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. The resulting CDT rates of molecular evolution also confirm rate heterogeneity over time and among taxa. Comparisons of expansion dates with ecological evidence confirm the inaccuracy of phylogenetically derived divergence rates when dating population-level events. The CDT method opens opportunities for addressing issues such as demographic responses to past climate change and the origin of rate heterogeneity related to taxa, genes, time and genetic information content.分子钟假说（molecular clock hypothesis）是进化生物学的核心理论之一，其通过假定分子进化速率恒定，为进化过程构建了时间框架。然而，越来越多的研究证据表明，推断得到的分子进化速率存在时间依赖性：利用近期校准方案得到的速率值往往偏高。由于多数物种几乎不存在近期的种群校准数据，研究人员通常会使用距今超过1 Ma的古老系统发育校准点，而这类校准点会高估种群参数。为获取适用于种群研究的更可靠分子进化速率，本文提出了种群转变校准法（Calibration of Demographic Transition, CDT）：该方法依托末次冰期暖期的气候变化时间节点，对不同物种的种群扩张事件进行校准。通过模拟实验与涵盖从软体动物到人类等多样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方法能够为种群遗传学研究提供稳健且普适性强的分子钟。基于CDT方法得到的分子进化速率同样证实了进化速率在时间维度与不同类群间存在异质性。将种群扩张时间与生态学证据进行对比后发现，利用系统发育方法得到的分化速率在推断种群水平事件的发生时间时准确性不足。CDT方法为解决诸多科学问题提供了新的契机，例如探究物种对过去气候变化的种群响应、解析与类群、基因、时间及遗传信息含量相关的速率异质性起源等。

搜集汇总

背景与挑战

背景概述

该数据集提出了一种名为“人口统计过渡校准”（CDT）的新方法，用于校准种群遗传学中的分子时钟，基于晚更新世气候变暖时期的时间框架来估计物种扩张事件。它通过模拟和多种物种（从软体动物到人类）的实证数据验证了该方法的稳健性和广泛适用性，并揭示了分子进化速率在时间和类群间的异质性，从而为研究过去气候变化的种群响应和速率异质性提供了新工具。