Data from: Genetic structure in the European endemic seabird, Phalacrocorax aristotelis, was shaped by a complex interaction of historical and contemporary, physical and non-physical drivers

Geographically separated populations tend to be less connected by gene flow, as a result of physical or non-physical barriers preventing dispersal, and this can lead to genetic structure. In this context, highly mobile organisms such as seabirds are interesting because the small effect of physical barriers means non-physical ones may be relatively more important. Here we use microsatellite and mitochondrial data to explore the genetic structure and phylogeography of Atlantic and Mediterranean populations of a European endemic seabird, the European Shag, Phalacrocorax aristotelis, and identify the primary drivers of their diversification. Analyses of mitochondrial markers revealed three phylogenetic lineages grouping the North Atlantic, Spanish/Corsican and Eastern Mediterranean populations, apparently arising from fragmentation during the Pleistocene followed by range expansion. These traces of historical fragmentation were also evident in the genetic structure estimated by microsatellite markers, despite significant contemporary gene flow among adjacent populations. Stronger genetic structure, probably promoted by landscape, philopatry and local adaptation, was found among distant populations and those separated by physical and ecological barriers. This study highlights the enduring effect of Pleistocene climatic changes on shag populations, especially within the Mediterranean Basin, and suggests a role for cryptic northern refugia, as well as known southern refugia, on the genetic structure of European seabirds. Finally, it outlines how contemporary ecological barriers and behavioral traits may maintain population divergence, despite long-distance dispersal triggered by extreme environmental conditions (e.g. population crashes).

地理隔离的种群往往因物理或非物理障碍阻碍扩散，导致基因交流（gene flow）受限，进而形成遗传结构（genetic structure）。在此背景下，具有高移动能力的生物（如海鸟（seabirds））便颇具研究价值——物理屏障的影响较弱，意味着非物理屏障的作用可能相对更为显著。本研究利用微卫星（microsatellite）与线粒体（mitochondrial）分子标记数据，探究欧洲特有海鸟——欧洲鸬鹚（European Shag，学名*Phalacrocorax aristotelis*）的大西洋与地中海种群的遗传结构与系统地理学（phylogeography）格局，并解析其物种分化的主要驱动因素。线粒体标记分析显示，北大西洋种群、西班牙/科西嘉种群以及东地中海种群可划分为三个系统发育谱系（phylogenetic lineages），这些谱系显然形成于更新世（Pleistocene）的种群片段化事件，随后发生了分布范围扩张。尽管相邻种群间存在显著的当代基因交流，但微卫星标记所推断的遗传结构中，同样可见历史片段化的痕迹。种群间距离越远，或被物理与生态屏障分隔时，其遗传结构往往更强——这一现象可能由景观格局、恋巢性（philopatry）以及局部适应所推动。本研究凸显了更新世气候变化对鸬鹚种群的持久影响，尤其是地中海盆地（Mediterranean Basin）内的种群，并表明隐秘的北方避难所与已知的南方避难所均对欧洲海鸟的遗传结构塑造具有重要作用。最后，本研究还阐明了：即便极端环境条件（如种群骤降）可触发长距离扩散，当代生态屏障与行为特征仍可维持种群间的分化。