Abstract
We are writing in response to a recent critique by Emerson & Hickerson ( ), 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 ( ) 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.