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）气候旋回与冰期事件，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。本研究依托多位点数据开展种群遗传分析，针对两种树松鼠姊妹物种——道格拉斯黄松鼠（Tamiasciurus douglasii）与哈德逊黄松鼠（Tamiasciurus hudsonicus）的分化、隔离与杂交现象展开探究，重点关注加拿大温哥华岛（Vancouver Island）上地理与遗传特征均具特殊性的哈德逊黄松鼠种群。这两个物种的分化时间仅约50万年前，处于更新世晚期。核基因组分析显示，该岛屿种群的系统发育地位嵌套于哈德逊黄松鼠类群中，但线粒体DNA（mtDNA）分析则将其归入道格拉斯黄松鼠类群。这一系统发育位置的冲突，更可能由历史杂交事件而非不完全谱系分选导致，且该岛屿种群与大陆上的两个物种均存在双向基因流。本研究的遗传分析结论与生物气候建模（bioclimatic modeling）结果一致：生物气候建模结果表明，在整个更新世晚期，两个物种均能在该区域存续。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冰期避难所（refugium）中存续。本研究结果揭示了更新世气候变化与栖息地变迁，如何在基因流存在的条件下推动类群产生初期分化。