Complex population structure in African village dogs and its implications for inferring dog domestication history

Abstract

High genetic diversity of East Asian village dogs has recently been used to argue for an East Asian origin of the domestic dog. However, global village dog genetic diversity and the extent to which semiferal village dogs represent distinct, indigenous populations instead of admixtures of various dog breeds has not been quantified. Understanding these issues is critical to properly reconstructing the timing, number, and locations of dog domestication. To address these questions, we sampled 318 village dogs from 7 regions in Egypt, Uganda, and Namibia, measuring genetic diversity >680 bp of the mitochondrial D-loop, 300 SNPs, and 89 microsatellite markers. We also analyzed breed dogs, including putatively African breeds (Afghan hounds, Basenjis, Pharaoh hounds, Rhodesian ridgebacks, and Salukis), Puerto Rican street dogs, and mixed breed dogs from the United States. Village dogs from most African regions appear genetically distinct from non-native breed and mixed-breed dogs, although some individuals cluster genetically with Puerto Rican dogs or United States breed mixes instead of with neighboring village dogs. Thus, African village dogs are a mosaic of indigenous dogs descended from early migrants to Africa, and non-native, breed-admixed individuals. Among putatively African breeds, Pharaoh hounds, and Rhodesian ridgebacks clustered with non-native rather than indigenous African dogs, suggesting they have predominantly non-African origins. Surprisingly, we find similar mtDNA haplotype diversity in African and East Asian village dogs, potentially calling into question the hypothesis of an East Asian origin for dog domestication.

Fig. 1.

Map of village dog sampling locations. Colors denote each distinct region and dots show approximate range of sampling within each region. See Table S1 for full description.

Fig. 2.

STRUCTURE analysis across 389 SNP and microsatellite loci in African village and American mixed breed dogs.

Fig. 3.

Principal component analysis of indigenous African village dogs. (A) PCA with the 89 microsatellite loci (n = 152). (B) PCA with the 300 SNP loci (n = 126).

Fig. 4.

Principal component analysis of village dogs and dogs from 5 putatively African and Middle Eastern breeds across 300 SNP markers in 186 village dog and 105 breed dogs.

Fig. 5.

Number of haplotypes (excluding indels) versus number of dogs sampled within Africa and East Asian geographic regions. Note log scale of x axis. East Asian samples from (6); African samples from this study or by (10). See Table S4 for a list of the areas used to construct this figure. The blue line depicts the expected number of haplotypes from Ewens's sampling formula (29), which assumes an infinite alleles model; E(K)=Σ_j=0ⁿ⁻¹θ /(j+θ). Using Levenberg-Marquardt nonlinear regression, we estimate θ to be 8.654 (95% C.I. = [7.41, 9.89]).