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 two 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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了解复杂历史产生的物种边界：斑点鞭尾蜥蜴物种形成连续体的基因流


不同谱系之间的基因流动挑战了物种边界的解析以及对最近辐射中进化历史的理解。在这里，我们整合系统发育和合并工具来解决多样化的网状模式，并使用专注于进化机制的视角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类群之一的系统学问题：Aspidoscelis 属的斑点鞭尾蜥蜴（A. gularis 复合体）。鞭尾鱼包含所有脊椎动物中已知数量最多的单性物种，而斑点鞭尾鱼复合体在通过杂交物种形成产生这种多样性方面发挥了关键作用。因此，了解谱系边界以及该群体内分歧和网状的进化历史是了解鞭尾鱼单性多样性产生的关键。尽管如此重要，但长期以来对其系统学的困惑阻碍了对哪些雌雄异体物种促成了单性谱系的形成的理解。使用简化的代表性基因组数据，我们解决了斑点鞭尾鱼内的分歧和基因流模式，并阐明了杂交物种形成的模式。我们发现的证据表明，生物地理结构的生态和环境变异对于形态和遗传多样化以及该系统中物种边界的维护非常重要。 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如何使物种界定的实践产生偏差，并导致在不同框架下工作的分类学家得出不同的结论（在这里，我们提出两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以及系统生物学领域长期存在的分类学挑战的方法提供了概念和方法论见解。