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.

研究背景：利用遗传数据推断种群与物种历史以及种群分层，对于区分不同物种形成场景、正确解读全基因组扫描中适应性进化与性状关联的信号均具有重要意义。本研究采用了两个近缘物种——斑姬鹟（pied flycatcher）与领姬鹟（collared flycatcher）——的种群样本中24个内含子位点的重测序数据。研究结果：我们应用隔离-迁移（Isolation-Migration）模型、群体归属分析方法，估算了物种间以及物种种内种群间的遗传分化与遗传多样性水平。数据表明，两个物种的分化时间不足100万年，显著短于此前基于线粒体DNA（mtDNA）得到的估算结果；结果指向单向基因流从斑姬鹟流向领姬鹟的物种分化场景，并暗示在新近建立的杂交带中，杂交障碍仍具有一定通透性。此外，我们检测到显著的种群分层现象，主要表现为西班牙种群与其他斑姬鹟种群之间的分化。研究结论：本研究结果进一步为“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证据。同时我们认为，针对这类生态模式物种开展的后续基因型-表型关联分析，应当将种群分层因素纳入考量进行设计。