Figure 2.

Hominid deletion phylogeny. (A) Neighbor-joining tree constructed from pairwise edit distance of genotypes for fixed and segregating deletions >5 kb. Branch length confidence estimates were generated by repeatedly subsampling 50% of the variants and regenerating the topology. All species and subspecies relationships are reconstructed with high confidence and are concordant with the topology identified from SNPs with the exception of Central chimpanzees, which form an outgroup to the other chimpanzee subspecies as a result of their increased diversity. SNP-based trees cluster Central and Eastern chimpanzees on a single clade. Among chimpanzees, the three individuals Yolanda, Andromeda, and Vincent, the Eastern-most individuals assessed in this study from Gombe National Reserve in Tanzania, cluster together with strong support. Additionally, the individuals Tobi and Julie, a distinct subpopulation of Nigerian chimpanzees by SNP analysis, cluster together. Eastern lowland gorillas form an outgroup to the gorilla clade and the Cross River gorilla clusters as an outgroup to Western lowland gorillas. The archaic Denisova individual clusters as an outgroup to all humans with 97% support. (B) PCA of segregating deletion genotypes recapitulates intrapopulation relationships and additionally the relative diversity within the populations assessed.