Nene Data Setnene_mt.const.xmlBison Data Setbison.bsp.xmlCave Bear Data Setcavebear.const.xmlBrown Bear Data Setbrownbear.const.xmlBowhead Whale Data Setbowheadwhale.const.xmlCave Lion Data Setcavelion.const.xmlCow Data Setcow.bsp.xmlCave Hyaena Data Setcavehyaena.bsp.xmlMuskox Data Setmuskox.const.xmlMaize Data Setmaize.const.xmlTuco-Tuco Data Settucotuco.const.xmlHorse Data Sethorse.expon.xmlWoolly Mammoth Data Setwoollymammoth.const.xmlArctic Fox Data SetBEAST input files for ancient DNA data sets. Substitution models were selected by comparison of Akaike Information Criterion scores, and coalescent priors were chosen using Bayes Factor analysis.arcticfox.const.xmlAdelie Penguin Data SetBEAST input files for ancient DNA data sets. Substitution models were selected by comparison of Akaike Information Criterion scores, and coalescent priors were chosen using Bayes Factor analysis.adeliepenguin.const.xmlChlorobium Data Setchlorobium.expon.xmlData Sets and Population Genetic StatisticsSummary and neutrality statistics, model abbreviations, and data sources.rsbl20070377supp1.docBoar Data Setboar.const.xmlMoa Data Setmoa.const.xmlAurochs Data SetBEAST input files for ancient DNA data sets. Substitution models were selected by comparison of Akaike Information Criterion scores, and coalescent priors were chosen using Bayes Factor analysis.aurochs.bsp.xml

Ancient DNA sequences are able to offer valuable insights into molecular evolutionary processes, which are not directly accessible via modern DNA. They are particularly suitable for the estimation of substitution rates because their ages provide calibrating information in phylogenetic analyses, circumventing the difficult task of choosing independent calibration points. The substitution rates obtained from such datasets have typically been high, falling between the rates estimated from pedigrees and species phylogenies. Many of these estimates have been made using a Bayesian phylogenetic method that explicitly accommodates heterochronous data. Stimulated by recent criticism of this method, we present a comprehensive simulation study that validates its performance. For datasets of moderate si ze, i t produces accurate estimates of rates, while appearing robust to assumpti ons about demographic history. We then analyse a large collection of 749 ancient and 727 modern DNA sequences from 19 species of animals, plants and bacteria. Our new estimates confirm that the substitution rates estimated from ancient DNA sequences are elevated above long-term phylogenetic levels.