School of Applied Sciences, University of Huddersfield, Quennsgate, Huddersfield, UK.
AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Department of Zoology, Linköping University, Linköping, Sweden.
BMC Genomics. 2020 Mar 18;21(1):241. doi: 10.1186/s12864-020-6603-3.
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 F<0.086.
Our study demonstrates the feasibility of ddRAD-seq in Apodemus and provides the first insights into the population genomics of the species.
田鼠属的老鼠是古北区最常见的哺乳动物之一。尽管它们分布广泛，生态观察历史悠久，但田鼠属仍没有全基因组数据，这限制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。
本研究通过对来自波兰北部 500 公里范围内四个种群的 72 只黄胸鼠和 10 只大林姬鼠进行双酶切限制性位点相关 DNA 测序（ddRAD-seq），提供了结果。我们的数据清楚地显示了这两个物种的遗传分化，基于 21377 个共同基因座，平均 p 距离为 1.51%，突变率为 0.0011-0.0019 个替换/位点/百万年。我们提供了 117 个高度分化的基因座目录，这些基因座能够在波兰区分这两个物种，并在很大程度上区分来自欧洲几个国家和突尼斯的 20 个无关样本。我们还证明了三个黄胸鼠种群之间存在混合，但表明它们的平均种群结构可以忽略不计，最大的成对 F 值为 0.086。
本研究证明了 ddRAD-seq 在田鼠属中的可行性，并首次提供了该物种群体基因组学的见解。
