Dire wolves were the last of an ancient New World canid lineage

doi:10.1038/s41586-020-03082-x

. 2021 Mar;591(7848):87-91.

doi: 10.1038/s41586-020-03082-x. Epub 2021 Jan 13.

Dire wolves were the last of an ancient New World canid lineage

Angela R Perri^#¹, Kieren J Mitchell^#², Alice Mouton^#³, Sandra Álvarez-Carretero^#⁴, Ardern Hulme-Beaman^{5

6}, James Haile⁷, Alexandra Jamieson⁷, Julie Meachen⁸, Audrey T Lin^{7

9

10}, Blaine W Schubert¹¹, Carly Ameen¹², Ekaterina E Antipina¹³, Pere Bover¹⁴, Selina Brace¹⁵, Alberto Carmagnini⁴, Christian Carøe¹⁶, Jose A Samaniego Castruita¹⁶, James C Chatters¹⁷, Keith Dobney^{5

18

19

20}, Mario Dos Reis⁴, Allowen Evin²¹, Philippe Gaubert²², Shyam Gopalakrishnan¹⁶, Graham Gower²³, Holly Heiniger²³, Kristofer M Helgen²⁴, Josh Kapp²⁵, Pavel A Kosintsev^{26

27}, Anna Linderholm^{7

28}, Andrew T Ozga^{29

30

31}, Samantha Presslee³², Alexander T Salis²³, Nedda F Saremi²⁵, Colin Shew³, Katherine Skerry³⁰, Dmitry E Taranenko³³, Mary Thompson³⁴, Mikhail V Sablin³⁵, Yaroslav V Kuzmin^{36

37}, Matthew J Collins^{16

38}, Mikkel-Holger S Sinding^{16

39}, M Thomas P Gilbert^{16

40}, Anne C Stone^{29

30

41}, Beth Shapiro^{25

42}, Blaire Van Valkenburgh³, Robert K Wayne³, Greger Larson⁷, Alan Cooper⁴³, Laurent A F Frantz^{44

45}

Affiliations

¹ Department of Archaeology, Durham University, Durham, UK. angela.r.perri@durham.ac.uk.
² Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia. kieren.mitchell@adelaide.edu.au.
³ Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.
⁴ School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
⁵ Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK.
⁶ School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK.
⁷ The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK.
⁸ Department of Anatomy, Des Moines University, Des Moines, IA, USA.
⁹ Department of Zoology, University of Oxford, Oxford, UK.
¹⁰ Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
¹¹ Center of Excellence in Paleontology & Department of Geosciences, East Tennessee State University, Johnson City, TN, USA.
¹² Department of Archaeology, University of Exeter, Exeter, UK.
¹³ Institute of Archaeology, Russian Academy of Sciences, Moscow, Russia.
¹⁴ ARAID Foundation, Instituto Universitario de Investigación en Ciencias Ambientales (IUCA) - Aragosaurus Group, Universidad de Zaragoza, Zaragoza, Spain.
¹⁵ Department of Earth Sciences, Natural History Museum, London, UK.
¹⁶ Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
¹⁷ Applied Paleoscience, Bothell, WA, USA.
¹⁸ Department of Archaeology, University of Sydney, Sydney, New South Wales, Australia.
¹⁹ Department of Archaeology, University of Aberdeen, Aberdeen, UK.
²⁰ Department of Archaeology, Simon Fraser University, Burnaby, Canada.
²¹ Institut des Sciences de l'Evolution - Montpellier, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France.
²² Laboratoire Evolution & Diversité Biologique, UPS/CNRS/IRD, Université Paul Sabatier, Toulouse, France.
²³ Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
²⁴ Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.
²⁵ Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.
²⁶ Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of Sciences, Yekaterinburg, Russia.
²⁷ Ural Federal University, Yekaterinburg, Russia.
²⁸ Department of Anthropology, Texas A&M University, College Station, TX, USA.
²⁹ Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.
³⁰ School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.
³¹ Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, USA.
³² Department of Archaeology, University of York, York, UK.
³³ Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
³⁴ Idaho Museum of Natural History, Idaho State University, Pocatello, ID, USA.
³⁵ Zoological Institute of the Russian Academy of Sciences, St Petersburg, Russia.
³⁶ Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
³⁷ Tomsk State University, Tomsk, Russia.
³⁸ McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK.
³⁹ Greenland Institute of Natural Resources, Nuuk, Greenland.
⁴⁰ NTNU University Museum, Trondheim, Norway.
⁴¹ Institute of Human Origins, Arizona State University, Tempe, AZ, USA.
⁴² Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA.
⁴³ South Australian Museum, Adelaide, South Australia, Australia.
⁴⁴ School of Biological and Chemical Sciences, Queen Mary University of London, London, UK. laurent.frantz@gmail.com.
⁴⁵ Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany. laurent.frantz@gmail.com.

^# Contributed equally.

PMID: 33442059
DOI: 10.1038/s41586-020-03082-x

Free article

Dire wolves were the last of an ancient New World canid lineage

Angela R Perri et al. Nature. 2021 Mar.

Free article

. 2021 Mar;591(7848):87-91.

doi: 10.1038/s41586-020-03082-x. Epub 2021 Jan 13.

Authors

Affiliations

¹ Department of Archaeology, Durham University, Durham, UK. angela.r.perri@durham.ac.uk.
² Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia. kieren.mitchell@adelaide.edu.au.
³ Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.
⁴ School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
⁵ Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK.
⁶ School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK.
⁷ The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK.
⁸ Department of Anatomy, Des Moines University, Des Moines, IA, USA.
⁹ Department of Zoology, University of Oxford, Oxford, UK.
¹⁰ Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
¹¹ Center of Excellence in Paleontology & Department of Geosciences, East Tennessee State University, Johnson City, TN, USA.
¹² Department of Archaeology, University of Exeter, Exeter, UK.
¹³ Institute of Archaeology, Russian Academy of Sciences, Moscow, Russia.
¹⁴ ARAID Foundation, Instituto Universitario de Investigación en Ciencias Ambientales (IUCA) - Aragosaurus Group, Universidad de Zaragoza, Zaragoza, Spain.
¹⁵ Department of Earth Sciences, Natural History Museum, London, UK.
¹⁶ Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
¹⁷ Applied Paleoscience, Bothell, WA, USA.
¹⁸ Department of Archaeology, University of Sydney, Sydney, New South Wales, Australia.
¹⁹ Department of Archaeology, University of Aberdeen, Aberdeen, UK.
²⁰ Department of Archaeology, Simon Fraser University, Burnaby, Canada.
²¹ Institut des Sciences de l'Evolution - Montpellier, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France.
²² Laboratoire Evolution & Diversité Biologique, UPS/CNRS/IRD, Université Paul Sabatier, Toulouse, France.
²³ Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
²⁴ Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.
²⁵ Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.
²⁶ Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of Sciences, Yekaterinburg, Russia.
²⁷ Ural Federal University, Yekaterinburg, Russia.
²⁸ Department of Anthropology, Texas A&M University, College Station, TX, USA.
²⁹ Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.
³⁰ School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.
³¹ Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, USA.
³² Department of Archaeology, University of York, York, UK.
³³ Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
³⁴ Idaho Museum of Natural History, Idaho State University, Pocatello, ID, USA.
³⁵ Zoological Institute of the Russian Academy of Sciences, St Petersburg, Russia.
³⁶ Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
³⁷ Tomsk State University, Tomsk, Russia.
³⁸ McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK.
³⁹ Greenland Institute of Natural Resources, Nuuk, Greenland.
⁴⁰ NTNU University Museum, Trondheim, Norway.
⁴¹ Institute of Human Origins, Arizona State University, Tempe, AZ, USA.
⁴² Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA.
⁴³ South Australian Museum, Adelaide, South Australia, Australia.
⁴⁴ School of Biological and Chemical Sciences, Queen Mary University of London, London, UK. laurent.frantz@gmail.com.
⁴⁵ Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany. laurent.frantz@gmail.com.

^# Contributed equally.

PMID: 33442059
DOI: 10.1038/s41586-020-03082-x

Abstract

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America¹, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae^2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.

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References

1. Dundas, R. G. Quaternary records of the dire wolf, Canis dirus, in North and South America. Boreas 28, 375–385 (1999). - DOI
1. vonHoldt, B. M. et al. Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf. Sci. Adv. 2, e1501714 (2016). - DOI
1. Gopalakrishnan, S. et al. Interspecific gene flow shaped the evolution of the genus Canis. Curr. Biol. 28, 3441–3449 (2018). - DOI
1. Meachen, J. A., Brannick, A. L. & Fry, T. J. Extinct Beringian wolf morphotype found in the continental U.S. has implications for wolf migration and evolution. Ecol. Evol. 6, 3430–3438 (2016). - DOI
1. Leonard, J. A. et al. Megafaunal extinctions and the disappearance of a specialized wolf ecomorph. Curr. Biol. 17, 1146–1150 (2007). - DOI

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[1] Dundas, R. G. Quaternary records of the dire wolf, Canis dirus, in North and South America. Boreas 28, 375–385 (1999). - DOI

[2] Dundas, R. G. Quaternary records of the dire wolf, Canis dirus, in North and South America. Boreas 28, 375–385 (1999). - DOI

[3] vonHoldt, B. M. et al. Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf. Sci. Adv. 2, e1501714 (2016). - DOI

[4] vonHoldt, B. M. et al. Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf. Sci. Adv. 2, e1501714 (2016). - DOI

[5] Gopalakrishnan, S. et al. Interspecific gene flow shaped the evolution of the genus Canis. Curr. Biol. 28, 3441–3449 (2018). - DOI

[6] Gopalakrishnan, S. et al. Interspecific gene flow shaped the evolution of the genus Canis. Curr. Biol. 28, 3441–3449 (2018). - DOI

[7] Meachen, J. A., Brannick, A. L. & Fry, T. J. Extinct Beringian wolf morphotype found in the continental U.S. has implications for wolf migration and evolution. Ecol. Evol. 6, 3430–3438 (2016). - DOI

[8] Meachen, J. A., Brannick, A. L. & Fry, T. J. Extinct Beringian wolf morphotype found in the continental U.S. has implications for wolf migration and evolution. Ecol. Evol. 6, 3430–3438 (2016). - DOI

[9] Leonard, J. A. et al. Megafaunal extinctions and the disappearance of a specialized wolf ecomorph. Curr. Biol. 17, 1146–1150 (2007). - DOI

[10] Leonard, J. A. et al. Megafaunal extinctions and the disappearance of a specialized wolf ecomorph. Curr. Biol. 17, 1146–1150 (2007). - DOI

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Dire wolves were the last of an ancient New World canid lineage

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Dire wolves were the last of an ancient New World canid lineage

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