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Time‐dependent estimates of molecular evolutionary rates: evidence and causes
Author(s) -
Ho Simon Y. W.,
Duchêne Sebastián,
Molak Martyna,
Shapiro Beth
Publication year - 2015
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1111/mec.13450
Subject(s) - biology , range (aeronautics) , reliability (semiconductor) , estimation , evolutionary biology , taxon , econometrics , statistics , ecology , mathematics , economics , management , quantum mechanics , composite material , power (physics) , physics , materials science
We are writing in response to a recent critique by Emerson & Hickerson ([Emerson BC, 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 ([Emerson BC, 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.