Data from: Diversification and gene flow in nascent lineages of island and mainland North American tree squirrels (Tamiasciurus)

Pleistocene climate cycles and glaciations had profound impacts on taxon diversification in the Boreal Forest Biome. Using population genetic analyses with multilocus data we examined diversification, isolation, and hybridization in two sibling species of tree squirrels (Tamiasciurus douglasii and T. hudsonicus) with special attention to the geographically and genetically enigmatic population of T. hudsonicus on Vancouver Island, Canada. The two species differentiated only about 500,000 years ago, in the late Pleistocene. The island population is phylogenetically nested within T. hudsonicus according to our nuclear analysis but within T. douglasii according to mtDNA. This conflict is more likely due to historical hybridization than to incomplete lineage sorting, and it appears that bidirectional gene flow occurred between the island population and both species on the mainland. This interpretation of our genetic analyses is consistent with our bioclimatic modeling, which demonstrates that both species were able to occupy this region throughout the late Pleistocene. The divergence of the island population 40,000 years ago suggests that tree squirrels persisted in a refugium on Vancouver Island at the Last Glacial Maximum, 20,000 years ago. Our observations demonstrate how Pleistocene climate change and habitat shifts have created incipient divergence in the presence of gene flow.

更新世（Pleistocene）气候旋回与冰期对北方森林生物群系（Boreal Forest Biome）内的类群分化产生了深远影响。本研究采用基于多位点数据（multilocus data）的种群遗传分析（population genetic analyses）方法，对两种树松鼠的姊妹物种（sibling species）——道格拉斯美洲红松鼠（Tamiasciurus douglasii）与哈德逊美洲红松鼠（Tamiasciurus hudsonicus）的分化、隔离与杂交现象展开研究，重点关注加拿大温哥华岛上地理与遗传特征均较为特殊的哈德逊美洲红松鼠种群。两个物种的分化时间仅约50万年前，处于更新世晚期。基于核基因组分析，该岛屿种群的系统发育位置嵌套于哈德逊美洲红松鼠类群中；但基于线粒体DNA（mtDNA）分析，其系统发育位置则嵌套于道格拉斯美洲红松鼠类群中。这种系统发育冲突更可能源于历史杂交事件，而非不完全谱系分选（incomplete lineage sorting），且该岛屿种群与大陆上的两个物种均存在双向基因流（gene flow）。本研究的遗传分析结果与生物气候模拟（bioclimatic modeling）结果相符，模拟结果显示，更新世晚期两个物种均可在此区域栖息存续。该岛屿种群的分化时间约为4万年前，这表明在2万年前的末次盛冰期（Last Glacial Maximum），树松鼠曾在温哥华岛的避难所中存活繁衍。本研究结果阐明了更新世气候变化与栖息地变迁如何在存在基因流的情况下催生了初期物种分化。