Genomic divergence
To identify the extent of genetic divergence among sites, we used two
approaches: 1) Principal Component Analysis (PCA) was used to explore
genetic clustering of Mývatn stickleback, and 2) a model-based admixture
analysis was used to determine population genetic structure by
calculating the proportion of an individual’s genome that originates
from different hypothetical ancestral gene pools (i.e., admixture
coefficients). PCA was conducted in ADEGENET package , and as suggested
by 100% of the initial PCs were retained when identifying the number of
clusters. Admixture analyses were run using SNMF, which estimates
admixture coefficients using non-negative matrix algorithms and makes no
assumptions about drift or Hardy-Weinberg equilibrium (HWE). SNMF was
run using the LEA package in R for number of ancestral populations (K) 1
– 10. Pairwise genome-wide Nei’s FSTs were calculated
between all sites and habitats using VCFTOOLS. Contemporary effective
population size (Ne ) was estimated using the
LD-based method, as implemented in NeEstimator v2 . To remove physical
linkage (as required in this method), we first thinned the SNPs across
10KB windows using VCFTOOLS. To provide confidence intervals of
estimates of Ne , we calculated Ne across each chromosome
independently.