Institut de Mathématiques de Toulouse, Université de Toulouse, Institut National des Sciences Appliquées, 31077, Toulouse, France.
Facultad de Matemática y Computación, Universidad de La Habana, La Havana, Cuba.
Heredity (Edinb). 2018 Dec;121(6):663-678. doi: 10.1038/s41437-018-0148-0. Epub 2018 Oct 7.
In the last years, a wide range of methods allowing to reconstruct past population size changes from genome-wide data have been developed. At the same time, there has been an increasing recognition that population structure can generate genetic data similar to those produced under models of population size change. Recently, Mazet et al. (Heredity 116:362-371, 2016) showed that, for any model of population structure, it is always possible to find a panmictic model with a particular function of population size changes, having exactly the same distribution of T (the coalescence time for a sample of size two) as that of the structured model. They called this function IICR (Inverse Instantaneous Coalescence Rate) and showed that it does not necessarily correspond to population size changes under non-panmictic models. Besides, most of the methods used to analyse data under models of population structure tend to arbitrarily fix that structure and to minimise or neglect population size changes. Here, we extend the seminal work of Herbots (PhD thesis, University of London, 1994) on the structured coalescent and propose a new framework, the Non-Stationary Structured Coalescent (NSSC) that incorporates demographic events (changes in gene flow and/or deme sizes) to models of nearly any complexity. We show how to compute the IICR under a wide family of stationary and non-stationary models. As an example we address the question of human and Neanderthal evolution and discuss how the NSSC framework allows to interpret genomic data under this new perspective.
在过去的几年中，已经开发出了广泛的方法，可以从全基因组数据中重建过去的种群大小变化。与此同时，人们越来越认识到，种群结构可以产生类似于种群大小变化模型产生的遗传数据。最近，Mazet 等人（Heredity 116:362-371, 2016）表明，对于任何种群结构模型，总是可以找到一个具有特定种群大小变化函数的混合模型，其合并时间（两个样本的合并时间）的分布与结构模型完全相同。他们将此函数称为 IICR（Inverse Instantaneous Coalescence Rate），并表明它不一定对应于非混合模型下的种群大小变化。此外，用于分析种群结构模型下数据的大多数方法往往任意固定该结构，并最小化或忽略种群大小变化。在这里，我们扩展了 Herbots（伦敦大学博士论文，1994 年）关于结构合并的开创性工作，并提出了一个新的框架，即非平稳结构合并（NSSC），该框架将人口流动和/或种群大小变化等人口统计学事件纳入几乎任何复杂程度的模型中。我们展示了如何在广泛的稳态和非稳态模型族下计算 IICR。作为一个例子，我们解决了人类和尼安德特人进化的问题，并讨论了 NSSC 框架如何允许从这个新的角度解释基因组数据。
