Late-glacial demographic expansion motivates a clock overhaul for population genetics

The molecular clock hypothesis is fundamental in evolutionary biology as by assuming constancy of the molecular rate it provides a time frame for evolution. However, increasing evidence shows time dependence of inferred molecular rates with inflated values obtained using recent calibrations. As recent demographic calibrations are virtually non-existent in most species, older phylogenetic calibration points (>1 Ma) are commonly used, which overestimate demographic parameters. To obtain more reliable rates of molecular evolution for population studies, I propose the Calibration of Demographic Transition (CDT) method, which uses the timing of climatic changes over the late glacial warming period to calibrate expansions in various species. Simulation approaches and empirical datasets from a diversity of species (from mollusk to humans) confirm that, when compared to other genealogy-based calibration methods, the CDT provides a robust and broadly applicable clock for population genetics. ...分子钟假说（molecular clock hypothesis）是进化生物学的核心理论之一：通过假定分子进化速率恒定，该假说为进化过程搭建了时间框架。然而，越来越多的研究证据表明，推断得到的分子进化速率具有时间依赖性——使用近期校准得到的速率往往存在高估情况。由于多数物种几乎不存在近期的种群统计学校准数据，学界通常采用距今较久的系统发育校准点（>1 Ma），但这类校准点会高估种群统计学参数。为了获得种群研究中更可靠的分子进化速率，本文提出了种群转变校准（Calibration of Demographic Transition, CDT）方法，该方法利用末次冰期晚期暖期的气候变化时间节点，对不同物种类群的种群扩张事件进行校准。通过模拟实验与涵盖软体动物至人类等多样物种类群的实证数据集验证，相较于其他基于谱系的校准方法，CDT方法可为种群遗传学研究提供稳健且普适性极强的分子钟工具。