Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada.
J Mol Evol. 2018 Feb;86(2):118-137. doi: 10.1007/s00239-018-9831-2. Epub 2018 Feb 10.
During the past 50 years, the molecular clock has become one of the main tools for providing a time scale for the history of life. In the era of robust molecular evolutionary analysis, clock calibration is still one of the most basic steps needing attention. When fossil records are limited, well-dated geological events are the main resource for calibration. However, biogeographic calibrations have often been used in a simplistic manner, for example assuming simultaneous vicariant divergence of multiple sister lineages. Here, we propose a novel iterative calibration approach to define the most appropriate calibration date by seeking congruence between the dates assigned to multiple allopatric divergences and the geological history. Exploring patterns of molecular divergence in 16 trans-Bering sister clades of echinoderms, we demonstrate that the iterative calibration is predominantly advantageous when using complex geological or climatological events-such as the opening/reclosure of the Bering Strait-providing a powerful tool for clock dating that can be applied to other biogeographic calibration systems and further taxa. Using Bayesian analysis, we observed that evolutionary rate variability in the COI-5P gene is generally distributed in a clock-like fashion for Northern echinoderms. The results reveal a large range of genetic divergences, consistent with multiple pulses of trans-Bering migrations. A resulting rate of 2.8% pairwise Kimura-2-parameter sequence divergence per million years is suggested for the COI-5P gene in Northern echinoderms. Given that molecular rates may vary across latitudes and taxa, this study provides a new context for dating the evolutionary history of Arctic marine life.
在过去的 50 年里，分子钟已成为提供生命史时间尺度的主要工具之一。在稳健的分子进化分析时代，钟校准仍然是最需要注意的基本步骤之一。当化石记录有限时，经过良好标定的地质事件是校准的主要资源。然而，生物地理校准经常被简单地使用，例如假设多个姐妹谱系的同时分歧。在这里，我们提出了一种新的迭代校准方法，通过寻求分配给多个异域分歧的日期与地质历史之间的一致性来定义最合适的校准日期。通过探索棘皮动物 16 个跨白令海峡姐妹群的分子分歧模式，我们证明，当使用复杂的地质或气候事件（例如白令海峡的开放/关闭）时，迭代校准主要是有利的，为时钟定年提供了一种强大的工具，可应用于其他生物地理校准系统和进一步的分类群。使用贝叶斯分析，我们观察到 COI-5P 基因中的进化率变异性通常以类似钟的方式分布在北方棘皮动物中。结果揭示了广泛的遗传分歧，与多次穿越白令海峡的迁徙一致。建议北方棘皮动物 COI-5P 基因的 K2P 序列分歧率为每百万年 2.8%。鉴于分子速率可能在纬度和分类群之间变化，本研究为北极海洋生物进化史的定年提供了新的背景。
