Data from: Inferring the demographic history of European Ficedula flycatcher populations

Background: Inference of population and species histories and population stratification using genetic data is important for discriminating between different speciation scenarios and for correct interpretation of genome scans for signs of adaptive evolution and trait association. Here we use data from 24 intronic loci re-sequenced in population samples of two closely related species, the pied flycatcher and the collared flycatcher. Results: We applied Isolation-Migration models, assignment analyses and estimated the genetic differentiation and diversity between species and between populations within species. The data indicate a divergence time between the species of < 1 million years, significantly shorter than previous estimates using mtDNA, point to a scenario with unidirectional gene-flow from the pied flycatcher into the collared flycatcher and imply that barriers to hybridisation are still permeable in a recently established hybrid zone. Furthermore, we detect significant population stratification, predominantly between the Spanish population and other pied flycatcher populations. Conclusions: Our results provide further evidence for a divergence process where different genomic regions may be at different stages of speciation. We also conclude that forthcoming analyses of genotype-phenotype relations in these ecological model species should be designed to take population stratification into account.**背景**：利用遗传数据推断种群与物种演化历史以及种群分层，对于区分不同物种形成情景、正确解读基因组扫描中适应性进化信号与性状关联的结果具有重要意义。本研究使用了两个近缘物种——斑姬鹟（pied flycatcher）和领姬鹟（collared flycatcher）的种群样本中24个内含子位点的重测序数据。 **结果**：本研究采用隔离-迁移模型（Isolation-Migration model）与群体归属分析方法，评估了物种间以及物种种群内的遗传分化与遗传多样性。数据显示，两个物种的分化时间不足100万年，显著短于此前利用线粒体DNA（mtDNA）得到的估算结果；研究结果指向一种单向基因流模式——即基因从斑姬鹟流向领姬鹟，同时表明在新近形成的杂交带中，杂交生殖障碍仍具有可渗透性。此外，本研究检测到显著的种群分层现象，主要存在于西班牙种群与其他斑姬鹟种群之间。 **结论**：本研究结果为「不同基因组区域可能处于物种形成的不同阶段」这一分化过程提供了进一步的证据。同时，我们认为后续针对这些生态模式物种的基因型-表型关联分析，应当设计为纳入种群分层因素的研究方案。