Genomic divergence
Using 1 205 604 SNP markers across 186 individuals, principal component
analysis (PCA), pairwise FST and admixture
analyses all revealed little genome-wide differentiation. First, the
first two principal components (PC1 and PC2) explained only 0.009 and
0.008% of variance, respectively (see supplement). There was some
clustering of individuals along PC1 (Fig S4), which could be indicative
of clustering based on genotype (associated with, for example, spatial
structure, sex or phenotype), on areas of low recombination or,
alternatively, arise as a statistical artefact. Our PCA did not cluster
individuals according to any a priori hypotheses for which we had
data (i.e., according to basin, habitat type, site, sex, phenotype or
tapeworm presence). Second, pairwise Nei’s Fstwere very low at both habitat and site level (Table S3). Third,
admixture analyses using snmf revealed that the model with K =
1 had the lowest cross-entropy score, suggesting that K = 1 best
predicted the population genetic structure in our dataset (Figure 3).
This suggests that Mývatn stickleback form one panmictic population. The
effective populations size (Ne) for the
population was estimated as 1976 (± 640).