Complex speciation, involving rapid divergence and multiple bouts of post-divergence gene flow, can obfuscate phylogenetic relationships and species limits. In North America, cases of complex speciation are common, due at least in part to the cyclical Pleistocene glacial history of the continent. Scrub-jays in the genus Aphelocoma provide a useful case study in complex speciation because their range throughout North America is structured by phylogeographic barriers with multiple cases of secondary contact between divergent lineages. Here, we show that a comprehensive approach to genomic reconstruction of evolutionary history, i.e., synthesizing results from species delimitation, species tree reconstruction, demographic model testing, and tests for gene flow, is capable of clarifying evolutionary history despite complex speciation. We find concordant evidence across all statistical approaches for the distinctiveness of an endemic southern Mexico lineage (A. w. sumichrasti), culminating in support for the species status of this lineage under any commonly applied species concept. We also find novel genomic evidence for the species status of a Texas endemic lineage A. w. texana, for which equivocal species delimitation results were clarified by demographic modeling and spatially explicit models of gene flow. Finally, we find that complex signatures of both ancient and modern gene flow between the non-sister California Scrub-Jay (A. californica) and Woodhouse’s Scrub-Jay (A. woodhouseii), result in discordant gene trees throughout the species’ genomes despite clear support for their overall isolation and species status. In sum, we find that a multi-faceted approach to genomic analysis can increase our understanding of complex speciation histories, even in well-studied groups. Given the emerging recognition that complex speciation is relatively commonplace, the comprehensive framework that we demonstrate for interrogation of species limits and evolutionary history using genomic data can provide a necessary roadmap for disentangling the impacts of gene flow and incomplete lineage sorting to better understand the systematics of other groups with similarly complex evolutionary histories.

中文翻译：

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将物种界定、物种树和基因流测试相结合，可以阐明 Scrub-Jays 中的复杂物种形成

复杂的物种形成，涉及快速分歧和分歧后基因流的多次发作，可以混淆系统发育关系和物种限制。在北美，复杂物种形成的情况很常见，至少部分是由于该大陆的周期性更新世冰川历史。Aphelocoma 属的 Scrub-jays 为复杂物种形成提供了一个有用的案例研究，因为它们在整个北美的范围是由系统地理障碍构成的，在不同的谱系之间存在多个二次接触的案例。在这里，我们展示了进化历史基因组重建的综合方法，即综合物种界定、物种树重建、人口模型测试和基因流测试的结果，能够阐明进化历史，尽管存在复杂的物种形成。我们在所有统计方法中找到了一致的证据来证明墨西哥南部特有谱系 (A. w. sumichrasti) 的独特性，最终在任何常用的物种概念下支持该谱系的物种状态。我们还发现了德克萨斯地方性血统 A. w. 物种状况的新基因组证据。德克萨斯州，通过人口统计模型和基因流的空间显式模型澄清了模棱两可的物种划界结果。最后，我们发现在非姐妹加利福尼亚 Scrub-Jay (A. californica) 和 Woodhouse's Scrub-Jay (A. woodhouseii) 之间的古代和现代基因流动的复杂特征导致整个物种基因组中的基因树不一致，尽管明确支持它们的整体隔离和物种状态。总共，我们发现，基因组分析的多方面方法可以增加我们对复杂物种形成历史的理解，即使在经过充分研究的群体中也是如此。鉴于人们逐渐认识到复杂物种形成相对普遍，我们展示的使用基因组数据询问物种限制和进化历史的综合框架可以提供必要的路线图，用于解开基因流和不完整谱系分类的影响，以更好地理解其他具有类似复杂进化历史的群体。