Sequencing results and parasite information
We kept 1277 stickleback from 26 sites for subsequent analyses, after excluding 160 individuals whose genotype calls may have under-represented their actual diversity due to low read depth (<450 reads each; Figure S1). These 26 sites were from 7 different watersheds (sample site information is in Table S1). The habitat types included 21 lakes, two rivers, and three estuaries. Each sample site had an average sample size of about 50 fish, with a range from 18 to 78 (Mean = 49.11, SD=14.7). We identified a total of 1115 unique MHC alleles, 820 (73.54%) of which were private alleles found in only one population. On average, each fish had seven distinct MHC alleles, with a range from 3- 15 (M=6.94, SD=1.87). 4.6% variation of MHC allelic richness could be explained by habitat type (ANOVA, habitat term, p < 2e-16), 1.7% variation could be explained by watershed (ANOVA, watershed term, p = 4.38e-05), and 23.0% of variation was explained by sample site (ANOVA, watershed/site term, p < 2e-16). Fish from river (M=8.38, SD=1.98) and estuary (M=7.1, SD=1.81) habitat had higher MHC allelic diversity than fish from lake habitat (M=6.77, SD=1.82).
In total, we identified 33 parasite taxa (parasite information is in Table S2). On average, each fish 2.5 different parasite taxa, with a range from 0 to 10 (Mean = 2.53, SD=1.74). Fish from river (M=1.94, SD=1.6) and estuary (M=1.15, SD=0.76) habitat had lower parasite burdens than fish from lake habitat (M=2.82, SD=1.74). 11.8% variation in parasite richness could be explained by habitat type, 4.9% variation could be explained by watershed (ANOVA, habitat term, p < 2e-16), while 28.3% of variation could be explained by sample site (ANOVA, watershed/site term, p < 2e-16). See Bolnick et al. (2019 and 2020) for further analysis of ecological factors structuring the parasite metacommunity (diversity, composition, co-occurrence) within and among lakes.