Population structure
Population structure was analyzed using principal components as well as
hierarchical clustering analysis. A covariance matrix was calculated
using PCAngsd and then we used RStudio v. 1.3.1093 (RStudio Team, 2018)
with R v. 3.6.0 (R Core Team, 2019) to conduct eigenvector decomposition
and created plots comparing principal components axes (PCs). We used
clustering in NGSadmix to infer the “best” number of populations and
estimate ancestry proportions. We ran NGSadmix five times each with
population numbers (i.e. K values) ranging from one to six. We
used the Evanno method implemented in CLUMPAK to determine the best fit
K value (accessed at http://clumpak.tau.ac.il/bestK.html).