Range shifts during the Pleistocene shaped the unique phylogeographical structures of many species. Pleistocene range shifts gave currently allopatric species opportunities to occur in sympatry, likely resulting in ancient introgressions between related taxa. In our study, we investigate the range shifts and introgression patterns of three Japanese Abies species (A. firma, A. homolepis, and A. veitchii) by employing an extensive survey of 43 populations. This survey includes comprehensive analysis of both mitochondrial (mtDNA) and nuclear (18 microsatellites) genomes, in combination with species distribution modeling (SDM). It is important to note that these two types of markers provide distinct and complementary information, as they have different modes of inheritance and mutation rates. Bayesian clustering analysis indicates that the three species were clearly separated, with the exception of the A. homolepis var. umbellata population, which is considered a natural hybrid between A. homolepis and A. firma. However, mtDNA haplotypes of the four northern populations of A. firma were entirely replaced by two major haplotypes of A. homolepis and A. veitchii. The results of neighbor-net, NewHybrids, STRUCTURE analyses, and SDM suggest that historical introgression between species occurred in each geographic region, with mtDNA capture being the likely mechanism. However, contrary to these findings, the ABC coalescent analysis did not support an ancient introgression. Therefore, further validation with genome-wide level data is needed to clarify this issue. Our conclusion is that climate-induced range shifts during the Pleistocene/Holocene likely played a crucial role in the observed patterns of introgression in these species.

更新世期间的范围变化塑造了许多物种独特的系统发育地理学结构。更新世范围的变化为当前的异域物种提供了共生的机会，可能导致相关类群之间的古代基因渗入。在我们的研究中，我们研究了三种日本冷杉物种（A.firma、A.homolepis和A.veitchii）的范围变化和渗入模式）通过对 43 个人进行广泛调查。这项调查包括对线粒体 (mtDNA) 和核（18 个微卫星）基因组的综合分析，并结合物种分布模型 (SDM)。值得注意的是，这两类标记提供了独特且互补的信息，因为它们具有不同的遗传模式和突变率。贝叶斯聚类分析表明，除了A. homolepis var. 以外，这三个物种明显分开。umbellata群体，被认为是A.homolepis和A.firma之间的自然杂交种。然而， A. Firma的四个北方种群的 mtDNA 单倍型完全被A. homolepis和A. veitchii两种主要单倍型所取代。neighbour-net、NewHybrids、STRUCTURE 分析和 SDM 的结果表明，每个地理区域都发生过物种间的历史渗入，其中 mtDNA 捕获是可能的机制。然而，与这些发现相反，ABC 联合分析并不支持古老的基因渗入。因此，需要进一步验证全基因组水平的数据来澄清这个问题。我们的结论是，更新世/全新世期间气候引起的范围变化可能在观察到的这些物种的渗入模式中发挥了至关重要的作用。