Data from: Phylogeographic diversification of antelope squirrels (Ammospermophilus) across North American deserts

We investigated the biogeographic history of antelope squirrels, genus Ammospermophilus, which are widely distributed across the deserts and other arid lands of western North America. We combined range-wide sampling of all currently recognized species of Ammospermophilus with a multilocus data set to infer phylogenetic relationships. We then estimated divergence times within identified clades of Ammospermophilus using fossil-calibrated and rate-calibrated molecular clocks. Lastly, we explored generalized distributional changes of Ammospermophilus since the last glacial maximum using species distribution models, and assessed responses to Quaternary climate change by generating demographic parameter estimates for the three wide-ranging clades of A. leucurus. From our phylogenetic estimates we inferred strong phylogeographic structure within Ammospermophilus and the presence of three well-supported major clades. Initial patterns of historical divergence were coincident with dynamic alterations in the landscape of western North America, and the formation of regional deserts during the Late Miocene and Pliocene. Species distribution models and demographic parameter estimates revealed patterns of recent population expansion in response to glacial retreat. When combined with evidence from co-distributed taxa, the historical biogeography of Ammospermophilus provides additional insight into the mechanisms that impacted diversification of arid-adapted taxa across the arid lands of western North America. We propose species recognition of populations of the southern Baja California peninsula to best represent our current understanding of evolutionary relationships among genetic units of Ammospermophilus.本研究针对羚羊松鼠属（Ammospermophilus）的生物地理历史展开探究。该属物种广泛分布于北美洲西部的荒漠与其他干旱生境中。本研究结合了对羚羊松鼠属所有当前已确认物种的全分布区采样，以及多位点数据集，以推断其系统发育关系。随后，本研究借助化石校准与速率校准的分子钟（molecular clocks）模型，对已鉴定的羚羊松鼠属演化支内部的分化时间进行估算。最后，本研究通过物种分布模型（species distribution models），探究了自末次冰盛期以来羚羊松鼠属的整体分布变化；同时针对分布范围广泛的三个白尾羚羊松鼠（A. leucurus）演化支，通过生成种群动态参数估算值，评估了其对第四纪气候变化的响应。基于系统发育分析结果，本研究推断羚羊松鼠属内部存在显著的系统地理结构，且存在三个得到充分支持的主要演化支。历史分化的初始模式与北美洲西部地貌的动态变迁，以及晚中新世至上新世期间区域性荒漠的形成时间相吻合。物种分布模型与种群动态参数估算结果显示，种群近期呈现出响应冰川消退的扩张模式。结合同分布区类群的相关证据，羚羊松鼠属的历史生物地理学研究，可为深入解析影响北美洲西部干旱生境中适应干旱类群分化的机制提供新的视角。本研究建议将下加利福尼亚半岛南部的种群划分为独立物种，以最贴合当前我们对羚羊松鼠属遗传单元间演化关系的认知。