Data from: 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 DQB04
allele also gave this population the highest nucleotide diversity for DQB.
Strong differentiation was evident for DQA, DQB, and DQA-DQB haplotypes
between the regional populations of Hector’s dolphins (FST>0.213)
and both subspecies (FST>0.311). Differentiation was generally
greater than observed at neutral microsatellite loci, suggesting the
influence of selection between geographically proximate East and West
Coast populations. This might be the result of spatial differences in
directional selection on those opposite coastlines. Additionally, measures
of the ratio of non-synonymous to synonymous substitutions (dN/dS) were
consistent with balancing selection over evolutionary time. Together,
these results suggest a complex interplay of balancing selection,
directional selection, local fidelity, and genetic drift.