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.

Ecological speciation within the mormyrid genus Campylomormyrus resulted in sympatric species exhibiting divergence in their feeding apparatus and electric organ discharge (EOD). This study documents the overall diet of the genus Campylomormyrus and examines the hypothesis that Campylomormyrus radiation is caused by an adaptation to different food sources. We performed diet assessment of five sympatric Campylomormyrus species (C. alces, C. compressirostris, C. curvirostris, C. tshokwe, C. numenius) and their sister taxon Gnathonemus petersii with markedly different snout morphologies and EODs using hybrid capture/HTS DNA metabarcoding of their stomach contents. Our approach allowed for high taxonomic resolution of prey items, including benthic invertebrates, allochthonous invertebrates, and vegetation. Comparisons of the diet compositions using quantitative measures and diet overlap indices revealed that all species are able to exploit multiple food niches in their habitats, i.e., fauna at the bottom, the water surface, and the water column. Major part of the diet is larvae of aquatic insects, such as dipterans, coleopterans, and trichopterans, known to occur in holes and interstitial spaces of the substrate. The results showed that different snout morphologies and the associated divergence in the EOD translate into different prey spectra. This suggests that the diversification in EOD and the morphology of the feeding apparatus is under functional adaptation.

Ecological speciation within the mormyrid genus Campylomormyrus resulted in sympatric species exhibiting divergence in their feeding apparatus and electric organ discharge (EOD). This study provides direct evidence to support the suggested ecological speciation scenario that Campylomormyrus radiation is caused by an adaptation to different food sources. We performed diet assessment of sympatric Campylomormyrus species with markedly different snout morphologies and EODs using hybrid capture/NGS DNA metabarcoding of their stomach contents. Our approach allowed for high taxonomic resolution of prey items, including benthic invertebrates, allochthonous invertebrates, and vegetation. Comparisons of the diet compositions using quantitative measures and diet overlap indices revealed that all species are able to exploit multiple food niches in their habitats, i.e. fauna at the bottom, the water surface, and the water column. The major part of the diet is larvae of aquatic insects, such as dipterans, coleopterans, and trichopterans, known to occur in holes and interstitial spaces of the substrate. The results showed that different snout morphologies and the associated divergence in the EOD translate into different prey spectra. This suggests that the diversification in EOD and the morphology of the feeding apparatus is under functional adaptation.