Data from: Speciation in mountain refugia: phylogeography and demographic history of the pine siskin and black-capped siskin complex

Following Pleistocene glacial maxima, species that adapted to temperate climates in low-latitude refugia had to modify their ranges as climate changed, expanding either latitudinally towards the poles, or altitudinally to higher elevations in mountainous regions. Within just a few thousand years, populations taking alternative routes during interglacials became isolated from each other and subjected to different selection pressures, often leading to lineage divergence and speciation. The pine siskin (Spinus pinus) is a common and widespread songbird showing relative phenotypic uniformity across the North American continent. One exception is the subspecies found in the highlands of northern Central America (S. p. perplexus), which shows marked differentiation in plumage color and shares some traits with the endemic and partly sympatric black-capped siskin (S. atriceps), suggesting potential introgression or even a hybrid origin of perplexus. Relationships and species limits among pinus, perplexus and atriceps have been controversial for decades. We provide new molecular evidence to help resolve the evolutionary history of the group. Phylogenetic analysis of mitochondrial DNA and nuclear intron sequences revealed three distinct lineages within the complex, corresponding to: (1) S. pinus individuals from Canada through central Mexico (S. p. pinus and S. p. macropterus), (2) individuals from the highlands of Guatemala and Chiapas (S. p. perplexus), and (3) S. atriceps. Pine siskins across North America show evidence of a recent postglacial population expansion and extremely low levels of diversity and structure. In contrast, S. p. perplexus shows evidence of demographic stasis, reflecting long-term isolation and restricted dispersal. Marked and diagnostic genetic differences among the three lineages in mtDNA and at least one intron, suggest that a hybrid origin of S. p. perplexus is unlikely, yet some degree of introgression between S. p. perplexus and S. atriceps cannot be ruled out in localities where they occur in sympatry.更新世冰盛期（Pleistocene glacial maxima）结束后，在低纬度避难所适应温带气候的物种需随气候变化调整分布范围：或沿纬度方向向极地扩张，或沿海拔向山区更高海拔区域拓展。仅数千年时间内，间冰期选择不同扩散路径的种群彼此隔离，并承受不同的选择压力，这往往会引发谱系分化（lineage divergence）与物种形成（speciation）。 松金翅雀（pine siskin，*Spinus pinus*）是一种分布广泛的常见鸣禽，在北美大陆整体呈现相对一致的表型特征。唯有中美洲北部高地的亚种S. p. perplexus例外：该亚种羽色存在显著分化，且与特有且部分同域分布（sympatric）的黑顶金翅雀（black-capped siskin，*S. atriceps*）共享部分性状，这暗示perplexus可能存在基因渐渗（introgression），甚至可能起源于杂交（hybrid origin）。 数十年来，pinus、perplexus与atriceps三者间的演化关系及物种界定一直存在争议。本研究提供全新的分子证据，以厘清该类群的演化历史。对线粒体DNA（mitochondrial DNA, mtDNA）与核内含子（nuclear intron）序列开展的系统发育分析（phylogenetic analysis）显示，该类群复合体中存在3个独立的谱系，分别对应：（1）分布于加拿大至墨西哥中部的S. pinus种群（S. p. pinus与S. p. macropterus）；（2）分布于危地马拉与恰帕斯高地的种群（S. p. perplexus）；（3）S. atriceps。 全北美范围内的松金翅雀种群均显示出近期冰期后种群扩张（postglacial population expansion）的信号，且遗传多样性与群体结构水平极低。与之形成鲜明对比的是，S. p. perplexus种群呈现种群动态停滞（demographic stasis）的特征，这反映其长期处于隔离状态且扩散能力受限。三个谱系在线粒体DNA与至少一个核内含子区域存在显著且具诊断性的遗传差异，这表明S. p. perplexus的杂交起源可能性极低，但在二者同域分布的区域，S. p. perplexus与S. atriceps之间仍存在一定程度基因渐渗的可能，无法完全排除。