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）展开生物地理历史研究，该属物种俗称羚羊松鼠，广泛分布于北美西部的沙漠及其他干旱生境中。我们结合了对该属所有当前公认物种的全分布区采样与多位点数据集，以推断其系统发育关系。随后，我们利用化石校准与速率校准的分子钟，估算了该属已识别演化支内部的分化时间。最后，我们借助物种分布模型（Species Distribution Models）探究了自末次冰盛期以来该属的整体分布变化，并通过对白尾羚羊松鼠（Ammospermophilus leucurus，缩写为A. leucurus）三个广布演化支的种群参数估算，评估了其对第四纪气候变化的响应。基于系统发育推断结果，我们发现羚羊松鼠属内部存在显著的系统地理结构，且存在三个得到强力支持的主要演化支。该属的早期历史分化格局与北美西部地貌的剧烈变动以及晚中新世、上新世时期区域沙漠的形成相吻合。物种分布模型与种群参数估算结果显示，该类群在冰期消退后出现了近期的种群扩张现象。结合同分布类群的相关证据，羚羊松鼠属的历史生物地理学研究可为解析北美西部干旱生境中适旱类群多样化的影响机制提供新的认知。我们建议将下加利福尼亚半岛南部的种群认定为独立物种，以最贴合当前我们对该属遗传单元间演化关系的认知。