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）气候旋回与冰川作用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。本研究采用搭载多位点数据的种群遗传学分析方法，对两种树松鼠（tree squirrels）的姊妹物种——道格拉斯松鼠（Tamiasciurus douglasii）与美洲红松鼠（Tamiasciurus hudsonicus）的分化、隔离与杂交事件展开探究，重点关注加拿大温哥华岛上的美洲红松鼠地理与遗传特征均较为模糊的种群。这两个物种的分化时间仅约50万年前，处于更新世晚期。本研究的核基因分析结果显示，该岛屿种群在系统发育上嵌入美洲红松鼠分支内，但线粒体DNA（mtDNA）分析则将其归类于道格拉斯松鼠分支中。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，且该岛屿种群与大陆上的两个物种间均存在双向基因流。本研究的遗传分析结论与生物气候建模结果一致，该建模结果证实更新世晚期两个物种均可在该区域存续。该岛屿种群约4万年前的分化时间表明，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（refugium）中持续存活。本研究结果揭示了更新世气候变化与生境变迁如何在基因流存在的条件下推动物种发生初期分化。