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).