Data from: Population genomic evidence for multiple Pliocene refugia in a montane-restricted harvestman (Arachnida, Opiliones, Sclerobunus robustus) from the southwestern United States

The integration of ecological niche modeling into phylogeographic analyses has allowed for the identification and testing of potential refugia under a hypothesis-based framework, where the expected patterns of higher genetic diversity in refugial populations and evidence of range expansion of non refugial populations are corroborated with empirical data. In this study we focus on a montane-restricted cryophilic harvestman, <i>Sclerobunus robustus</i>, distributed throughout the heterogeneous Southern Rocky Mountains and Intermontane Plateau (SRMIP) of southwestern North America. We identified hypothetical refugia using ecological niche models (ENMs) across three time periods, corroborated these refugia with population genetic methods using double-digest RAD-seq data, and conducted population level phylogenetic and divergence dating analyses. ENMs identify two large temporally persistent regions in the mid-latitude highlands. Genetic patterns support these two hypothesized refugia with higher genetic diversity within refugial populations and evidence for range expansion in populations found outside of hypothesized refugia. Phylogenetic analyses identify five to six genetically divergent, geographically cohesive clades of <i>S. robustus</i>. Divergence dating analyses suggest that these separate refugia date to the Pliocene and that divergence between clades predates the late Pleistocene glacial cycles, while diversification within clades was likely driven by these cycles. Population genetic analyses reveal effects of both isolation by distance (IBD) and isolation by environment (IBE), with IBD more important in the continuous mountainous portion of the distribution, while IBE was stronger in the populations inhabiting the isolated sky islands of the south. Using model-based coalescent approaches, we find support for post-divergence migration between clades from separate refugia.

将生态位模型（ecological niche modeling, ENMs）整合进系统地理学分析，使得研究者能够在基于假设的框架下识别并检验潜在冰期避难所：即通过实证数据验证「避难种群具有更高遗传多样性、非避难种群存在种群扩张」这一预期模式。本研究以分布于北美西南部异质性生境南落基山脉与山间高原（Southern Rocky Mountains and Intermontane Plateau, SRMIP）的山地专性嗜寒盲蜘蛛——*强壮硬盲蛛（Sclerobunus robustus）*为研究对象。我们通过三个时间尺度的生态位模型识别了潜在避难所，并利用双酶切限制性位点关联DNA测序（double-digest RAD-seq, ddRAD-seq）数据结合种群遗传学方法验证了这些避难所，同时开展了种群水平的系统发育与分化时间估算分析。生态位模型在中纬度高地识别出两个长期稳定存在的大型区域。种群遗传模式支持这两个假说中的避难所：避难种群内遗传多样性更高，而非避难种群则表现出种群扩张的迹象。系统发育分析识别出强壮硬盲蛛的5至6个遗传分化显著且地理分布集中的支系。分化时间估算结果显示，这些独立避难所的形成时间可追溯至上新世，支系间的分化早于晚更新世冰期，而支系内部的物种分化则大概率由该时期的冰期事件驱动。种群遗传分析同时揭示了距离隔离（isolation by distance, IBD）与环境隔离（isolation by environment, IBE）的共同作用：在分布区连续的山地生境中，距离隔离的效应更为显著；而在西南部孤立天空岛种群中，环境隔离的作用更强。本研究通过基于模型的溯祖分析方法，发现来自不同避难所的支系间存在分化后的基因流。