Principal component analysis
The PCA for genomic variation in the 191 Swedish accessions in Figure 2E
was performed using a compressed mixed linear model run in R
implementing the GAPIT package (Lipka et al., 2012; Zhang et al., 2010).
Genotype data was downloaded from the 1001 genomes dataset filtered for
bialleleic SNPs with >5% MAF (minor allele frequency). The
first two PCs were used to split the accessions into the categories in
Figure 2D and F.