Data from: The hidden history of the snowshoe hare, Lepus americanus: extensive mitochondrial DNA introgression inferred from multilocus genetic variation

Hybridization drives the evolutionary trajectory of many species or local populations, and assessing the geographic extent and genetic impact of interspecific gene flow may provide invaluable clues to understand population divergence or the adaptive relevance of admixture. In North America, hares (Lepus spp.) are key species for ecosystem dynamics and their evolutionary history may have been affected by hybridization. Here we reconstructed the speciation history of the three most widespread hares in North America - the snowshoe hare (Lepus americanus), the white-tailed jackrabbit (L. townsendii) and the black-tailed jackrabbit (L. californicus) - by analyzing sequence variation at eight nuclear markers and one mitochondrial DNA (mtDNA) locus (6 240 bp; 94 specimens). A multilocus-multispecies coalescent-based phylogeny suggests that L. americanus diverged ~2.7 Mya and that L. californicus and L. townsendii split more recently (~1.2 Mya). Within L. americanus a deep history of cryptic divergence (~2.0 Mya) was inferred, which coincides with major speciation events in other North American species. While the isolation-with-migration model suggested that nuclear gene flow was generally rare or absent among species or major genetic groups, coalescent simulations of mtDNA divergence revealed historical mtDNA introgression from L. californicus into the Pacific Northwest populations of L. americanus. This finding marks a history of past reticulation between these species, which may have affected other parts of the genome and influence the adaptive potential of hares during climate change.杂交驱动着诸多物种或局域种群的进化轨迹，评估种间基因流的地理范围与遗传影响，可为解析种群分化或遗传混杂的适应价值提供关键线索。在北美区域，兔属（Lepus spp.）类群是生态系统动态的关键物种类群，其进化历史或受杂交作用影响。本研究通过分析8个核标记（nuclear markers）与1个线粒体DNA（mtDNA）位点的序列变异（总长度6240 bp，涵盖94份标本），重建了北美分布最广的三种兔类的物种形成历史——美洲兔（Lepus americanus，雪兔）、白尾长耳大野兔（L. townsendii）与黑尾长耳大野兔（L. californicus）。基于多位点-多物种溯祖（multilocus-multispecies coalescent）的系统发育分析显示，美洲兔的分化时间约为270万年前，而加州长耳大野兔与白尾长耳大野兔的分化时间更近，约为120万年前。在美洲兔类群内部，研究推断出一段约200万年前的隐秘分化历史，这与其他北美物种的主要物种形成事件高度吻合。尽管隔离与基因流（isolation-with-migration）模型表明，物种间或主要遗传类群之间的核基因流普遍较为稀少甚至不存在，但针对线粒体DNA分化的溯祖模拟结果显示，曾发生过从加州长耳大野兔向美洲兔太平洋西北种群的历史线粒体DNA渐渗事件。这一发现揭示了这些类群间曾存在网状演化历史，该历史或影响基因组的其他区域，并将在气候变化背景下影响兔类的适应潜能。