Figure 4.

Modeling the Ancestry of African Golden Wolves

(A) TreeMix tree with all samples, estimated using the pairwise correlation of allele frequencies between all groups of samples. This tree is fit with three migration edges. The first three migration edges all indicate extensive gene flow from the gray and Ethiopian wolves into the African golden wolves, suggesting a hybrid origin for this species.

(B and C) The QP graph is an admixture graph estimated using all pairwise D statistics between samples. Estimated genetic drift is shown along the solid lines in units of f2 distance (parts per thousand), and estimated mixture proportions are given along the dotted lines. Names of specific modern populations are shown in full, whereas hypothetical ancestral individuals are represented by letters.

(B) This tree shows all the possible placements—highlighted in red—for the Northwestern African golden wolf, chosen due to their low levels of gene flow with the Ethiopian wolf. These were modeled as possible internal and external nodes and as an admixed group from all possible node pairs.

(C) The best fitting graph with a Z value closest to 0, modeling the Ethiopian wolf-like and gray wolf-like ancestry of Northwestern and Eastern African golden wolves, as well as gene flow into modern Ethiopian wolves from the Eastern African golden wolves. This admixture graph suggests that the African golden wolves are probably a species of hybrid origin, derived from the gray wolf and Ethiopian wolf as the parental species. Further, Figure S4 shows admixture graphs showing potential gene flow from a “ghost” basal canid lineage into the ancestor of wolves and dogs.