d. Neutral evolution
We previously generated reduced representation genomic sequence data for
the populations in this study, using ddRADseq following the protocol of
Peterson, Weber, Kay, Fisher, & Hoekstra (2012) modified as described
in Stuart et al. (2017). From these data we estimated genome-wide mean
heterozygosity for each individual fish, and from this population-level
mean heterozygosity. We also calculated pairwise Weir-Cockerham adjusted
FST between each pair of populations.
If MHC polymorphism is strongly affected by bottlenecks or other neutral
population genetic processes, then we may expect that MHC diversity
would be positively correlated with genomic mean heterozygosity. We
tested whether the average number of MHC alleles (per fish) in each
population varied as a function of the mean heterozygosity. We might
then also expect that between-population MHC divergence is primarily a
reflection of shared ancestry due to colonization processes or ongoing
gene flow. To test this, we used a Mantel test to evaluate correlations
between among-population MHC distance matrix and the FSTmatrix.