Abstract
BackgroundMost genetic analyses of ancient and modern dogs have focused on variation in the autosomes or on the mitochondria. Mitochondrial DNA is more easily obtained from ancient samples than nuclear DNA and mitochondrial analyses have revealed important insights into the evolutionary history of canids. Utilizing a recently published dog Y-chromosome reference, we analyzed Y-chromosome sequence across a diverse collection of canids and determined the Y haplogroup of three ancient European dogs.ResultsWe identified 1121 biallelic Y-chromosome SNVs using whole-genome sequences from 118 canids and defined variants diagnostic to distinct dog Y haplogroups. Similar to that of the mitochondria and previous more limited studies of Y diversity, we observe several deep splits in the Y-chromosome tree which may be the result of retained Y-chromosome diversity which predates dog domestication or post-domestication admixture with wolves. We find that Y-chromosomes from three ancient European dogs (4700–7000 years old) belong to distinct clades.ConclusionsWe estimate that the time to the most recent comment ancestor of dog Y haplogroups is 68–151 thousand years ago. Analysis of three Y-chromosomes from the Neolithic confirms long stranding population structure among European dogs.
Highlights
Most genetic analyses of ancient and modern dogs have focused on variation in the autosomes or on the mitochondria
The mitochondria A and B haplogroups are most common in contemporary European dogs, surveys of ancient samples indicate that the majority of ancient European dogs carried the C or D mitochondrial haplotype
The coyote mask is nearly identical to that obtained from the combined canid dataset, suggesting that divergence between coyote and dog will not lead to largescale errors in read mapping for this analysis
Summary
Most genetic analyses of ancient and modern dogs have focused on variation in the autosomes or on the mitochondria. The time of the most recent common ancestor (TMRCA) of haplogroups A-D significantly predates estimates for domestication based on archeological and genetic evidence [1, 4, 6, 9, 11, 12] Instead, these clades may represent variation present among the founding population of the dog lineage or the results of wolf introgressions into dog populations. The mitochondria A and B haplogroups are most common in contemporary European dogs, surveys of ancient samples indicate that the majority of ancient European dogs carried the C or D mitochondrial haplotype This apparent turnover in mitochondrial haplogroups may reflect the migration of a distinct dog population into Europe over the past 15,000 years [9]
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