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Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds
Stockholms universitet, Humanistiska fakulteten, Institutionen för arkeologi och antikens kultur. Harvard Medical School, USA; Broad Institute of Harvard and MIT, USA.
Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen. Swedish Museum of Natural History, Sweden.
Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen. Swedish Museum of Natural History, Sweden.ORCID-id: 0000-0001-7382-7509
Antal upphovsmän: 42015 (Engelska)Ingår i: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 25, nr 11, s. 1515-1519Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

The origin of domestic dogs is poorly understood [1-15], with suggested evidence of dog-like features in fossils that predate the Last Glacial Maximum [6, 9, 10, 14, 16] conflicting with genetic estimates of a more recent divergence between dogs and worldwide wolf populations [13, 15, 17-19]. Here, we present a draft genome sequence from a 35,000 year-old wolf from the Taimyr Peninsula in northern Siberia. We find that this individual belonged to a population that diverged from the common ancestor of present-day wolves and dogs very close in time to the appearance of the domestic dog lineage. We use the directly dated ancient wolf genome to recalibrate the molecular timescale of wolves and dogs and find that the mutation rate is substantially slower than assumed by most previous studies, suggesting that the ancestors of dogs were separated from present-day wolves before the Last Glacial Maximum. We also find evidence of introgression from the archaic Taimyr wolf lineage into present-day dog breeds from northeast Siberia and Greenland, contributing between 1.4% and 27.3% of their ancestry. This demonstrates that the ancestry of present-day dogs is derived from multiple regional wolf populations.

Ort, förlag, år, upplaga, sidor
2015. Vol. 25, nr 11, s. 1515-1519
Nationell ämneskategori
Evolutionsbiologi
Forskningsämne
zoologisk systematik och evolutionsforskning
Identifikatorer
URN: urn:nbn:se:su:diva-119054DOI: 10.1016/j.cub.2015.04.019ISI: 000355556600028OAI: oai:DiVA.org:su-119054DiVA, id: diva2:846565
Tillgänglig från: 2015-08-17 Skapad: 2015-07-27 Senast uppdaterad: 2020-03-04Bibliografiskt granskad
Ingår i avhandling
1. Large carnivore population turnover and ecological change during the Late Quaternary
Öppna denna publikation i ny flik eller fönster >>Large carnivore population turnover and ecological change during the Late Quaternary
2016 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
Abstract [en]

The cave lion (Panthera spelaea), the grey wolf (Canis lupus) and the brown bear (Ursus arctos) all shared an intercontinental distribution across the northern hemisphere during most of the Late Quaternary, and experienced repeated events of climate change. The cave lion went extinct at the end of the Pleistocene and although the wolf and the bear have survived until present day, recent human persecution has caused demographic bottlenecks and local extinctions. In this thesis, mitochondrial and nuclear DNA was analyzed from ancient and modern samples in order to study spatiotemporal changes in genetic diversity in the three species. Mitochondrial sequences analyzed from 48 radiocarbon dated cave lion remains revealed two haplogroups, of which the more genetically diverse seemingly disappeared around 41,000 years BP. Serial coalescent simulations on the data supported a population bottleneck in Beringia between roughly 47-18,000 years BP. Its long duration prevents a specific causal factor to be singled out, but the early onset and overlapping declines of other large mammals in the region suggests that major environmental changes greatly impacted the fauna of Beringia during this time. Using a similar genetic marker, a set of 126 modern wolves and two Siberian wolf remains of Late Pleistocene age were analyzed. The sequences yielded from the latter samples pertained to a basal haplogroup, which contained all Late Pleistocene wolves from previous studies. As data from both modern and ancient wolves were combined, a pattern of decreasing genetic diversity was identified around the Pleistocene-Holocene transition. This decrease was further tested by serial coalescent simulations, which supported a bottleneck in northern North America around this time. Further analyses were applied to one of the ancient wolf remains from Siberia, producing a draft genome sequence and a complete mitochondrial genome. Given the radiocarbon date of the Siberian wolf, a slower mutation rate could be inferred, which pushed back the split between the lineages leading to modern wolves and dogs to at least 27,000 years BP. The Siberian wolf was positioned close to the split but basal to these lineages. A global comparison with modern dogs indicated a closer genetic affiliation between the Siberian wolf and some arctic breeds. For the brown bear, phylogeographic changes in Europe were studied over the last 50,000 years, using radiocarbon dating and mitochondrial sequences. When concatenated and compared with published data, the mtDNA revealed a turnover event just before the LGM, while the dating confirmed a presence of brown bears at relatively high latitudes during this period. Marked shifts in population size were also inferred. Furthermore, data of stable isotope levels confirmed a dietary shift to increasing herbivory around the LGM. Finally, a recent anthropogenic bottleneck among Scandinavian brown bears was studied. While no change in genetic structure could be detected, mitochondrial and microsatellite markers showed a decline in genetic diversity, especially pronounced in the southern subpopulation. ABC simulations supported a bottleneck taking place across all of Scandinavia. Taken together, this thesis have identified and elucidated several impacts on genetic diversity in the past populations of large carnivores. The use of different genetic markers has enabled comparisons with published data, but also revealed their comparatively different benefits and limitations. Overall, the presented studies compose a synthesis of past population dynamics in large carnivores, uniquely revealed by ancient DNA.

Ort, förlag, år, upplaga, sidor
Stockholm: Department of Zoology, Stockholm University, 2016
Nationell ämneskategori
Evolutionsbiologi
Forskningsämne
zoologisk systematik och evolutionsforskning
Identifikatorer
urn:nbn:se:su:diva-127845 (URN)978-91-7649-380-9 (ISBN)
Disputation
2016-04-29, De Geersalen, Geovetenskapens hus, Svante Arrhenius väg 14, Stockholm, 13:00 (Engelska)
Opponent
Handledare
Anmärkning

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 4: Manuscript.

Tillgänglig från: 2016-04-06 Skapad: 2016-03-13 Senast uppdaterad: 2020-03-30Bibliografiskt granskad

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Skoglund, PontusErsmark, ErikPalkopoulou, Eleftheria
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