Robust Time Estimation Reconciles Views of the Antiquity of Placental Mammals 英文参考文献.docVIP

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Robust Time Estimation Reconciles Views of the Antiquity of Placental Mammals 英文参考文献.doc

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Robust Time Estimation Reconciles Views of the Antiquity of Placental Mammals 英文参考文献

RobustTimeEstimationReconcilesViewsofthe AntiquityofPlacentalMammals YasuhiroKitazoe1*,HirohisaKishino2,PeterJ.Waddell2,3,NoriakiNakajima1,TakahisaOkabayashi1,TeruakiWatabe1,YoshiyasuOkuhara1 1CenterofMedicalInformationScience,KochiMedicalSchool,Nankoku,Kochi,Japan,2GraduateSchoolofAgriculturalandLifeSciences,University ofTokyo,Tokyo,Japan,3SouthCarolinaCancerCenter(SCCC),UniversityofSouthCarolina,Columbia,SouthCarolina,UnitedStatesofAmerica Background. Molecular studies have reported divergence times of modern placental orders long before the Cretaceous– Tertiary boundary and far older than paleontological data. However, this discrepancy may not be real, but rather appear becauseoftheviolationofimplicitassumptionsintheestimationprocedures,suchasnon-gradualchangeofevolutionaryrate and failure to correct for convergent evolution. Methodology/Principal Findings. New procedures for divergence-time estimation robust to abrupt changes in the rate of molecular evolution are described. We used a variant of the multidimensionalvectorspace(MVS)proceduretotakeaccountofpossibleconvergentevolution.Numericalsimulationsof abrupt rate change and convergent evolution showed good performance of the new procedures in contrast to current methods.Applicationtocompletemitochondrialgenomesidentifiedmarkedrateaccelerationsanddecelerations,whichare notobtainedwithcurrentmethods. Therootofplacentalmammalsisestimatedtobe ,18millionyearsmorerecent than whenassumingalogBrownianmotionmodel.CorrectingthepairwisedistancesforconvergentevolutionusingMVSlowers theageoftherootaboutanother20millionyearscomparedtousingstandardmaximumlikelihoodtreebranchlengths.These twoprocedurescombinedrevisetheroottimeofplacentalmammalsfromaround122millionyearsagotocloseto84million yearsago.Asaresult,theestimateddistributionofmoleculardivergencetimesisbroadlyconsistentwithquantitativeanalysis of the North American fossil recordand traditional morphological views. Conclusions/Significance. By including the du