—Gene flow between diverging lineages challenges the resolution of species boundaries and the understanding of evolutionary history in recent radiations. Here, we integrate phylogenetic and coalescent tools to resolve reticulate patterns of diversification and use a perspective focused on evolutionary mechanisms to distinguish interspecific and intraspecific taxonomic variation. We use this approach to resolve the systematics for one of the most intensively studied but difficult to understand groups of reptiles: the spotted whiptail lizards of the genus Aspidoscelis (A. gularis complex). Whiptails contain the largest number of unisexual species known within any vertebrate group and the spotted whiptail complex has played a key role in the generation of this diversity through hybrid speciation. Understanding lineage boundaries and the evolutionary history of divergence and reticulation within this group is therefore key to understanding the generation of unisexual diversity in whiptails. Despite this importance, long-standing confusion about their systematics has impeded understanding of which gonochoristic species have contributed to the formation of unisexual lineages. Using reduced representation genomic data, we resolve patterns of divergence and gene flow within the spotted whiptails and clarify patterns of hybrid speciation. We find evidence that biogeographically structured ecological and environmental variation has been important in morphological and genetic diversification, as well as the maintenance of species boundaries in this system. Our study elucidates how gene flow among lineages and the continuous nature of speciation can bias the practice of species delimitation and lead taxonomists operating under different frameworks to different conclusions (here we propose that a 2 species arrangement best reflects our current understanding). In doing so, this study provides conceptual and methodological insights into approaches to resolving diversification patterns and species boundaries in rapid radiations with complex histories, as well as long-standing taxonomic challenges in the field of systematic biology.

中文翻译：

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了解复杂历史中出现的物种边界：斑点鞭尾蜥蜴物种形成连续体的基因流动


—不同谱系之间的基因流动挑战了物种边界的解析和对近期辐射中进化历史的理解。在这里，我们整合了系统发育和聚结工具来解决多样化的网状模式，并使用专注于进化机制的观点来区分种间和种内分类变异。我们使用这种方法来解决研究最深入但难以理解的爬行动物群之一的系统学：Aspidoscelis 属的斑点鞭尾蜥蜴 （A. gularis complex）。鞭尾鞭尾包含任何脊椎动物群中已知数量最多的单性物种，而斑点鞭尾复合体在通过杂交物种形成产生这种多样性中发挥了关键作用。因此，了解该群体内的谱系边界以及分化和网状的进化历史是理解鞭尾鱼单性多样性产生的关键。尽管如此重要，但长期以来对它们的系统学的混淆阻碍了对哪些性腺物种有助于单性谱系的形成的理解。使用减少代表性的基因组数据，我们解析了斑点鞭尾内的分化和基因流动模式，并阐明了杂交物种形成的模式。我们发现证据表明，生物地理结构的生态和环境变异在形态和遗传多样化以及维持该系统中的物种边界方面很重要。 我们的研究阐明了谱系之间的基因流动和物种形成的连续性质如何使物种划定的做法产生偏差，并导致在不同框架下操作的分类学家得出不同的结论（在这里，我们提出 2 个物种的排列最能反映我们目前的理解）。在此过程中，本研究为解决具有复杂历史的快速辐射中的多样化模式和物种边界的方法以及系统生物学领域长期存在的分类学挑战提供了概念和方法论见解。