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首页> 外文期刊>PLoS Genetics >Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data
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Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data

机译：从全基因组重测序数据推算出的捕蝇器和领捕蝇器的人口差异历史

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Profound knowledge of demographic history is a prerequisite for the understanding and inference of processes involved in the evolution of population differentiation and speciation. Together with new coalescent-based methods, the recent availability of genome-wide data enables investigation of differentiation and divergence processes at unprecedented depth. We combined two powerful approaches, full Approximate Bayesian Computation analysis (ABC) and pairwise sequentially Markovian coalescent modeling (PSMC), to reconstruct the demographic history of the split between two avian speciation model species, the pied flycatcher and collared flycatcher. Using whole-genome re-sequencing data from 20 individuals, we investigated 15 demographic models including different levels and patterns of gene flow, and changes in effective population size over time. ABC provided high support for recent (mode 0.3 my, range <0.7 my) species divergence, declines in effective population size of both species since their initial divergence, and unidirectional recent gene flow from pied flycatcher into collared flycatcher. The estimated divergence time and population size changes, supported by PSMC results, suggest that the ancestral species persisted through one of the glacial periods of middle Pleistocene and then split into two large populations that first increased in size before going through severe bottlenecks and expanding into their current ranges. Secondary contact appears to have been established after the last glacial maximum. The severity of the bottlenecks at the last glacial maximum is indicated by the discrepancy between current effective population sizes (20,000–80,000) and census sizes (5–50 million birds) of the two species. The recent divergence time challenges the supposition that avian speciation is a relatively slow process with extended times for intrinsic postzygotic reproductive barriers to evolve. Our study emphasizes the importance of using genome-wide data to unravel tangled demographic histories. Moreover, it constitutes one of the first examples of the inference of divergence history from genome-wide data in non-model species. Author Summary Demographic processes leave specific and detectable signatures within species genomes. Analysis of patterns of variation within and between closely related species can be used to unravel their divergence history and is crucial for understanding evolutionary processes such as speciation. We applied a set of novel population-genomic tools to investigate patterns of natural variation and infer demographic history of two avian speciation model species: pied flycatcher and collared flycatcher. The analysis supported a scenario consistent with allopatric speciation with recent, postglacial secondary contact. Most likely the ancestral species persisted through one of the glacial periods of the middle Pleistocene and then split into two large descendent populations that appear to have increased in size before experiencing severe bottlenecks during expansion into their current ranges. The two species established secondary contact after the last glacial maximum. This resulted in unidirectional gene flow from pied flycatcher to collared flycatcher. The results are consistent with a scenario where pied flycatcher recolonized northern Europe more rapidly than collared flycatcher. Our study increases the knowledge about the dynamics of the speciation process and constitutes one of the first examples of the inference of complex demographic history using information from genome-wide data in non-model species.
机译：对人口历史的深刻了解是了解和推断与人口分化和物种形成有关的过程的先决条件。与基于聚结的新方法一起，最近可获得的全基因组数据使得能够以前所未有的深度研究分化和发散过程。我们结合了两种强大的方法，即完整的近似贝叶斯计算分析（ABC）和成对的顺序马尔可夫聚结建模（PSMC），以重构两个鸟类物种形成模型物种（斑驳的捕蝇器和领捕蝇器）之间的人口统计学历史。使用来自20个个体的全基因组重新测序数据，我们研究了15种人口统计学模型，包括不同水平和模式的基因流以及有效人群数量随时间的变化。 ABC为最近（模式0.3 my，范围<0.7 my）物种的分化，两个物种自初始分化以来两个物种的有效种群数量的减少以及最近的单向基因捕获（从斑捕蝇器到圈状捕蝇器）的单向提供了高支持。在PSMC结果的支持下，估计的发散时间和种群大小变化表明，祖先物种在中更新世中的一个冰川期持续存在，然后分裂为两个大种群，这些种群的大小先增加，然后经历严重的瓶颈并扩展为它们的种群。当前范围。上次冰期最大值之后似乎建立了辅助接触。这两个物种目前的有效种群数量（20,000–80,000）与人口普查规模（5–5,000万只鸟）之间的差异表明了最后一次冰川最大期的瓶颈严重程度。最近的分歧时间对以下假设提出了挑战，即鸟类物种形成是一个相对缓慢的过程，内在的合子后生殖障碍的进化时间延长。我们的研究强调了使用全基因组数据解开混杂的人口历史的重要性。此外，它是从非模型物种的全基因组数据中推论历史差异的第一个例子。作者摘要人口统计过程在物种基因组内留下了特定且可检测的特征。对密切相关物种内部和之间的变异模式的分析可用于揭示其发散历史，对于理解物种形成等进化过程至关重要。我们应用了一套新颖的种群基因组学工具来调查自然变异的模式并推断两个鸟类物种形成模型物种：斑pie捕蝇器和领捕蝇器的人口统计历史。分析支持一种与最近发生的冰川后次生接触的异相物种形成一致的情况。祖先物种最有可能在整个中更新世的一个冰川期中持续存在，然后分裂为两个大型后代种群，这些种群的大小似乎有所增加，然后在扩展到当前范围时遇到了严重的瓶颈。这两个物种在最后一次冰期结束后建立了第二次接触。这导致单方向的基因流从斑pie捕蝇器转移到领捕蝇器。该结果与一种情形是一致的，即pie式捕蝇器比领捕蝇器更快地重新定居了北欧。我们的研究增加了有关物种形成过程动力学的知识，并使用非模型物种中全基因组数据的信息，构成了复杂的人口历史推断的第一个例子。

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