Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe

Carnivores tend to exhibit a lack of (or less pronounced) genetic
structure at continental scales in both a geographic and temporal sense
using various mitochondrial DNA markers on modern and/or ancient
specimens. This tends to confound the identification of refugial areas and
post-glacial colonization patterns in this group. In this study we used
Genotyping-by-Sequencing (GBS) to reconstruct the phylogeographic history
of a widespread carnivore, the red fox (Vulpes vulpes), in Europe by
investigating broad-scale patterns of genomic variation, differentiation
and admixture amongst contemporary populations. Using 15,003 single
nucleotide polymorphisms (SNPs) from 524 individuals allowed us to
identify the importance of refugial regions for the red fox in terms of
endemism (e.g. Iberia) and sources of post-glacial re-expansion (e.g.
Carpathians and Balkans) across northern regions of the continent. In
addition, we tested multiple post-glacial re-colonization scenarios of
previously glaciated regions during the Last Glacial Maximum using an
Approximate Bayesian Computation (ABC) approach. We identified the role of
ancient and temporary land-bridges in the colonization of Scandinavia and
the British Isles, with a natural colonization of Ireland deemed more
likely than an ancient human-mediated introduction as has previously been
proposed. Using genome-wide data has allowed us to tease apart broad-scale
patterns of structure and diversity in a widespread carnivore in Europe
that was not always evident from using more limited marker sets.

基于现代或古生物标本的多种线粒体DNA（mitochondrial DNA）标记分析显示，食肉动物在大陆尺度的地理与时间维度上，普遍缺乏遗传结构（或遗传结构较弱）。这一特征常会干扰该类群冰期避难所区域及冰期后拓殖模式的鉴定。本研究通过基因分型测序（Genotyping-by-Sequencing, GBS），对欧洲广布食肉动物赤狐（Vulpes vulpes）的系统地理历史进行重建，分析了当代种群间基因组变异、分化与基因交流的大尺度格局。本研究基于524个个体的15003个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）位点，明确了欧洲北部区域赤狐冰期避难所的重要性：包括特有性热点区域（如伊比利亚半岛），以及冰期后种群再扩张的起源地（如喀尔巴阡山脉与巴尔干半岛）。此外，本研究采用近似贝叶斯计算（Approximate Bayesian Computation, ABC）方法，对末次盛冰期以来曾受冰川覆盖区域的多种冰期后再拓殖情景进行了检验。研究发现，古代与临时性陆桥在斯堪的纳维亚半岛与不列颠群岛的赤狐拓殖过程中发挥了关键作用；相较于此前提出的人类远古介导引入假说，爱尔兰的赤狐种群更可能通过自然拓殖形成。相较于使用有限分子标记的既往研究，全基因组数据帮助我们厘清了欧洲广布食肉动物种群结构与多样性的大尺度格局，而该格局在以往研究中往往难以被清晰识别。