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

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 09/2009; 106(33):13903-8. DOI: 10.1073/pnas.0902129106
Source: PubMed


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.

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Available from: Marius Hedimbi, Jul 30, 2014
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    • "Exists as commensal and feral populations over much of tropical Asia and on islands as far as New Guinea (Miklouho-Maclay, 1882) and historically Polynesia, including Hawaii and New Zealand (Oskarsson et al., 2012). Pre-Colombian American breeds, Canaan breed of the Middle East, and some (but not all) native African and East Asian breeds also belong to this subspecies (Boyko et al., 2009; von Holdt et al., 2010; Larson et al., 2012). Feral Dogs of this subspecies reverse to Dingo-like rather than Gray Wolf-like appearance (Dinets, Rotshild, 1998). "

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    • "Mitochondrial DNA (mtDNA) mainly used for phylogenetic population studies in the domestic dog (Canis lupus familiaris) regarding their geographic and temporal origin (Savolainen et al. 2002; Boyko et al. 2009; Pang et al. 2009; Vonholdt et al. 2010) as well as their evolutionary history (Tsuda et al. 1997; Vilà et al. 2005) also provides information regarding maternal gene flow and phylogenetic relationships within and among purebred dog breeds because of its maternal pattern of inheritance. In addition, the paternally inherited Y chromosome allows conclusions about evolutionary events in paternal lineages of mammals. "
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    ABSTRACT: The Norwegian Lundehund breed of dog has undergone a severe loss of genetic diversity as a result of inbreeding and epizootics of canine distemper. As a consequence, the breed is extremely homogeneous and accurate sex identification is not always possible by standard screening of X-chromosomal loci. To improve our genetic understanding of the breed we genotyped 17 individuals using a genome-wide array of 170 000 single nucleotide polymorphisms (SNPs). Standard analyses based on expected homozygosity of X-chromosomal loci failed in assigning individuals to the correct sex, as determined initially by physical examination and confirmed with the Y-chromosomal marker, amelogenin. This demonstrates that identification of sex using standard SNP assays can be erroneous in highly inbred individual
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    • "Specifically a small set of genes associated with phenotypic traits related to morphology, coat texture, color and behavior have been identified that are common to breeds sharing a similar phenotype [1–5]. Other studies have also provided insight into the selective forces at play during the process of domestication [6–9], admixture with wild relatives [10, 11], or the population structure purebred and village dogs [12–14]. "
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