Time-dependent rates of molecular evolution

Authors

  • SIMON Y. W. HO,

    1. Centre for Macroevolution and Macroecology, Evolution Ecology & Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia
    2. School of Biological Sciences, Edgeworth David Building A11, University of Sydney, Sydney, NSW, Australia
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  • ROBERT LANFEAR,

    1. Centre for Macroevolution and Macroecology, Evolution Ecology & Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia
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  • LINDELL BROMHAM,

    1. Centre for Macroevolution and Macroecology, Evolution Ecology & Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia
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  • MATTHEW J. PHILLIPS,

    1. Centre for Macroevolution and Macroecology, Evolution Ecology & Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia
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    • Present address: Biogeosciences, Queensland University of Technology, Brisbane, Qld, Australia.

  • JULIEN SOUBRIER,

    1. Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, University of Adelaide, Adelaide, SA, Australia
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  • ALLEN G. RODRIGO,

    1. Department of Biology, Duke University, Durham, NC, USA
    2. Bioinformatics Institute and School of Biological Sciences, University of Auckland, Auckland, New Zealand
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  • ALAN COOPER

    1. Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, University of Adelaide, Adelaide, SA, Australia
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Simon Y. W. Ho, Fax: +61 2 91140979; E-mail: simon.ho@sydney.edu.au

Abstract

For over half a century, it has been known that the rate of morphological evolution appears to vary with the time frame of measurement. Rates of microevolutionary change, measured between successive generations, were found to be far higher than rates of macroevolutionary change inferred from the fossil record. More recently, it has been suggested that rates of molecular evolution are also time dependent, with the estimated rate depending on the timescale of measurement. This followed surprising observations that estimates of mutation rates, obtained in studies of pedigrees and laboratory mutation-accumulation lines, exceeded long-term substitution rates by an order of magnitude or more. Although a range of studies have provided evidence for such a pattern, the hypothesis remains relatively contentious. Furthermore, there is ongoing discussion about the factors that can cause molecular rate estimates to be dependent on time. Here we present an overview of our current understanding of time-dependent rates. We provide a summary of the evidence for time-dependent rates in animals, bacteria and viruses. We review the various biological and methodological factors that can cause rates to be time dependent, including the effects of natural selection, calibration errors, model misspecification and other artefacts. We also describe the challenges in calibrating estimates of molecular rates, particularly on the intermediate timescales that are critical for an accurate characterization of time-dependent rates. This has important consequences for the use of molecular-clock methods to estimate timescales of recent evolutionary events.

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