomes of its close relatives to construct a readily interpretable characterizationoftheeffectsofpositiveselection:theshapeofaverageneutraldiversityaroundaminoacidsubstitutions. As expected under recurrent selective sweeps, we find a trough in diversity levels around amino acid but not around synonymoussubstitutions,adistinctivepatternthatisnotexpectedunderalternativemodels.Thischaracterizationisricher thanpreviousapproaches,whichreliedonlimitedsummariesofthedata(e.g.,theslopeofascatterplot),andrelatesto underlying selection parameters in a straightforward way, allowing us to make more reliable inferences about the prevalenceandstrengthofadaptation.Specifically,wedevelopacoalescent-basedmodelfortheshapeoftheentirecurve and use it to infer adaptive parameters by maximum likelihood. Our inference suggests that ,13% of amino acid substitutionscauseselectivesweeps.Interestingly,itrevealstwoclassesofbeneficialfixations:aminority(approximately 3%)thatappearstohavehadlargeselectiveeffectsandaccountsformostofthereductionindiversity,andtheremaining 10%,whichseemtohavehadveryweakselectiveeffects.Theseestimatesthereforehelptoreconciletheapparentconflict among previously published estimates of the strength of selection. More generally, ou