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 2 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
2 markers previously developed for the red fox from dog Y-chromosome
sequence. The markers were genotyped in 76 male red foxes from 4
populations: 7 foxes from Newfoundland (eastern Canada), 12 from Maryland
(eastern United States), 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 2 previously known markers alone would
have identified only 10 haplotypes. The haplotypes from the 4 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.

红狐（Vulpes vulpes）基因组的从头测序组装（de novo assembly），有力推动了该物种种组学研究工具的研发。此前，由于缺乏红狐Y染色体序列相关信息，针对北美红狐种群历史的研究一度受限。不过近期在参考基因组的2个支架序列（scaffold）中，已鉴定出一段长度达1兆碱基（Mb）的红狐Y染色体序列。本研究对上述支架序列开展重复基序扫描，共发现194个潜在微卫星位点。研究人员从中选取23个位点进行引物开发，经筛选验证后获得11个新型分子标记；同时结合2个此前基于犬Y染色体序列开发的红狐Y染色体标记，构建起一套完整的标记面板。利用该标记面板，研究人员对来自4个种群的76只雄性红狐进行了基因分型：其中7只采自加拿大东部的纽芬兰岛、12只采自美国东部的马里兰州、9只采自大不列颠岛，另有48只为已知北美起源的圈养红狐，饲养于俄罗斯新西伯利亚的实验农场中。整套标记面板共鉴定出22种红狐单倍型，而使用此前的2个标记仅能区分10种单倍型。4个种群的单倍型主要按大陆聚类，但来自大不列颠岛种群与实验农场种群的单向基因流，或对马里兰州种群的单倍型多样性产生影响。本研究开发的新型标记提升了红狐Y染色体多样性分析的分辨率，同时为解析雄性个体对红狐种群多样性的贡献以及系统地理学格局提供了全新视角。

搜集汇总

背景与挑战

背景概述

该数据集聚焦于红狐Y染色体标记的开发与应用，基于红狐基因组组装开发了11个新的微卫星标记，并结合已有标记对76只雄性红狐进行基因分型，识别出22种单倍型，增强了红狐种群多样性和系统地理学分析的能力。数据包括原始片段分析文件，适用于校准新样本或种群中的标记调用，为研究红狐雄性贡献的种群历史提供了关键工具。