CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
Syst Biol. 2012 May;61(3):367-81. doi: 10.1093/sysbio/syr114. Epub 2011 Dec 26.
Understanding recent speciation history requires merging phylogenetic and population genetics approaches, taking into account the persistence of ancestral polymorphism and possible introgression. The emergence of a clear phylogeny of hares (genus Lepus) has been hampered by poor genomic sampling and possible occurrence of mitochondrial DNA (mtDNA) introgression from the arctic/boreal Lepus timidus into several European temperate and possibly American boreal species. However, no formal test of introgression, taking also incomplete lineage sorting into account, has been done. Here, to clarify the yet poorly resolved species phylogeny of hares and test hypotheses of mtDNA introgression, we sequenced 14 nuclear DNA and 2 mtDNA fragments (8205 and 1113 bp, respectively) in 50 specimens from 11 hare species from Eurasia, North America, and Africa. By applying an isolation-with-migration model to the nuclear data on subsets of species, we find evidence for very limited gene flow from L. timidus into most temperate European species, and not into the American boreal ones. Using a multilocus coalescent-based method, we infer the species phylogeny, which we find highly incongruent with mtDNA phylogeny using parametric bootstrap. Simulations of mtDNA evolution under the speciation history inferred from nuclear genes did not support the hypothesis of mtDNA introgression from L. timidus into the American L. townsendii but did suggest introgression from L. timidus into 4 temperate European species. One such event likely resulted in the complete replacement of the aboriginal mtDNA of L. castroviejoi and of its sister species L. corsicanus. It is remarkable that mtDNA introgression in hares is frequent, extensive, and always from the same donor arctic species. We discuss possible explanations for the phenomenon in relation to the dynamics of range expansions and species replacements during the climatic oscillations of the Pleistocene.
理解最近的物种形成历史需要合并系统发育和种群遗传学方法，同时考虑到祖先多态性的持久性和可能的基因渗入。由于基因组采样不足以及可能存在来自北极/北方的 Lepus timidus 的线粒体 DNA（mtDNA）基因渗入到几个欧洲温带和可能的美洲北方物种中，兔属（Lepus）的清晰系统发育一直受到阻碍。然而，还没有进行正式的基因渗入测试，也没有考虑不完全谱系分选。在这里，为了阐明兔属物种系统发育仍不明确的情况，并检验 mtDNA 基因渗入的假说，我们对来自欧亚大陆、北美洲和非洲的 11 种兔属的 50 个标本进行了 14 个核 DNA 和 2 个 mtDNA 片段（分别为 8205 和 1113 bp）的测序。通过在核数据子集上应用隔离-迁移模型，我们发现有证据表明来自 L. timidus 的基因流非常有限，进入大多数欧洲温带物种，但不进入美洲北方物种。使用基于多基因合并的方法，我们推断了物种系统发育，发现与使用参数自举的 mtDNA 系统发育高度不一致。在从核基因推断的物种形成历史下对 mtDNA 进化进行模拟，并不支持 L. timidus 的 mtDNA 从北极物种渗入到美洲 L. townsendii 的假说，但确实表明从 L. timidus 渗入到 4 个欧洲温带物种。其中一个事件可能导致了 L. castroviejoi 和其姊妹种 L. corsicanus 的原始 mtDNA 的完全替代。值得注意的是，兔属中的 mtDNA 基因渗入非常频繁、广泛，并且总是来自同一个北极物种。我们将讨论与更新世气候振荡期间的范围扩张和物种更替动态有关的现象的可能解释。
