title: Time-dependent estimates of molecular evolutionary rates: evidence and causes.
abstract: We are writing in response to a recent critique by Emerson & Hickerson (2015), who challenge the evidence of a time-dependent bias in molecular rate estimates. This bias takes the form of a negative relationship between inferred evolutionary rates and the ages of the calibrations on which these estimates are based. Here, we present a summary of the evidence obtained from a broad range of taxa that supports a time-dependent bias in rate estimates, with a consideration of the potential causes of these observed trends. We also describe recent progress in improving the reliability of evolutionary rate estimation and respond to the concerns raised by Emerson & Hickerson (2015) about the validity of rates estimated from time-structured sequence data. In doing so, we hope to dispel some misconceptions and to highlight several research directions that will improve our understanding of time-dependent biases in rate estimates.
authors.affiliation: School of Biological Sciences, University of Sydney, Sydney, NSW, Australia.
authors.forename: Simon Y W
authors.initials: SY
authors.lastname: Ho
authors.affiliation: School of Biological Sciences, University of Sydney, Sydney, NSW, Australia.
authors.forename: Sebastián
authors.initials: S
authors.lastname: Duchêne
authors.affiliation: Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland.
authors.forename: Martyna
authors.initials: M
authors.lastname: Molak
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, USA.|UCSC Genomics Institute, University of California, Santa Cruz, California, USA.
authors.forename: Beth
authors.initials: B
authors.lastname: Shapiro
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D006801:Humans; D008957:Models, Genetic; D059645:Mutation Rate
keywords: Bayesian phylogenetics; ancient DNA; calibration; mutation rate; pedigree; substitution rate