Abstract
Evolutionary timescales can be estimated from genetic data using the molecular clock, often calibrated by fossil or geological evidence. However, estimates of molecular rates in mitochondrial DNA appear to scale negatively with the age of the clock calibration. Although such a pattern has been observed in a limited range of data sets, it has not been studied on a large scale in metazoans. In addition, there is uncertainty over the temporal extent of the time-dependent pattern in rate estimates. Here we present a meta-analysis of 239 rate estimates from metazoans, representing a range of timescales and taxonomic groups. We found evidence of time-dependent rates in both coding and non-coding mitochondrial markers, in every group of animals that we studied. The negative relationship between the estimated rate and time persisted across a much wider range of calibration times than previously suggested. This indicates that, over long time frames, purifying selection gives way to mutational saturation as the main driver of time-dependent biases in rate estimates. The results of our study stress the importance of accounting for time-dependent biases in estimating mitochondrial rates regardless of the timescale over which they are inferred.
Highlights
Understanding the tempo and mode of the molecular evolutionary process is one of the fundamental goals of biological research
Our analyses demonstrate a consistent pattern of time-dependent biases in rate estimates in mitochondrial DNA across metazoan taxa
Our finding of a prolonged decay in molecular rate estimates is consistent with recent evidence from a large-scale analysis of substitution rates in viruses, which revealed a time-dependent bias in rate estimates across a temporal scale spanning 10 orders of magnitude (Duchene, Holmes & Ho, 2014)
Summary
Understanding the tempo and mode of the molecular evolutionary process is one of the fundamental goals of biological research. Molecular estimates of evolutionary timescales are made using the molecular clock, which assumes that DNA evolves at a constant rate among lineages (Zuckerkandl & Pauling, 1962). With improving knowledge of the evolutionary process, molecularclock methods have undergone considerable development over the past five decades (Ho, 2014; Kumar, 2005), with various forms of rate variation being able to be taken into account (Ho & Duchene, 2014). To estimate evolutionary rates from DNA sequence data, molecular clocks need to be calibrated. This involves using independent information to constrain the age of one or
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