distribution of particularly informative SNPs for each PC axis provides one method to inspect whether the apparent differences in substructure are due to a single or very limited number of genomic intervals. For the first two axes of the PCA the particularly informative SNPs, ESAIMs, are widely distributed (Tables S1 and S2). Deletion of subsets of particularly informative markers (e.g. SNPs in lactase and MHC regions) did not change the patterns observed using these ESAIMs for either PC1 or PC2. Since we observed that the Chromosome 8 inversion affected the PCA, we also examined the common European inversion on chromosome 17 [27]. Here, deletion of this chromosomal interval had no effect on the first 10 PCs presumably due to the smaller size of this inversion, 900 kb compared to ∼4Mb for the Chromosome 8 inversion.
