The influence of selection on MHC DQA and DQB haplotypes in the endemic New Zealand Hector’s and Māui dolphins

Strong balancing selection on the Major Histocompatibility Complex (MHC) can lead to different patterns in gene frequencies and neutral genomic variation within species. We investigated diversity and geographic structure of MHC genes DQA and DQB, as well as their inferred functional haplotypes, from two regional populations (East and West Coast) of the endangered Hector’s dolphin (Cephalorhynchus hectori hectori) and the critically endangered Māui dolphin (Cephalorhynchus hectori maui) (West Coast, North Island), and contrasted these results with patterns from neutral microsatellites. The Māui had the lowest number of alleles for DQA (2) and DQB (3), consistent with strong genetic drift acting on this remnant population. However, the two retained DQA alleles are amongst the most divergent combinations of all four alleles found across the Hector’s metapopulation, potentially reflecting the retention of divergent alleles due to balancing selection. The high frequency of the divergent DQB0...