Nuclear genetic analysis of the red fox across its trans-Pacific range

The red fox (Vulpes vulpes) occurs on multiple continents in diverse habitats, making it an informative system for evolutionary genomic research. However, its phylogeography remains unclear. Previously, mitochondrial DNA and small numbers of nuclear loci provided discordant views. Both markers indicated deep divergence (~ 0.5 MY) between Eurasian and southern North American populations but differed in the apparent continental affinity of Alaskan red foxes, implying some degree of gene exchange during secondary contact (~0.1 MY). We assayed >173,000 nuclear genomic sites in 52 red foxes, along with 2 Rueppell’s (V. rueppellii) foxes and a gray wolf (Canis lupus) using the Illumina CanineHD BeadChip. We obtained 5,107 SNPs that were polymorphic in the foxes. Consistent with the Afro-Eurasian origins of red foxes, genetic diversity was higher in Eurasian than North American samples. Phylogenetic trees indicated that Alaskan and southern North American red foxes formed a monophyletic...

赤狐（Vulpes vulpes）广泛分布于多个大陆的多样生境中，是进化基因组学研究的优质模式体系。然而其系统地理学（phylogeography）研究仍存在诸多不明之处。此前，线粒体DNA（mitochondrial DNA）与少量核基因座的研究结论存在分歧：两类标记均显示欧亚种群与北美南部种群间存在约0.5百万年的深度分化，但在阿拉斯加赤狐的大陆亲缘关系判定上存在差异，这暗示在约0.1百万年前的二次接触过程中存在一定程度的基因交流。本研究借助Illumina犬科高密度基因芯片（Illumina CanineHD BeadChip），对52只赤狐、2只吕佩尔狐（V. rueppellii）以及1只灰狼（Canis lupus）进行基因检测，共获取超过173,000个核基因组位点，最终筛选得到5107个在狐类中呈多态性的单核苷酸多态性（Single Nucleotide Polymorphism，SNPs）。与赤狐起源于非洲-欧亚大陆的推论相符，欧亚采样种群的遗传多样性高于北美采样种群。系统发育树分析显示，阿拉斯加赤狐与北美南部赤狐构成单系群……