Figure 3

Phylogeny based on P/A regions as group-wise markers. A bootstrap network tree based on Jaccard’s distances of binary markers based on regions with consistent within-group presence/absence of reads. The tree topology, though more unstable, entirely overlaps with that produced by the SNPs in Figure 2. This suggests that distances deriving from P/A regions are primarily based on elements with segregation patterns similar to those of genetic variation, probably transposable elements and regions of DNA methylation.