Data from: Y-chromosome markers for the red fox

The de novo assembly of the red fox (Vulpes vulpes) genome has facilitated the development of genomic tools for the species. Efforts to identify the population history of red foxes in North America have previously been limited by a lack of information about the red fox Y-chromosome sequence. However, a megabase of red fox Y-chromosome sequence was recently identified over two scaffolds in the reference genome. Here, these scaffolds were scanned for repeated motifs, revealing 194 likely microsatellites. Twenty-three of these loci were selected for primer development and, after testing, produced a panel of 11 novel markers that were analyzed alongside two markers previously developed for the red fox from dog Y-chromosome sequence. The markers were genotyped in 76 male red foxes from four populations: 7 foxes from Newfoundland (eastern Canada), 12 from Maryland (eastern USA), and 9 from the island of Great Britain, as well as 48 foxes of known North American origin maintained on an experimental farm in Novosibirsk, Russia. The full marker panel revealed 22 haplotypes among these red foxes, whereas the two previously known markers alone would have identified only 10 haplotypes. The haplotypes from the four populations clustered primarily by continent, but unidirectional gene flow from Great Britain and farm populations may influence haplotype diversity in the Maryland population. The development of new markers has increased the resolution at which red fox Y-chromosome diversity can be analyzed and provides insight into the contribution of males to red fox population diversity and patterns of phylogeography.

赤狐（Vulpes vulpes）基因组的从头组装（de novo assembly）推动了该物种种组学工具的开发。此前，由于缺乏赤狐Y染色体序列相关信息，针对北美赤狐种群历史的研究曾受到限制。不过，近期在参考基因组的两个支架（scaffold）上，已鉴定出一段兆碱基级别的赤狐Y染色体序列。本研究对这两个支架进行了重复基序扫描，共发现194个潜在微卫星（microsatellites）。研究人员从中选取23个位点开发引物，经测试后得到一套包含11个新型分子标记的检测面板，并与此前基于犬科Y染色体序列为赤狐开发的2个标记一同开展分析。我们对来自4个种群的76只雄性赤狐进行了基因分型：7只来源于加拿大东部的纽芬兰岛、12只来源于美国东部的马里兰州、9只来源于大不列颠岛，另有48只来源于已知北美种群、饲养于俄罗斯新西伯利亚市一处实验农场的赤狐。整套标记面板共鉴定出22个单倍型（haplotypes），而仅使用此前已知的2个标记仅能识别10个单倍型。这4个种群的单倍型主要按大陆聚类，但从大不列颠岛和实验种群向马里兰州种群的单向基因流可能影响了当地的单倍型多样性。本研究开发的新型标记提升了赤狐Y染色体多样性研究的分辨率，同时为解析雄性个体对赤狐种群多样性的贡献以及系统地理学（phylogeography）格局提供了新的视角。