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).

地理隔离的种群通常因物理或非物理障碍阻碍扩散，导致基因交流减少，进而形成遗传结构。在这一研究背景下，具有高移动性的生物（如海鸟）颇具研究价值，因为物理屏障的影响较弱，非物理障碍的作用可能相对更为突出。本研究利用微卫星标记（microsatellite）与线粒体数据，探究欧洲特有海鸟——欧洲鸬鹚（European Shag，学名Phalacrocorax aristotelis）大西洋种群与地中海种群的遗传结构及系统地理学（phylogeography）特征，并明确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、西班牙/科西嘉以及东地中海种群可分为三个系统发育支系，其形成疑似源于更新世（Pleistocene）时期的种群片段化事件，随后伴随种群范围扩张。尽管相邻种群间存在显著的当代基因流，但通过微卫星标记估算的遗传结构中，同样能观察到这类历史片段化的痕迹。在距离较远的种群，以及被物理与生态屏障分隔的种群中，检测到更强的遗传结构，这一现象大概率由景观格局、恋巢习性（philopatry）与局部适应共同促进形成。本研究凸显了更新世气候变化对鸬鹚种群的持久影响，尤其是地中海盆地内的种群，并表明隐秘的北方冰期避难所与已知的南方冰期避难所，均对欧洲海鸟的遗传结构塑造具有作用。最后，本研究还阐明了，尽管极端环境条件（如种群崩溃）可触发长距离扩散，但当代生态屏障与行为特征仍可维持种群分化。