Abstract
The Harbour porpoise (Phocoena phocoena ) is a highly mobile
cetacean species which primarily occurs in coastal and shelf waters
across the Northern hemisphere. It inhabits heterogeneous seascapes that
vary broadly in salinity and temperature. Here we produced 74 whole
genomes at intermediate coverage to study Harbour porpoise’s
evolutionary history and investigate the role of local adaptation in the
diversification into subspecies and populations. We identified
~6 million high quality SNPs sampled at 8 localities
across the North Atlantic and adjacent waters, which we used for
population structure, demographic, and genotype-environment association
analyses. Our results support a genetic differentiation between three
subspecies, and three distinct populations within the subspeciesP.p. phocoena : Atlantic, Belt Sea and Proper Baltic Sea.
Effective population size and Tajima’s D levels suggest a population
contraction in both Black Sea and Iberian porpoises while a population
expansion in the P.p. phocoena populations. Phylogenetic trees
indicate a post-glacial colonization of Harbour porpoises from a
southern refugium. Genotype-environment association analysis identified
salinity as a major driver in genomic variation and we identified
candidate genes putatively underlying adaptation to different salinity
levels. Our study highlights the value of whole genome resequencing to
unravel subtle population structure in highly mobile species and shows
how strong environmental gradients and local adaptation may lead to
population differentiation. The results have great conservation
implications as we found major levels of inbreeding and low genetic
diversity in the endangered Black Sea subspecies and identified the
critically endangered Proper Baltic Sea porpoises as a separate
population.
Keywords: Harbour Porpoise, Genomics, Genetic Structure, Local
Adaptation, Conservation