Data from: Eurasian house mouse (Mus musculus L.) differentiation at microsatellite loci identifies the Iranian plateau as a phylogeographic hotspot

Background The phylogeography of the house mouse (Mus musculus L.), an emblematic species for genetic and biomedical studies, is only partly understood, essentially because of a sampling bias towards its most peripheral populations in Europe, Asia and the Americas. Moreover, the present-day phylogeographic hypotheses stem mostly from the study of mitochondrial lineages. In this article, we complement the mtDNA studies with a comprehensive survey of nuclear markers (19 microsatellite loci) typed in 963 individuals from 47 population samples, with an emphasis on the putative Middle-Eastern centre of dispersal of the species. Results Based on correspondence analysis, distance and allele-sharing trees, we find a good coherence between geographical origin and genetic make-up of the populations. We thus confirm the clear distinction of the three best described peripheral subspecies, M. m. musculus, M. m. domesticus and M. m. castaneus. A large diversity was found in the Iranian populations, which have had an unclear taxonomic status to date. In addition to samples with clear affiliation to M. m. musculus and M. m. domesticus, we find two genetic groups in Central and South East Iran, which are as distinct from each other as they are from the south-east Asian M. m. castaneus. These groups were previously also found to harbor distinct mitochondrial haplotypes. Conclusion We propose that the Iranian plateau is home to two more taxonomic units displaying complex primary and secondary relationships with their long recognized neighbours. This central region emerges as the area with the highest known diversity of mouse lineages within a restricted geographical area, designating it as the focal place to study the mechanisms of speciation and diversification of this species.

背景 作为遗传与生物医学研究的标志性模式物种，小家鼠（*Mus musculus* L.）的系统地理学（phylogeography）研究至今仍未被完全阐明，其核心原因在于现有研究多偏向于采集欧洲、亚洲及美洲的边缘种群，存在显著采样偏差。此外，当前主流的系统地理学假说大多基于线粒体谱系的研究结果。
本文中，我们通过对覆盖47个种群样本、共计963个个体的核标记（19个微卫星位点（microsatellite loci））开展全面基因分型分析，以补充线粒体DNA（mtDNA）的相关研究，并重点聚焦于该物种推测的中东扩散起源中心。

结果 基于对应分析（correspondence analysis）、距离树及等位基因共享树的分析结果，我们发现种群的地理起源与其遗传构成之间存在显著一致性。据此，我们明确验证了三个已被广泛研究的边缘亚种——小家鼠（*Mus musculus musculus*）、小家鼠（*Mus musculus domesticus*）与小家鼠（*Mus musculus castaneus*）——之间的清晰分化。
伊朗境内的小家鼠种群展现出极高的遗传多样性，其分类学地位至今仍未明确。除了明确隶属于上述两个亚种的种群样本外，我们在伊朗中部及东南部地区还发现了两个独立的遗传类群；这两个类群之间的分化程度，与它们同东南亚小家鼠（*Mus musculus castaneus*）之间的分化程度相当。此前已有研究证实，这两个遗传类群携带独特的线粒体单倍型。

结论 我们提出：伊朗高原存在另外两个分类学单元，它们与长期以来被认知的近缘类群之间存在复杂的一级与二级演化关系。该区域也成为目前已知的、有限地理范围内小家鼠谱系多样性最高的区域，因此成为研究该物种种形成与演化分化机制的核心研究位点。