The Major Histocompatibility Complex (MHC) is a central element in the vertebrate immune system. While MHC genes are a common target of conservation genomic studies, it has been challenging to reliably amplify locus-specific alleles, which is especially problematic when studying endangered lineages, like some Harbour porpoise (Phocoena phocoena) populations and subspecies. Here, we manually annotated all MHC II genes in the Harbour porpoise genome, and genotyped every exon 2 in 94 individuals spanning six geographical regions, including the endangered Black Sea porpoise subspecies (Phocoena phocoena relicta) and the endangered Proper Baltic Sea population of the North Atlantic subspecies (P. p. phocoena). We performed gene-wise analyses of diversity and selection, and put the results into perspective with 24 available Harbour porpoise genomes. Furthermore, we characterized all MHC II genes in 19 available long-read cetacean and terrestrial outgroups genomes to study the MHC II evolution across the cetacean diversification. From the 10 MHC II loci annotated in the Harbour porpoise genome, two (DRB1 and DQB) exhibited inflated allelic diversity and signatures of positive selection. Interestingly, DRB genes followed different evolutionary trajectories in mysticetes and odontocetes. Our results have significant conservation implications since we identified reduced MHC II diversity in the endangered Black Sea subspecies, and provide a case study for reliable MHC II genotyping in other species. Further, our study demonstrates the need for long-read genomes to understand the genomic architecture of MHC and to accurately assess its diversity and evolution.

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 subspecies P.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.