AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France.
Heredity (Edinb). 2019 Aug;123(2):176-191. doi: 10.1038/s41437-019-0182-6. Epub 2019 Jan 22.
Predominantly selfing populations are expected to have reduced effective population sizes due to nonrandom sampling of gametes, demographic stochasticity (bottlenecks or extinction-recolonization), and large scale hitchhiking (reduced effective recombination). Thus, they are expected to display low genetic diversity, which was confirmed by empirical studies. The structure of genetic diversity in predominantly selfing species is dramatically different from outcrossing ones, with populations often dominated by one or a few multilocus genotypes (MLGs) coexisting with several rare genotypes. Therefore, multilocus diversity indices are relevant to describe diversity in selfing populations. Here, we use simulations to provide analytical expectations for multilocus indices and examine whether selfing alone can be responsible for the high-frequency MLGs persistent through time in the absence of selection. We then examine how combining single and multilocus indices of diversity may be insightful to distinguish the effects of selfing, population size, and more complex demographic events (bottlenecks, migration, admixture, or extinction-recolonization). Finally, we examine how temporal changes in MLG frequencies can be insightful to understand the evolutionary trajectory of a given population. We show that combinations of selfing and small demographic sizes can result in high-frequency MLGs, as observed in natural populations. We also show how different demographic scenarios can be distinguished by the parallel analysis of single and multilocus indices of diversity, and we emphasize the importance of temporal data for the study of predominantly selfing populations. Finally, the comparison of our simulations with empirical data on populations of Medicago truncatula confirms the pertinence of our simulation framework.
自交为主的种群由于配子的非随机抽样、种群数量的随机波动（瓶颈或灭绝-再定居）和大规模的 hitchhiking（有效重组减少），预计其有效种群规模会减小。因此，它们的遗传多样性预计会较低，这一点已被实证研究证实。自交为主的物种的遗传多样性结构与异交物种显著不同，种群通常由一个或少数几个多基因座基因型（MLG）主导，同时存在几个罕见的基因型。因此，多基因座多样性指数与描述自交种群的多样性有关。在这里，我们使用模拟来提供多基因座指数的分析预期，并检验在没有选择的情况下，自交本身是否可以解释高频 MLG 随着时间的推移持续存在的原因。然后，我们研究了如何结合单基因座和多基因座多样性指数可以有助于区分自交、种群大小以及更复杂的种群动态事件（瓶颈、迁移、混合或灭绝-再定居）的影响。最后，我们研究了 MLG 频率的时间变化如何有助于理解给定种群的进化轨迹。我们表明，自交和小种群大小的组合可能导致高频 MLG，就像在自然种群中观察到的那样。我们还展示了如何通过对单基因座和多基因座多样性指数的平行分析来区分不同的种群动态场景，并强调了时间数据对于研究自交为主的种群的重要性。最后，将我们的模拟结果与 Medicago truncatula 种群的实证数据进行比较，证实了我们的模拟框架的相关性。
