Data from: Multiple refugia and barriers explain the phylogeography of the Valais shrew, Sorex antinorii (Mammalia: Soricomorpha)

The aim of the present study was to investigate the genetic structure of the Valais shrew (Sorex antinorii) by a combined phylogeographical and landscape genetic approach, and thereby to infer the locations of glacial refugia and establish the influence of geographical barriers. We sequenced part of the mitochondrial cytochrome b (cyt b) gene of 179 individuals of S. antinorii sampled across the entire species' range. Six specimens attributed to S. arunchi were included in the analysis. The phylogeographical pattern was assessed by Bayesian molecular phylogenetic reconstruction, population genetic analyses, and a species distribution modelling (SDM)-based hindcasting approach. We also used landscape genetics (including isolation-by-resistance) to infer the determinants of current intra-specific genetic structure. The phylogeographical analysis revealed shallow divergence among haplotypes and no clear substructure within S. antinorii. The starlike structure of the median-joining network is consistent with population expansion from a single refugium, probably located in the Apennines. Long branches observed on the same network also suggest that another refugium may have existed in the north-eastern part of Italy. This result is consistent with SDM, which also suggests several habitable areas for S. antinorii in the Italian peninsula during the LGM. Therefore S. antinorii appears to have occupied disconnected glacial refugia in the Italian peninsula, supporting previous data for other species showing multiple refugia within southern refugial areas. By coupling genetic analyses and SDM, we were able to infer how past climatic suitability contributed to genetic divergence of populations. The genetic differentiation shown in the present study does not support the specific status of S. arunchi.

本研究旨在通过系统地理学与景观遗传学相结合的方法，探究瓦莱鼩（Sorex antinorii）的遗传结构，进而推断其冰期避难所的分布位置，并明确地理屏障对种群遗传结构的影响。我们对采自该物种全分布范围内的179只瓦莱鼩个体的线粒体细胞色素b（cyt b）基因片段进行了测序，同时纳入了6个被归为阿伦奇鼩（S. arunchi）的标本进行分析。本研究通过贝叶斯分子系统发育重建、种群遗传分析以及基于物种分布模型（species distribution modelling, SDM）的回推预测方法，对其系统地理格局进行了评估；此外还利用景观遗传学方法（包含抗性隔离分析），推断了当前种内遗传结构的决定因素。系统地理分析结果显示，瓦莱鼩的单倍型间分化程度较浅，种群内部无明显的亚结构特征。中介连接网络图的星状结构与单一避难所的种群扩张模式相符，该避难所大概率位于亚平宁山脉；而该网络图中观察到的长分支也提示，意大利东北部可能也曾存在另一处冰期避难所。这一结果与物种分布模型的分析结果一致，后者同样显示，在末次盛冰期（Last Glacial Maximum, LGM），意大利半岛存在多处适合瓦莱鼩栖息的区域。由此可见，瓦莱鼩曾在意大利半岛占据过彼此隔离的冰期避难所，这为其他物种在南部避难区域内存在多处避难所的已有研究数据提供了支持。通过整合遗传分析与物种分布模型，本研究得以阐明过去的气候适宜性如何作用于种群的遗传分化过程。本研究揭示的遗传分化并不支持阿伦奇鼩（S. arunchi）的物种分类地位。