Mice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, hindering our ability to further exploit the genus in evolutionary and ecological genomics context. Here we present results from the double-digest restriction site-associated DNA sequencing (ddRAD-seq) on 72 individuals of A. flavicollis and 10 A. sylvaticus from four populations, sampled across 500 km distance in northern Poland. Our data present clear genetic divergence of the two species, with average p-distance, based on 21377 common loci, of 1.51% and a mutation rate of 0.0011 - 0.0019 substitutions per site per million years. We provide a catalogue of 117 highly divergent loci that enable genetic differentiation of the two species in Poland and to a large degree of 20 unrelated samples from several European countries and Tunisia. We also show evidence of admixture between the three A. flavicollis populations but demonstrate that they have negligible average population structure, with largest pairwise FST<0.086. Our study demonstrates the feasibility of ddRAD-seq in Apodemus and provides the first insights into the population genomics of the species.

中文翻译：

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基于RAD-seq的波兰北部淡淡姬鼠种群结构与比较

姬鼠属的小鼠是古太平洋地区最常见的哺乳动物之一。尽管其生态观测范围广泛且历史悠久，但尚无可用于姬鼠茅的全基因组数据，这阻碍了我们在进化和生态基因组学背景下进一步利用该属的能力。在这里，我们从波兰北部500 km的距离采样中，从四个种群的72个黄萎病曲霉和10个野生曲霉的双消化酶切位点相关DNA测序（ddRAD-seq）中获得了结果。我们的数据显示了这两个物种的明显遗传差异，基于21377个共同基因座的平均p距离为1.51％，每百万年每位点的突变率为0.0011-0.0019个替换。我们提供了117个高度不同位点的目录，这些位点可以使这两个物种在波兰进行遗传分化，并且可以在很大程度上从几个欧洲国家和突尼斯获得20个无关样本。我们还显示了三个黄曲霉种群之间混合的证据，但表明它们的平均种群结构微不足道，最大成对FST <0.086。我们的研究证明了ddRAD-seq在姬鼠属中的可行性，并提供了对该物种种群基因组学的初步见识。