Université de Toulouse, Institut National des Sciences Appliquées, Institut de Mathématiques de Toulouse, Toulouse, France.
Institut de Mathématiques de Toulouse; UMR5219. Université de Toulouse, Toulouse, France.
Heredity (Edinb). 2021 Jun;126(6):896-912. doi: 10.1038/s41437-021-00426-9. Epub 2021 Apr 12.
Inferring the demographic history of species is one of the greatest challenges in populations genetics. This history is often represented as a history of size changes, ignoring population structure. Alternatively, when structure is assumed, it is defined a priori as a population tree and not inferred. Here we propose a framework based on the IICR (Inverse Instantaneous Coalescence Rate). The IICR can be estimated for a single diploid individual using the PSMC method of Li and Durbin (2011). For an isolated panmictic population, the IICR matches the population size history, and this is how the PSMC outputs are generally interpreted. However, it is increasingly acknowledged that the IICR is a function of the demographic model and sampling scheme with limited connection to population size changes. Our method fits observed IICR curves of diploid individuals with IICR curves obtained under piecewise stationary symmetrical island models. In our models we assume a fixed number of time periods during which gene flow is constant, but gene flow is allowed to change between time periods. We infer the number of islands, their sizes, the periods at which connectivity changes and the corresponding rates of connectivity. Validation with simulated data showed that the method can accurately recover most of the scenario parameters. Our application to a set of five human PSMCs yielded demographic histories that are in agreement with previous studies using similar methods and with recent research suggesting ancient human structure. They are in contrast with the view of human evolution consisting of one ancestral population branching into three large continental and panmictic populations with varying degrees of connectivity and no population structure within each continent.
推断物种的人口历史是群体遗传学中最大的挑战之一。这个历史通常被表示为大小变化的历史，忽略了种群结构。或者，当假设结构时，它被预先定义为种群树，而不是推断出来。在这里，我们提出了一个基于 IICR（反向瞬时合并率）的框架。可以使用 Li 和 Durbin（2011）的 PSMC 方法，为单个二倍体个体估计 IICR。对于一个孤立的混合种群，IICR 与种群大小历史相匹配，这就是 PSMC 输出通常的解释方式。然而，越来越多的人认识到，IICR 是人口模型和抽样方案的函数，与种群大小变化的联系有限。我们的方法拟合了二倍体个体的观测 IICR 曲线与分段平稳对称岛屿模型下获得的 IICR 曲线。在我们的模型中，我们假设在基因流动恒定的固定时间段内有一个固定数量的时间段，但允许在时间段之间改变基因流动。我们推断出岛屿的数量、大小、连通性变化的时间段以及相应的连通性变化率。模拟数据的验证表明，该方法可以准确地恢复大多数场景参数。我们将该方法应用于五个人类 PSMC，得出的人口历史与使用类似方法的先前研究以及最近的研究结果一致，这些研究结果表明了古代人类的结构。这与人类进化的观点形成了鲜明的对比，后者认为人类进化是由一个祖先种群分支为三个大型大陆和混合种群，其连通性程度不同，每个大陆内部没有种群结构。
