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，导致基因流连接性减弱，进而形成种群遗传结构。在此背景下，具备高移动能力的生物（如海鸟）颇具研究价值：物理障碍的影响微弱，意味着非物理障碍的作用可能相对更为显著。本研究利用微卫星（microsatellite）标记与线粒体数据，针对欧洲特有海鸟——欧洲沙格鸬鹚（European Shag，学名*Phalacrocorax aristotelis*）的大西洋与地中海种群开展遗传结构与系统地理学（phylogeography）分析，并解析其物种分化的核心驱动因子。线粒体标记分析显示，北大西洋种群、西班牙/科西嘉种群与东地中海种群可划分为三个系统发育支系，其形成过程推测为更新世时期的种群分化，随后伴随分布范围扩张。尽管相邻种群间存在显著的当代基因流，但基于微卫星标记推断的种群遗传结构中，同样能观测到上述历史分化的痕迹。在地理距离较远的种群，以及被物理与生态障碍分隔的种群中，观测到更强的遗传结构，其形成可能受景观格局、恋巢性（philopatry）与局部适应共同推动。本研究凸显了更新世气候变化对鸬鹚种群的长期影响，尤其在地中海盆地范围内，并提出隐秘的北部冰期避难所与已知的南部避难所，均可对欧洲海鸟的种群遗传结构产生塑造作用。最后，本研究阐明了：即便极端环境条件（如种群骤降）可触发长距离扩散，当代生态障碍与行为特征仍可维持种群间的分化格局。