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关键组成部分。本研究以分布于喀尔巴阡山脉沿线的西方松鸡（Western Capercaillie，鸟纲(Aves)雉科(Phasianidae)）为研究对象，分析其种群结构与遗传分化水平。此外，本研究还对比了喀尔巴阡山脉、巴尔干半岛（保加利亚）以及泰加林（俄罗斯与瑞典）地区松鸡的种群分化程度，以揭示可能影响其种群结构的历史与当前演化过程。本研究采集了组织样本、非侵入性粪便及羽毛样本，以及博物馆标本的趾垫样本，用于线粒体（mtDNA）序列分析以及9个核DNA(nDNA)微卫星位点的等位基因变异检测。线粒体DNA序列分析结果显示，北方支系内部存在一个南方亚支系。在北方支系内部，微卫星数据可将种群划分为两组：(1) 西喀尔巴阡种群；(2) 东喀尔巴阡种群与泰加林种群。保加利亚种群则构成第三个聚类群，对应系统发育分析中的南方亚支系。西喀尔巴阡种群表现出杂合子缺失现象。分析结果表明，数量充足的东喀尔巴阡种群与泰加林种群共享等位基因，提示二者自末次冰期以来拥有共同的起源。与之相反，西喀尔巴阡种群长期处于隔离状态，仅存在少量来自东部的个体迁入，因此与东部及北部种群产生了遗传分化。南方种群自末次冰盛期以来便与北方种群相互隔离。本研究的分子遗传学分析结果，不支持当前学界所认可的亚种层级分类划分。