| Summary: | Seabird populations worldwide have been declining dramatically over the last decades as a result of a range of environmental and anthropogenic stressors. Nevertheless, management of threatened seabirds is arguably hampered by the severe underutilization of whole genome sequencing (WGS) combined with a limited understanding of the interplay of complex ecological factors affecting population connectivity and contributing to the genetic population structure. By providing detailed genomic data, WGS allows to assess levels of connectivity and gene flow between distinct breeding populations and, thus, helps to identify relevant conservation units for seabirds. Atlantic puffins (Fratercula arctica) have been designated as vulnerable to extinction globally and listed as endangered in Europe. A lack of genetic data for puffins at all spatial scales obstructs efforts towards an assessment of dispersal barriers, limits our understanding of cause-and-effect dynamics between population trends, ecology and the marine ecosystem, and hinders the development of adapted large-scale conservation actions. Here, I present the first whole genome analysis of population structure, gene flow, demographic history and structural DNA variation of a pelagic, North Atlantic seabird. The analysis of 13 Atlantic puffin colonies throughout the majority of the species’ breeding range revealed four large, genetically distinct clusters, which broadly overlap with the currently recognized taxonomy that includes three subspecies (F. a. naumanni, F. a. arctica and F. a. grabae) (Paper I). Additionally, I found a hybrid population in the High Arctic resulting from interbreeding between the High Arctic, large-bodied subspecies F. a. naumanni and the temperate and smaller subspecies F. a. arctica (Paper I & Paper III). Using whole genome data from contemporary and museum specimens, I provide evidence that this hybridization started as recent as six to seven generations ago resulting from a southward range shift of F. a. naumanni and coinciding with ...
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