Data from: Genetic differentiation of western capercaillie in the Carpathian Mountains reveal the importance of post glacial expansions and habitat connectivity in understanding the present day European distribution

Population structure and barriers to gene flow are important components for understanding the evolutionary history of a species. Here we study population structure and differentiation in the western capercaillie (Aves: Phasianidae) along the Carpathian Mountains. Further, we compared the levels of population differentiation among capercaillie from the Carpathian Mountains, Balkans (Bulgaria) and the boreal forest (Russia and Sweden) in order to reveal past and current processes which may influence population structure. Tissue samples, non-invasive faeces and feathers and toe pads from museum specimens were used for genetic analyses of mitochondrial (mtDNA) sequences and allelic variation at nine nuclear DNA (nDNA) microsatellite loci. Analyses of mtDNA sequences revealed a southern subclade within the northern clade. Within the northern clade, microsatellite data distinguished two groups: (1) Western Carpathian populations; and (2) Eastern Carpathian and boreal forest populations. Bulgarian populations constituted a third cluster corresponding to the southern phylogenetic subclade. The Western Carpathian populations showed a heterozygote deficiency. The analyses indicate that the abundant Eastern Carpathian populations share alleles with populations from the boreal forest suggesting a common origin of these populations since the last glacial period. On the other hand, the Western Carpathian populations have been isolated over a long period with only a few migrants from the east, thereby becoming differentiated from the eastern and northern populations. The southern populations have been isolated from the northern populations since the last glacial maximum. The molecular analyses did not support the currently recognised taxonomy at the subspecies level.

种群结构与基因流屏障是解析物种演化历史的核心要素之一。本研究以沿喀尔巴阡山脉分布的西方松鸡（western capercaillie，鸟纲：雉科）为研究对象，分析其种群结构与遗传分化。此外，为揭示影响种群结构的古今演化过程，本研究对比了喀尔巴阡山脉、巴尔干半岛（保加利亚）以及寒温带针叶林（俄罗斯与瑞典）的松鸡种群间的遗传分化水平。本研究使用组织样本、非侵入式粪便与羽毛样本，以及博物馆标本的趾垫样本，对线粒体（mtDNA）序列以及9个核DNA（nDNA）微卫星位点的等位基因变异开展遗传分析。线粒体序列分析结果显示，北方演化支内部存在一个南方亚支。在北方演化支内，微卫星数据将种群划分为两个类群：（1）喀尔巴阡山西部种群；（2）喀尔巴阡山东部与寒温带针叶林种群。保加利亚种群则构成第三个类群，对应南方系统发育亚支。喀尔巴阡山西部种群表现出杂合子缺失现象。分析结果表明，数量丰富的喀尔巴阡山东部种群与寒温带针叶林种群共享等位基因，提示二者自末次冰期以来拥有共同起源。与之相反，喀尔巴阡山西部种群长期处于隔离状态，仅存在少量来自东部的基因交流，因此与东部及北部种群产生了遗传分化。南方种群自末次盛冰期以来便与北方种群相互隔离。本分子分析结果不支持当前公认的亚种分类层级划分。