Abstract
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 a period of rapid ecological change in the Arctic (Paper III). The presence of a hybrid population may also be a forecast of future scenarios throughout other parts of the Arctic illustrated by the sympatry of genetically distinct, but nonadmixing, puffin subspecies within a single High Arctic colony on the west coast of Greenland (Paper II). While genomic-based demographic reconstructions suggest that F. a. naumanni and F. a. arctica diverged due to climatic oscillations in the Pleistocene (Paper III), our understanding of the genomic basis of puffin subspecies differentiation and potential adaptive divergence is limited. Hence, I used single nucleotide polymorphisms, structural variants and short tandem repeats to identify genomic outlier loci that potentially contribute to intraspecific gene flow barriers and phenotypic differences between the subspecies (Paper IV). The results of this thesis highlight the importance of historical and modern whole genome data in understanding population structure and gene flow in seabirds, as well as the genomic basis of intraspecific, phenotypic differences and local adaptation. In light of a global biodiversity loss occurring at unprecedented rates, these findings should have implications for future seabird research and conservation management.