The organization in three separate clusters can also be observed in the principal component analysis (PCA; Figure 2B). The first two PCs (Figure 2A, left) explained 7.9 % and 5.0 % of the total variation. PC1 separates the West-East clusters from the Center, and PC2 partitions the Western cluster from the Eastern populations. Sampling locations do not form individual groups within the three main clusters, except for Madeira, Azores and partially Greece, reflecting the high amount of admixture observed in Figure 2A. PC3 further separated the individuals from Azores from those of Madeira (Figure 2A right).
The phylogenetic tree of complete mitogenomes shows two well supported clades at the extremes, with some haplotypes branching from the middle part of the tree (Figure 3 and Figure S2). This agrees with the genetic clusters observed for the nuclear data belonging to regions with low FST variance (Figure S3 and Figure S4). While the central haplotypes are more common in the West group, the groups of haplotypes at each extreme of the tree are not geographically confined to a region, suggestive of high gene flow between the Center and the East.