Ho Simon Y W, Duchêne Sebastián, Molak Martyna, Shapiro Beth
School of Biological Sciences, University of Sydney, Sydney, NSW, Australia.
Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland.
Mol Ecol. 2015 Dec;24(24):6007-12. doi: 10.1111/mec.13450.
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.
我们撰写此文章是为了回应艾默生和希克森（2015年）最近的一篇评论，他们对分子速率估计中时间依赖性偏差的证据提出了质疑。这种偏差表现为推断的进化速率与这些估计所基于的校准年龄之间呈负相关关系。在此，我们总结了从广泛的分类群中获得的证据，这些证据支持速率估计中存在时间依赖性偏差，并考虑了这些观察到的趋势的潜在原因。我们还描述了在提高进化速率估计可靠性方面的最新进展，并回应了艾默生和希克森（2015年）对从时间结构序列数据估计的速率的有效性所提出的担忧。通过这样做，我们希望消除一些误解，并突出几个研究方向，这些方向将增进我们对速率估计中时间依赖性偏差的理解。
