title: 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.
authors: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.
authors: Adam R
authors: AR
authors: Boyko
authors: Ryan H
authors: RH
authors: Boyko
authors: Corin M
authors: CM
authors: Boyko
authors: Heidi G
authors: HG
authors: Parker
authors: Marta
authors: M
authors: Castelhano
authors: Liz
authors: L
authors: Corey
authors: Jeremiah D
authors: JD
authors: Degenhardt
authors: Adam
authors: A
authors: Auton
authors: Marius
authors: M
authors: Hedimbi
authors: Robert
authors: R
authors: Kityo
authors: Elaine A
authors: EA
authors: Ostrander
authors: Jeffrey
authors: J
authors: Schoenebeck
authors: Rory J
authors: RJ
authors: Todhunter
authors: Paul
authors: P
authors: Jones
authors: Carlos D
authors: CD
authors: Bustamante
mesh_terms: D000349:Africa; D000818:Animals; D000829:Animals, Domestic / Q000235:genetics; D001947:Breeding; D004272:DNA, Mitochondrial / Q000235:genetics; D004285:Dogs / Q000235:genetics*; D014644:Genetic Variation; D005828:Genetics, Population; D018895:Microsatellite Repeats / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis
chemical_list: D004272:DNA, Mitochondrial