Dog domestication and the dual dispersal of people and dogs into the Americas.
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ABSTRACT:
SUBMITTER: Perri AR
PROVIDER: S-EPMC8017920 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description: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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Project description:BACKGROUND:Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and three dogs from Iran which covers the eastern part of the Fertile Crescent located in Southwest Asia where the independent domestication of most of the plants and animals has been documented and also high haplotype sharing between wolves and dog breeds has been reported. RESULTS:Higher diversity was found within the wolf genome compared with the dog genome. A total number of 12.45 million SNPs were detected in all individuals (10.45 and 7.82 million SNPs were identified for all the studied wolves and dogs, respectively) and a total number of 3.49 million small Indels were detected in all individuals (3.11 and 2.24 million small Indels were identified for all the studied wolves and dogs, respectively). A total of 10,571 copy number variation regions (CNVRs) were detected across the 6 individual genomes, covering 154.65?Mb, or 6.41%, of the reference genome (canFam3.1). Further analysis showed that the distribution of deleterious variants in the dog genome is higher than the wolf genome. Also, genomic annotation results from intron and intergenic regions showed that the proportion of variations in the wolf genome is higher than that in the dog genome, while the proportion of the coding sequences and 3'-UTR in the dog genome is higher than that in the wolf genome. The genes related to the olfactory and immune systems were enriched in the set of the structural variants (SVs) identified in this work. CONCLUSIONS:Our results showed more deleterious mutations and coding sequence variants in the domestic dog genome than those in wolf genome. By providing the first Iranian dog and wolf variome map, our findings contribute to understanding the genetic architecture of the dog domestication.
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Project description:Studies of mitochondrial DNA (mtDNA) diversity indicate explicitly that dogs were domesticated, probably exclusively, in southern East Asia. However, Southwest Asia (SwAsia) has had poor representation and geographical coverage in these studies. Other studies based on archaeological and genome-wide SNP data have suggested an origin of dogs in SwAsia. Hence, it has been suspected that mtDNA evidence for this scenario may have remained undetected. In the first comprehensive investigation of genetic diversity among SwAsian dogs, we analyzed 582 bp of mtDNA for 345 indigenous dogs from across SwAsia, and compared with 1556 dogs across the Old World. We show that 97.4% of SwAsian dogs carry haplotypes belonging to a universal mtDNA gene pool, but that only a subset of this pool, five of the 10 principal haplogroups, is represented in SwAsia. A high frequency of haplogroup B, potentially signifying a local origin, was not paralleled with the high genetic diversity expected for a center of origin. Meanwhile, 2.6% of the SwAsian dogs carried the rare non-universal haplogroup d2. Thus, mtDNA data give no indication that dogs originated in SwAsia through independent domestication of wolf, but dog-wolf hybridization may have formed the local haplogroup d2 within this region. Southern East Asia remains the only region with virtually full extent of genetic variation, strongly indicating it to be the primary and probably sole center of wolf domestication. An origin of dogs in southern East Asia may have been overlooked by other studies due to a substantial lack of samples from this region.
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Project description:Dogs were present in the Americas before the arrival of European colonists, but the origin and fate of these precontact dogs are largely unknown. We sequenced 71 mitochondrial and 7 nuclear genomes from ancient North American and Siberian dogs from time frames spanning ~9000 years. Our analysis indicates that American dogs were not derived from North American wolves. Instead, American dogs form a monophyletic lineage that likely originated in Siberia and dispersed into the Americas alongside people. After the arrival of Europeans, native American dogs almost completely disappeared, leaving a minimal genetic legacy in modern dog populations. The closest detectable extant lineage to precontact American dogs is the canine transmissible venereal tumor, a contagious cancer clone derived from an individual dog that lived up to 8000 years ago.
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Project description:The history of dog domestication is still under debate, but it is doubtless the process of an ancient partnership between dogs (Canis familiaris) and humans. Although data on ancient DNA for dog diversity are still incomplete, it is clear that several regional dog populations had formed in Eurasia up to the Holocene. During the Neolithic Revolution and the transition from hunter-gatherer to farmer societies, followed by civilization changes in the Antiquity period, the dog population structure also changed. This process was due to replacement with newly formed dog populations. In this study, we present for the first time mitochondrial data of ancient dog remains from the Early Neolithic (8000 years before present (BP)) to Late Antiquity (up to 3th century AD) from southeastern Europe (the Balkans). A total of 16 samples were analyzed, using the mitochondrial D-loop region (HVR1). The results show the presence of A (70%) and B (25%) clades throughout the Early and Late Neolithic Period. In order to clarify the position of our results within the ancient dog population in Eneolithic Eurasia, we performed phylogenetic analysis with the available genetic data sets. This data showed a similarity of the ancient Bulgarian dogs to Italian (A, B, and C clades) and Iberian (clades A and C) dogs' populations. A clear border can be seen between southern European genetic dog structure, on the one hand, and on the other hand, central-western (clade C), eastern (clade D) and northern Europe (clades A and C). This corresponds to genetic data for European humans during the same period, without admixture between dog populations. Also, our data have shown the presence of clade B in ancient Eurasia. This is not unexpected, as the B haplogroup is widely distributed in extant Balkan dogs and wolves. The presence of this clade both in dogs and in wolves on the Balkans may be explained with hybridization events before the Neolithic period. The spreading of this clade across Europe, together with the A clade, is related to the possible dissemination of newly formed dog breeds from Ancient Greece, Thrace, and the Roman Empire.
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