Data from: Disentangling the complex evolutionary history of the Western Palearctic blue tits (Cyanistes spp.) – phylogenomic analyses suggest radiation by multiple colonisation events and subsequent isolation

Isolated islands and their often unique biota continue to play key roles for understanding the importance of drift, genetic variation and adaptation in the process of population differentiation and speciation. One island system that has inspired and intrigued evolutionary biologists is the blue tit complex (Cyanistes spp.) in Europe and Africa, in particular the complex evolutionary history of the multiple genetically distinct taxa of the Canary Islands. Understanding Afrocanarian colonization events is of particular importance because of recent unconventional suggestions that these island populations acted as source of the widespread population in mainland Africa. We investigated the relationship between mainland and island blue tits using a combination of Sanger sequencing at a population level (20 loci; 12 500 nucleotides) and next-generation sequencing of single population representatives (>3 200 000 nucleotides), analysed in coalescence and phylogenetic frameworks. We found (i) that Afrocanarian blue tits are monophyletic and represent four major clades, (ii) that the blue tit complex has a continental origin and that the Canary Islands were colonized three times, (iii) that all island populations have low genetic variation, indicating low long-term effective population sizes and (iv) that populations on La Palma and in Libya represent relicts of an ancestral North African population. Further, demographic reconstructions revealed (v) that the Canary Islands, conforming to traditional views, hold sink populations, which have not served as source for back colonization of the African mainland. Our study demonstrates the importance of complete taxon sampling and an extensive multimarker study design to obtain robust phylogeographical inferences.孤立岛屿及其通常兼具独特性的生物区系，在解析遗传漂变、遗传变异与适应在种群分化和物种形成进程中的核心作用方面，始终占据关键地位。令进化生物学家深受启发且着迷不已的岛屿系统之一，便是分布于欧洲与非洲的蓝山雀类群复合体（Cyanistes spp.），尤其是加那利群岛内多个遗传分化类群的复杂演化历史。解析非洲-加那利群岛的殖民扩散事件具有特殊研究价值，因近期有非传统观点提出，这些岛屿种群曾作为非洲大陆广布种群的起源来源。我们结合群体水平桑格测序（Sanger sequencing）（覆盖20个基因座、共计12500个核苷酸）与单种群代表样本的下一代测序（next-generation sequencing）（覆盖超过3200000个核苷酸），并在溯祖分析框架与系统发育分析框架下开展数据分析。本研究获得以下结果：（1）非洲-加那利群岛蓝山雀为单系群，可划分为4个主要演化支；（2）蓝山雀类群复合体起源于大陆，加那利群岛曾先后发生3次殖民事件；（3）所有岛屿种群的遗传变异水平均较低，表明其长期有效种群规模偏小；（4）拉帕尔马岛与利比亚的种群代表了北非祖先种群的孑遗类群；（5）种群动态历史重建结果进一步显示，与传统观点一致，加那利群岛的种群均为汇种群，并未充当非洲大陆的反向殖民来源。本研究证实，完整的类群采样与多标记物广泛测序的实验设计，对于获得可靠的系统地理学推断结果具有重要意义。