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.