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Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages

Ramos-Madrigal J 1 , Sinding MS 2 , Carøe C 3 , Mak SST 1 , Niemann J 3 , Samaniego Castruita JA 3 Show all authors , Fedorov S 4 , Kandyba A 5 , Germonpré M 6 , Bocherens H 7 , Feuerborn TR 8 , Pitulko VV 9 , Pavlova EY 10 , Nikolskiy PA 11 , Kasparov AK 9 , Ivanova VV 12 , Larson G 13 , Frantz LAF 14 , Willerslev E 15 , Meldgaard M 16 , Petersen B 17 , Sicheritz-Ponten T 17 , Bachmann L 18 , Wiig Ø 18 , Hansen AJ 8 , Gilbert MTP 19 , Gopalakrishnan S 20

Affiliations 

  • 1 Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
  • 2 Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Natural History Museum, University of Oslo, Oslo, Norway; The Qimmeq Project, University of Greenland, Nuussuaq, Greenland; Greenland Institute of Natural Resources, Nuuk, Greenland; Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
  • 3 Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
  • 4 Mammoth Museum of North-Eastern Federal University, Yakutsk, Russia
  • 5 Department of Stone Age Archeology, Institute of Archaeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
  • 6 Directorate Earth and History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
  • 7 Department of Geosciences, Biogeology, University of Tübingen, Tübingen, Germany; Senckenberg Centre for Human Evolution and Palaeoenvironment, Tübingen, Germany
  • 8 Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; The Qimmeq Project, University of Greenland, Nuussuaq, Greenland; Section for GeoGenetics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
  • 9 Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
  • 10 Arctic and Antarctic Research Institute, St. Petersburg, Russia
  • 11 Geological Institute, Russian Academy of Sciences, Moscow, Russia
  • 12 VNIIOkeangeologia Research Institute (The All-Russian Research Institute of Geology and Mineral Resources of the World Ocean), St. Petersburg, Russia
  • 13 The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
  • 14 School of Biological and Chemical Sciences, Queen Mary University of London, London, UK; Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
  • 15 Section for GeoGenetics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Danish Institute for Advanced Study (D-IAS), University of Southern Denmark, Odense, Denmark; Department of Zoology, University of Cambridge, Cambridge, UK; Wellcome Trust Sanger Institute, University of Cambridge, Cambridge, UK
  • 16 The Qimmeq Project, University of Greenland, Nuussuaq, Greenland; Section for GeoGenetics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
  • 17 Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
  • 18 Natural History Museum, University of Oslo, Oslo, Norway
  • 19 Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, Norwegian University of Science and Technology, Trondheim, Norway
  • 20 Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark. Electronic address: [email protected]
Curr Biol, 2021 01 11;31(1):198-206.e8.
PMID: 33125870 DOI: 10.1016/j.cub.2020.10.002

Abstract

Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian and American wolves and domestic dogs.1 Genetic studies have suggested these groups trace their origins to a wolf population that expanded during the last glacial maximum (LGM)1-3 and replaced local wolf populations.4 Moreover, ancient genomes from the Yana basin and the Taimyr peninsula provided evidence of at least one extinct wolf lineage that dwelled in Siberia during the Pleistocene.35 Previous studies have suggested that Pleistocene Siberian canids can be classified into two groups based on cranial morphology. Wolves in the first group are most similar to present-day populations, although those in the second group possess intermediate features between dogs and wolves.67 However, whether this morphological classification represents distinct genetic groups remains unknown. To investigate this question and the relationships between Pleistocene canids, present-day wolves, and dogs, we resequenced the genomes of four Pleistocene canids from Northeast Siberia dated between >50 and 14 ka old, including samples from the two morphological categories. We found these specimens cluster with the two previously sequenced Pleistocene wolves, which are genetically more similar to Eurasian wolves. Our results show that, though the four specimens represent extinct wolf lineages, they do not form a monophyletic group. Instead, each Pleistocene Siberian canid branched off the lineage that gave rise to present-day wolves and dogs. Finally, our results suggest the two previously described morphological groups could represent independent lineages similarly related to present-day wolves and dogs.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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