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

Angela Perri; Kieren J. Mitchell; Alice Mouton; Sandra Alvarez-Carretero; Ardern Hulme-Beaman; Jaimes Haile; Alexandra Jamieson; Julie Meachen; Audrey T. Lin; Blaine W. Schubert; Carly Ameen; Ekaterina E. Antipina; Pere Bover; Selina Brace; Alberto Carmagnini; Christian Carøe; Jose A. Samaniego Castruita; James C. Chatters; Keith Dobney; Mario dos Reis; Allowen Evin; Phillippe Gaubert; Shyam Gopalakrishnan; Graham Gower; Holly Heiniger; Kristofer M. Helgen; Josh Kapp; Pavel A. Kosintsev; Anna Linderholm; Andrew T. Ozga; Samantha Presslee; Alexander T. Salis; Nedda F. Saremi; Colin Shew; Katherine Skerry; Dmitry E. Taranenko; Mary Thompson; Mikhail V. Sablin; Yaroslav V. Kuzmin; Matthew J. Collins; Mikkel-Holger S. Sinding; M. Thomas P. Gilbert; Anne C. Stone; Beth Shapiro; Blaire Van Valkenburgh; Robert K. Wayne; Greger Larson; Alan Cooper; Laurent A. F. Frantz

doi:10.1038/s41586-020-03082-x

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

Angela Perri
, Kieren J. Mitchell
, Alice Mouton
, Sandra Alvarez-Carretero
, Ardern Hulme-Beaman
, Jaimes Haile
, Alexandra Jamieson
, Julie Meachen
, Audrey T. Lin
, Blaine W. Schubert
, Carly Ameen
, Ekaterina E. Antipina
, Pere Bover
, Selina Brace
, Alberto Carmagnini
, Christian Carøe
, Jose A. Samaniego Castruita
, James C. Chatters
, Keith Dobney
, Mario dos Reis

Allowen Evin, Phillippe Gaubert, Shyam Gopalakrishnan, Graham Gower, Holly Heiniger, Kristofer M. Helgen, Josh Kapp, Pavel A. Kosintsev, Anna Linderholm, Andrew T. Ozga, Samantha Presslee, Alexander T. Salis, Nedda F. Saremi, Colin Shew, Katherine Skerry, Dmitry E. Taranenko, Mary Thompson, Mikhail V. Sablin, Yaroslav V. Kuzmin, Matthew J. Collins, Mikkel-Holger S. Sinding, M. Thomas P. Gilbert, Anne C. Stone, Beth Shapiro, Blaire Van Valkenburgh, Robert K. Wayne, Greger Larson, Alan Cooper, Laurent A. F. Frantz

Department of Biological Sciences

Research output: Contribution to journal › Article › peer-review

68 Scopus citations

Abstract

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America 1 , 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.

Original language	American English
Pages (from-to)	87-91
Number of pages	5
Journal	Nature
Volume	591
DOIs	https://doi.org/10.1038/s41586-020-03082-x
State	Published - Jan 13 2021

Bibliographical note

Publisher Copyright:
© 2021, The Author(s), under exclusive licence to Springer Nature Limited.

Funding

Acknowledgements We thank the staff at the Carnegie Museum of Natural History, Cincinnati Museum Center, Danish Zoological Museum, Harrison Zoological Museum, Harvard Museum of Comparative Zoology, Idaho Museum of Natural History, Institute of Archaeology (Russian Academy of Sciences), Institute of Systematics and Animal Ecology (Russian Academy of Sciences), Institute of Zoology (Chinese Academy of Sciences), Instituto de Conservação da Natureza e das Florestas, Kansas Museum of Natural History, La Brea Tar Pits and Museum, Ludwig Maximilian University, McClung Museum, Museum of the Institute of Plant and Animal Ecology (Russian Academy of Sciences), Museum national d’Histoire naturelle, National Museums Scotland, Natural History Museum London, Naturalis Biodiversity Center, Naturhistorisches Museum Bern, Smithsonian National Museum of Natural History, Swedish Naturhistoriska Riksmuseet, SYLVATROP, US Bureau of Reclamation, University of California Museum of Paleontology, University of Texas at El Paso, University of Washington Burke Museum and the Zoological Institute (Russian Academy of Sciences; state assignment no. АААА-А19-119032590102-7) for access to specimens in their care; T. Barnosky, S. Bray, A. Farrell, R. Fischer, A. Harris, J. Harris, A. Henrici, P. Holroyd, R. MacPhee, T. Martin, A. Philpot, J. Saunders, J. Southon, G. Storrs, G. Takeuchi, X. Wang and C. Widga for assistance; and L. DeSantis for comments. A.M. used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group. DireGWC was sequenced using the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 OD018174 Instrumentation Grant. We acknowledge the assistance of the Danish National High-Throughput Sequencing Centre, BGI-Europe, the Garvan Institute of Medical Research and the Australian Cancer Research Foundation (ACRF) Cancer Genomics Facility for assistance in Illumina and BGIseq500 data generation. A.R.P. was supported by a Marie Curie COFUND Junior Research Fellowship (Durham University). A.M. was supported by an NSF grant (award number: 1457106) and the QCB Collaboratory Postdoctoral Fellowship (UCLA). L.A.F.F., J.H., A.H.-B. and G.L. were supported by either European Research Council grant (ERC-2013-StG-337574-UNDEAD and ERC-2019-StG-853272-PALAEOFARM) and/or Natural Environmental Research Council grants (NE/K005243/1 and NE/K003259/1). K.S. was supported by a grant from Barrett, the Honors College at Arizona State University. A.T.O. was supported by the Strategic Initiative Funds, Office of the President, Arizona State University to the Institute of Human Origins DNA and Human Origins at Arizona State University project. L.A.F.F. was supported by a Junior Research Fellowship (Wolfson College, University of Oxford) and L.A.F.F. and A. Carmagnini were supported by the Wellcome Trust (210119/Z/18/Z). S.G. was supported by Carlsbergfondet grant CF14–0995 and Marie Skłodowska-Curie Actions grant 655732-WhereWolf. M.T.P.G. was supported by ERC Consolidator grant 681396-Extinction Genomics. B.S. and J.K. were supported by IMLS MG-30-17-0045-17 and NSF DEB-1754451. A.H.-B. was supported by the Leverhulme Trust (ECF-2017-315). A. Cooper, K.J.M. and H.H. were supported by the Australian Research Council. A.T.S. and G.G. were supported by Australian Government Research Training Program Scholarships. A.T.L. was supported by the Peter Buck Postdoctoral Fellowship from the Smithsonian Institution’s National Museum of Natural History. Y.V.K. was supported by the by State Assignment of the Sobolev Institute of Geology and Mineralogy.

Funders	Funder number
Australian Research Council
Wolfson College, University of Oxford
University of California at Los Angeles
Arizona State University
National Museum of Natural History
National Institutes of Health
Durham University
Office of the President
Sobolev Institute of Geology and Mineralogy
NIH Office of the Director	S10OD018174
European Research Council	ERC-2013-StG-337574-UNDEAD, ERC-2019-StG-853272-PALAEOFARM
Leverhulme Trust	ECF-2017-315
Institute of Museum and Library Services	MG-30-17-0045-17, DEB-1754451
National Science Foundation	1457106, 1754451, 1425059
H2020 Marie Skłodowska-Curie Actions	655732-WhereWolf
Wellcome Trust	210119/Z/18/Z, CF14–0995
Natural Environment Research Council	NE/K003259/1, NE/K005243/1

ASJC Scopus Subject Areas

General

Keywords

Evolutionary genetics
Palaeontology
Plylogenetics
Speciation

Disciplines

Biology
Genetics and Genomics
Life Sciences

Access to Document

10.1038/s41586-020-03082-xLicense: Unspecified

Cite this

Perri, A., Mitchell, K. J., Mouton, A., Alvarez-Carretero, S., Hulme-Beaman, A., Haile, J., Jamieson, A., Meachen, J., Lin, A. T., Schubert, B. W., Ameen, C., Antipina, E. E., Bover, P., Brace, S., Carmagnini, A., Carøe, C., Samaniego Castruita, J. A., Chatters, J. C., Dobney, K., ... Frantz, L. A. F. (2021). Dire wolves were the last of an ancient New World canid lineage. Nature, 591, 87-91. https://doi.org/10.1038/s41586-020-03082-x

Perri, A, Mitchell, KJ, Mouton, A, Alvarez-Carretero, S, Hulme-Beaman, A, Haile, J, Jamieson, A, Meachen, J, Lin, AT, Schubert, BW, Ameen, C, Antipina, EE, Bover, P, Brace, S, Carmagnini, A, Carøe, C, Samaniego Castruita, JA, Chatters, JC, Dobney, K, dos Reis, M, Evin, A, Gaubert, P, Gopalakrishnan, S, Gower, G, Heiniger, H, Helgen, KM, Kapp, J, Kosintsev, PA, Linderholm, A, Ozga, AT, Presslee, S, Salis, AT, Saremi, NF, Shew, C, Skerry, K, Taranenko, DE, Thompson, M, Sablin, MV, Kuzmin, YV, Collins, MJ, Sinding, M-HS, Gilbert, MTP, Stone, AC, Shapiro, B, Van Valkenburgh, B, Wayne, RK, Larson, G, Cooper, A & Frantz, LAF 2021, 'Dire wolves were the last of an ancient New World canid lineage', Nature, vol. 591, pp. 87-91. https://doi.org/10.1038/s41586-020-03082-x

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title = "Dire wolves were the last of an ancient New World canid lineage",

abstract = " Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America 1 , 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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AB - Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America 1 , 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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Dire wolves were the last of an ancient New World canid lineage

Abstract

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