Grey wolf genomic history reveals a dual ancestry of dogs

Anders Bergström; David W. G. Stanton; Ulrike H. Taron; Laurent Frantz; Mikkel-Holger S. Sinding; Erik Ersmark; Saskia Pfrengle; Molly Cassatt-Johnstone; Ophélie Lebrasseur; Linus Girdland-Flink; Daniel M. Fernandes; Morgane Ollivier; Leo Speidel; Shyam Gopalakrishnan; Michael V. Westbury; Jazmin Ramos-Madrigal; Tatiana R. Feuerborn; Ella Reiter; Joscha Gretzinger; Susanne C. Münzel; Pooja Swali; Nicholas J. Conard; Christian Carøe; James Haile; Anna Linderholm; Semyon Androsov; Ian Barnes; Chris Baumann; Norbert Benecke; Hervé Bocherens; Selina Brace; Ruth F. Carden; Dorothée G. Drucker; Sergey Fedorov; Mihály Gasparik; Mietje Germonpré; Semyon Grigoriev; Pam Groves; Stefan T. Hertwig; Varvara V. Ivanova; Luc Janssens; Richard P. Jennings; Aleksei K. Kasparov; Irina V. Kirillova; Islam Kurmaniyazov; Yaroslav V. Kuzmin; Pavel A. Kosintsev; Martina Lázničková-Galetová; Charlotte Leduc; Pavel Nikolskiy; Marc Nussbaumer; Cóilín O’Drisceoil; Ludovic Orlando; Alan Outram; Elena Y. Pavlova; Angela R. Perri; Małgorzata Pilot; Vladimir V. Pitulko; Valerii V. Plotnikov; Albert V. Protopopov; André Rehazek; Mikhail Sablin; Andaine Seguin-Orlando; Jan Storå; Christian Verjux; Victor F. Zaibert; Grant Zazula; Philippe Crombé; Anders J. Hansen; Eske Willerslev; Jennifer A. Leonard; Anders Götherström; Ron Pinhasi; Verena J. Schuenemann; Michael Hofreiter; M. Thomas P. Gilbert; Beth Shapiro; Greger Larson; Johannes Krause; Love Dalén; Pontus Skoglund

doi:10.1038/s41586-022-04824-9

Grey wolf genomic history reveals a dual ancestry of dogs

Anders Bergström^* (Corresponding Author), David W. G. Stanton, Ulrike H. Taron, Laurent Frantz, Mikkel-Holger S. Sinding, Erik Ersmark, Saskia Pfrengle, Molly Cassatt-Johnstone, Ophélie Lebrasseur, Linus Girdland-Flink, Daniel M. Fernandes, Morgane Ollivier, Leo Speidel, Shyam Gopalakrishnan, Michael V. Westbury, Jazmin Ramos-Madrigal, Tatiana R. Feuerborn, Ella Reiter, Joscha Gretzinger, Susanne C. MünzelPooja Swali, Nicholas J. Conard, Christian Carøe, James Haile, Anna Linderholm, Semyon Androsov, Ian Barnes, Chris Baumann, Norbert Benecke, Hervé Bocherens, Selina Brace, Ruth F. Carden, Dorothée G. Drucker, Sergey Fedorov, Mihály Gasparik, Mietje Germonpré, Semyon Grigoriev, Pam Groves, Stefan T. Hertwig, Varvara V. Ivanova, Luc Janssens, Richard P. Jennings, Aleksei K. Kasparov, Irina V. Kirillova, Islam Kurmaniyazov, Yaroslav V. Kuzmin, Pavel A. Kosintsev, Martina Lázničková-Galetová, Charlotte Leduc, Pavel Nikolskiy, Marc Nussbaumer, Cóilín O’Drisceoil, Ludovic Orlando, Alan Outram, Elena Y. Pavlova, Angela R. Perri, Małgorzata Pilot, Vladimir V. Pitulko, Valerii V. Plotnikov, Albert V. Protopopov, André Rehazek, Mikhail Sablin, Andaine Seguin-Orlando, Jan Storå, Christian Verjux, Victor F. Zaibert, Grant Zazula, Philippe Crombé, Anders J. Hansen, Eske Willerslev, Jennifer A. Leonard, Anders Götherström, Ron Pinhasi, Verena J. Schuenemann, Michael Hofreiter, M. Thomas P. Gilbert, Beth Shapiro, Greger Larson, Johannes Krause, Love Dalén, Pontus Skoglund^* (Corresponding Author)

^*Corresponding author for this work

The Francis Crick Institute

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

39 Citations (Scopus)

2 Downloads (Pure)

Abstract

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.

Original language	English
Pages (from-to)	313–320
Number of pages	8
Journal	Nature
Volume	607
Early online date	29 Jun 2022
DOIs	https://doi.org/10.1038/s41586-022-04824-9
Publication status	Published - 14 Jul 2022

Bibliographical note

This work was supported by grants to P. Skoglund from the European Research Council (grant no. 852558), the Erik Philip Sörensen Foundation and the Science for Life Laboratory, Swedish Biodiversity Program, made available by support from the Knut and Alice Wallenberg Foundation. A.B., L.S., P. Swali and P. Skoglund were supported by Francis Crick Institute core funding (FC001595) from Cancer Research UK, the UK Medical Research Council and the Wellcome Trust. P. Skoglund was also supported by the Vallee Foundation, the European Molecular Biology Organisation and the Wellcome Trust (217223/Z/19/Z). Computations were supported by SNIC-UPPMAX. We also acknowledge support from Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, the National Genomics Infrastructure funded by the Swedish Research Council and the Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. We thank the Yukon gold mining community and First Nations, including the Tr’ondëk Hwëch’in, for continued support of our palaeontology research in the Yukon Territories, Canada. We thank the Danish National High-Throughput Sequencing Centre and BGI-Europe for assistance in sequencing data generation and the Danish National Supercomputer for Life Sciences–Computerome (https://computerome.dtu.dk) for computational resources. We thank National Museum Wales for continued sampling support. M. Germonpré acknowledges support from the Brain.be 2.0 ICHIE project (BELSPO B2/191/P2/ICHIE). M.T.P.G. was supported by the European Research Council (grant no. 681396). M.-H.S.S. was supported by the Velux Foundations through the Qimmeq Project, the Aage og Johanne Louis-Hansens Fond and the Independent Research Fund Denmark (8028-00005B). L.D. acknowledges support from FORMAS (2018-01640). D.W.G.S. received funding for this project from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 796877. M.P. was supported by the Polish National Agency for Academic Exchange–NAWA (grant no. PPN/PPO/2018/1/00037). V.J.S. was supported by the University of Zurich’s University Research Priority Program ‘Evolution in Action: From Genomes to Ecosystems’. This research was done with the participation of ZIN RAS (grant no. 075-15-2021-1069). We are grateful to the museum of the Institute of Plant and Animal Ecology UB RAS (Ekaterinburg, Russia) for provision of samples. R.P.J. and C.O’D. were supported by the Standing Committee for Archaeology of the Royal Irish Academy through the Archaeological Excavation Research Grant Scheme. E.Y.P., P.N. and V.V.P. are supported by the Russian Science Foundation (grant no. 16-18-10265-RNF and 21-18-00457-RNF). Y.V.K. was supported by the Russian Science Foundation (grant no. 20-17-00033). M.H. was supported by the European Research Council (consolidator grant GeneFlow no. 310763). M.L.-G. was supported by the Czech Science Foundation GAČR (grant no. 15-06446S) and institutional financing of the Moravian Museum from the Czech Ministry of Culture (IP DKRVO 2019-2023, MK000094862). L.S. is supported by the Sir Henry Wellcome fellowship (220457/Z/20/Z). We thank Staatliches Museum für Naturkunde Stuttgart for sample access. L.F. and G.L. were supported by European Research Council grants (ERC-2013-StG-337574-UNDEAD and ERC-2019-StG-853272-PALAEOFARM) and Natural Environmental Research Council grants (NE/K005243/1, NE/K003259/1, NE/S007067/1 and NE/S00078X/1). L.F. was also supported by the Wellcome Trust (210119/Z/18/Z). This research was funded in whole, or in part, by the Wellcome Trust (FC001595). For the purpose of open access, the author has applied a CC-BY public copyright licence to any author accepted manuscript version arising from this submission.

Data Availability Statement

The generated DNA sequencing data are available in the European Nucleotide Archive (ENA) under study accession PRJEB42199. Previously published genomic data analysed here are available under accession numbers PRJNA448733, PRJCA000335, PRJEB20635, PRJNA496590, PRJNA494815, PRJEB7788, PRJEB13070, PRJNA319283, PRJEB22026, PRJNA608847, PRJEB38079, PRJEB39580 and PRJEB41490, with individual genomes used listed in Supplementary Data 2. The canFam3.1 reference genome is available under NCBI assembly accession GCF_000002285.3.

Keywords

archaeology
ecological genetics
evolutionary genetics
population genetics
Animals
Genome/genetics
Europe
Genomics
Dogs
Domestication
Phylogeny
Wolves/genetics

Access to Document

10.1038/s41586-022-04824-9Licence: CC BY

Bergstrom_etal_Nat_Grey_Wolf_Economic_VOR
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Final published version, 13.9 MBLicence: CC BY

Cite this

Bergström, A., Stanton, D. W. G., Taron, U. H., Frantz, L., Sinding, M.-H. S., Ersmark, E., Pfrengle, S., Cassatt-Johnstone, M., Lebrasseur, O., Girdland-Flink, L., Fernandes, D. M., Ollivier, M., Speidel, L., Gopalakrishnan, S., Westbury, M. V., Ramos-Madrigal, J., Feuerborn, T. R., Reiter, E., Gretzinger, J., ... Skoglund, P. (2022). Grey wolf genomic history reveals a dual ancestry of dogs. Nature, 607, 313–320. https://doi.org/10.1038/s41586-022-04824-9

Bergström, A, Stanton, DWG, Taron, UH, Frantz, L, Sinding, M-HS, Ersmark, E, Pfrengle, S, Cassatt-Johnstone, M, Lebrasseur, O, Girdland-Flink, L, Fernandes, DM, Ollivier, M, Speidel, L, Gopalakrishnan, S, Westbury, MV, Ramos-Madrigal, J, Feuerborn, TR, Reiter, E, Gretzinger, J, Münzel, SC, Swali, P, Conard, NJ, Carøe, C, Haile, J, Linderholm, A, Androsov, S, Barnes, I, Baumann, C, Benecke, N, Bocherens, H, Brace, S, Carden, RF, Drucker, DG, Fedorov, S, Gasparik, M, Germonpré, M, Grigoriev, S, Groves, P, Hertwig, ST, Ivanova, VV, Janssens, L, Jennings, RP, Kasparov, AK, Kirillova, IV, Kurmaniyazov, I, Kuzmin, YV, Kosintsev, PA, Lázničková-Galetová, M, Leduc, C, Nikolskiy, P, Nussbaumer, M, O’Drisceoil, C, Orlando, L, Outram, A, Pavlova, EY, Perri, AR, Pilot, M, Pitulko, VV, Plotnikov, VV, Protopopov, AV, Rehazek, A, Sablin, M, Seguin-Orlando, A, Storå, J, Verjux, C, Zaibert, VF, Zazula, G, Crombé, P, Hansen, AJ, Willerslev, E, Leonard, JA, Götherström, A, Pinhasi, R, Schuenemann, VJ, Hofreiter, M, Gilbert, MTP, Shapiro, B, Larson, G, Krause, J, Dalén, L & Skoglund, P 2022, 'Grey wolf genomic history reveals a dual ancestry of dogs', Nature, vol. 607, pp. 313–320. https://doi.org/10.1038/s41586-022-04824-9

@article{bdcfc05d76db4fb9bd9767b64af6be8f,

title = "Grey wolf genomic history reveals a dual ancestry of dogs",

abstract = "The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.",

keywords = "archaeology, ecological genetics, evolutionary genetics, population genetics, Animals, Genome/genetics, Europe, Genomics, Dogs, Domestication, Phylogeny, Wolves/genetics",

author = "Anders Bergstr{\"o}m and Stanton, {David W. G.} and Taron, {Ulrike H.} and Laurent Frantz and Sinding, {Mikkel-Holger S.} and Erik Ersmark and Saskia Pfrengle and Molly Cassatt-Johnstone and Oph{\'e}lie Lebrasseur and Linus Girdland-Flink and Fernandes, {Daniel M.} and Morgane Ollivier and Leo Speidel and Shyam Gopalakrishnan and Westbury, {Michael V.} and Jazmin Ramos-Madrigal and Feuerborn, {Tatiana R.} and Ella Reiter and Joscha Gretzinger and M{\"u}nzel, {Susanne C.} and Pooja Swali and Conard, {Nicholas J.} and Christian Car{\o}e and James Haile and Anna Linderholm and Semyon Androsov and Ian Barnes and Chris Baumann and Norbert Benecke and Herv{\'e} Bocherens and Selina Brace and Carden, {Ruth F.} and Drucker, {Doroth{\'e}e G.} and Sergey Fedorov and Mih{\'a}ly Gasparik and Mietje Germonpr{\'e} and Semyon Grigoriev and Pam Groves and Hertwig, {Stefan T.} and Ivanova, {Varvara V.} and Luc Janssens and Jennings, {Richard P.} and Kasparov, {Aleksei K.} and Kirillova, {Irina V.} and Islam Kurmaniyazov and Kuzmin, {Yaroslav V.} and Kosintsev, {Pavel A.} and Martina L{\'a}zni{\v c}kov{\'a}-Galetov{\'a} and Charlotte Leduc and Pavel Nikolskiy and Marc Nussbaumer and C{\'o}il{\'i}n O{\textquoteright}Drisceoil and Ludovic Orlando and Alan Outram and Pavlova, {Elena Y.} and Perri, {Angela R.} and Ma{\l}gorzata Pilot and Pitulko, {Vladimir V.} and Plotnikov, {Valerii V.} and Protopopov, {Albert V.} and Andr{\'e} Rehazek and Mikhail Sablin and Andaine Seguin-Orlando and Jan Stor{\aa} and Christian Verjux and Zaibert, {Victor F.} and Grant Zazula and Philippe Cromb{\'e} and Hansen, {Anders J.} and Eske Willerslev and Leonard, {Jennifer A.} and Anders G{\"o}therstr{\"o}m and Ron Pinhasi and Schuenemann, {Verena J.} and Michael Hofreiter and Gilbert, {M. Thomas P.} and Beth Shapiro and Greger Larson and Johannes Krause and Love Dal{\'e}n and Pontus Skoglund",

note = "This work was supported by grants to P. Skoglund from the European Research Council (grant no. 852558), the Erik Philip S{\"o}rensen Foundation and the Science for Life Laboratory, Swedish Biodiversity Program, made available by support from the Knut and Alice Wallenberg Foundation. A.B., L.S., P. Swali and P. Skoglund were supported by Francis Crick Institute core funding (FC001595) from Cancer Research UK, the UK Medical Research Council and the Wellcome Trust. P. Skoglund was also supported by the Vallee Foundation, the European Molecular Biology Organisation and the Wellcome Trust (217223/Z/19/Z). Computations were supported by SNIC-UPPMAX. We also acknowledge support from Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, the National Genomics Infrastructure funded by the Swedish Research Council and the Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. We thank the Yukon gold mining community and First Nations, including the Tr{\textquoteright}ond{\"e}k Hw{\"e}ch{\textquoteright}in, for continued support of our palaeontology research in the Yukon Territories, Canada. We thank the Danish National High-Throughput Sequencing Centre and BGI-Europe for assistance in sequencing data generation and the Danish National Supercomputer for Life Sciences–Computerome (https://computerome.dtu.dk) for computational resources. We thank National Museum Wales for continued sampling support. M. Germonpr{\'e} acknowledges support from the Brain.be 2.0 ICHIE project (BELSPO B2/191/P2/ICHIE). M.T.P.G. was supported by the European Research Council (grant no. 681396). M.-H.S.S. was supported by the Velux Foundations through the Qimmeq Project, the Aage og Johanne Louis-Hansens Fond and the Independent Research Fund Denmark (8028-00005B). L.D. acknowledges support from FORMAS (2018-01640). D.W.G.S. received funding for this project from the European Union{\textquoteright}s Horizon 2020 research and innovation programme under Marie Sk{\l}odowska-Curie grant agreement no. 796877. M.P. was supported by the Polish National Agency for Academic Exchange–NAWA (grant no. PPN/PPO/2018/1/00037). V.J.S. was supported by the University of Zurich{\textquoteright}s University Research Priority Program {\textquoteleft}Evolution in Action: From Genomes to Ecosystems{\textquoteright}. This research was done with the participation of ZIN RAS (grant no. 075-15-2021-1069). We are grateful to the museum of the Institute of Plant and Animal Ecology UB RAS (Ekaterinburg, Russia) for provision of samples. R.P.J. and C.O{\textquoteright}D. were supported by the Standing Committee for Archaeology of the Royal Irish Academy through the Archaeological Excavation Research Grant Scheme. E.Y.P., P.N. and V.V.P. are supported by the Russian Science Foundation (grant no. 16-18-10265-RNF and 21-18-00457-RNF). Y.V.K. was supported by the Russian Science Foundation (grant no. 20-17-00033). M.H. was supported by the European Research Council (consolidator grant GeneFlow no. 310763). M.L.-G. was supported by the Czech Science Foundation GA{\v C}R (grant no. 15-06446S) and institutional financing of the Moravian Museum from the Czech Ministry of Culture (IP DKRVO 2019-2023, MK000094862). L.S. is supported by the Sir Henry Wellcome fellowship (220457/Z/20/Z). We thank Staatliches Museum f{\"u}r Naturkunde Stuttgart for sample access. L.F. and G.L. were supported by European Research Council grants (ERC-2013-StG-337574-UNDEAD and ERC-2019-StG-853272-PALAEOFARM) and Natural Environmental Research Council grants (NE/K005243/1, NE/K003259/1, NE/S007067/1 and NE/S00078X/1). L.F. was also supported by the Wellcome Trust (210119/Z/18/Z). This research was funded in whole, or in part, by the Wellcome Trust (FC001595). For the purpose of open access, the author has applied a CC-BY public copyright licence to any author accepted manuscript version arising from this submission.",

year = "2022",

month = jul,

day = "14",

doi = "10.1038/s41586-022-04824-9",

language = "English",

volume = "607",

pages = "313–320",

journal = "Nature",

issn = "1476-4687",

publisher = "Nature Publishing Group",

}

TY - JOUR

T1 - Grey wolf genomic history reveals a dual ancestry of dogs

AU - Bergström, Anders

AU - Stanton, David W. G.

AU - Taron, Ulrike H.

AU - Frantz, Laurent

AU - Sinding, Mikkel-Holger S.

AU - Ersmark, Erik

AU - Pfrengle, Saskia

AU - Cassatt-Johnstone, Molly

AU - Lebrasseur, Ophélie

AU - Girdland-Flink, Linus

AU - Fernandes, Daniel M.

AU - Ollivier, Morgane

AU - Speidel, Leo

AU - Gopalakrishnan, Shyam

AU - Westbury, Michael V.

AU - Ramos-Madrigal, Jazmin

AU - Feuerborn, Tatiana R.

AU - Reiter, Ella

AU - Gretzinger, Joscha

AU - Münzel, Susanne C.

AU - Swali, Pooja

AU - Conard, Nicholas J.

AU - Carøe, Christian

AU - Haile, James

AU - Linderholm, Anna

AU - Androsov, Semyon

AU - Barnes, Ian

AU - Baumann, Chris

AU - Benecke, Norbert

AU - Bocherens, Hervé

AU - Brace, Selina

AU - Carden, Ruth F.

AU - Drucker, Dorothée G.

AU - Fedorov, Sergey

AU - Gasparik, Mihály

AU - Germonpré, Mietje

AU - Grigoriev, Semyon

AU - Groves, Pam

AU - Hertwig, Stefan T.

AU - Ivanova, Varvara V.

AU - Janssens, Luc

AU - Jennings, Richard P.

AU - Kasparov, Aleksei K.

AU - Kirillova, Irina V.

AU - Kurmaniyazov, Islam

AU - Kuzmin, Yaroslav V.

AU - Kosintsev, Pavel A.

AU - Lázničková-Galetová, Martina

AU - Leduc, Charlotte

AU - Nikolskiy, Pavel

AU - Nussbaumer, Marc

AU - O’Drisceoil, Cóilín

AU - Orlando, Ludovic

AU - Outram, Alan

AU - Pavlova, Elena Y.

AU - Perri, Angela R.

AU - Pilot, Małgorzata

AU - Pitulko, Vladimir V.

AU - Plotnikov, Valerii V.

AU - Protopopov, Albert V.

AU - Rehazek, André

AU - Sablin, Mikhail

AU - Seguin-Orlando, Andaine

AU - Storå, Jan

AU - Verjux, Christian

AU - Zaibert, Victor F.

AU - Zazula, Grant

AU - Crombé, Philippe

AU - Hansen, Anders J.

AU - Willerslev, Eske

AU - Leonard, Jennifer A.

AU - Götherström, Anders

AU - Pinhasi, Ron

AU - Schuenemann, Verena J.

AU - Hofreiter, Michael

AU - Gilbert, M. Thomas P.

AU - Shapiro, Beth

AU - Larson, Greger

AU - Krause, Johannes

AU - Dalén, Love

AU - Skoglund, Pontus

N1 - This work was supported by grants to P. Skoglund from the European Research Council (grant no. 852558), the Erik Philip Sörensen Foundation and the Science for Life Laboratory, Swedish Biodiversity Program, made available by support from the Knut and Alice Wallenberg Foundation. A.B., L.S., P. Swali and P. Skoglund were supported by Francis Crick Institute core funding (FC001595) from Cancer Research UK, the UK Medical Research Council and the Wellcome Trust. P. Skoglund was also supported by the Vallee Foundation, the European Molecular Biology Organisation and the Wellcome Trust (217223/Z/19/Z). Computations were supported by SNIC-UPPMAX. We also acknowledge support from Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, the National Genomics Infrastructure funded by the Swedish Research Council and the Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. We thank the Yukon gold mining community and First Nations, including the Tr’ondëk Hwëch’in, for continued support of our palaeontology research in the Yukon Territories, Canada. We thank the Danish National High-Throughput Sequencing Centre and BGI-Europe for assistance in sequencing data generation and the Danish National Supercomputer for Life Sciences–Computerome (https://computerome.dtu.dk) for computational resources. We thank National Museum Wales for continued sampling support. M. Germonpré acknowledges support from the Brain.be 2.0 ICHIE project (BELSPO B2/191/P2/ICHIE). M.T.P.G. was supported by the European Research Council (grant no. 681396). M.-H.S.S. was supported by the Velux Foundations through the Qimmeq Project, the Aage og Johanne Louis-Hansens Fond and the Independent Research Fund Denmark (8028-00005B). L.D. acknowledges support from FORMAS (2018-01640). D.W.G.S. received funding for this project from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 796877. M.P. was supported by the Polish National Agency for Academic Exchange–NAWA (grant no. PPN/PPO/2018/1/00037). V.J.S. was supported by the University of Zurich’s University Research Priority Program ‘Evolution in Action: From Genomes to Ecosystems’. This research was done with the participation of ZIN RAS (grant no. 075-15-2021-1069). We are grateful to the museum of the Institute of Plant and Animal Ecology UB RAS (Ekaterinburg, Russia) for provision of samples. R.P.J. and C.O’D. were supported by the Standing Committee for Archaeology of the Royal Irish Academy through the Archaeological Excavation Research Grant Scheme. E.Y.P., P.N. and V.V.P. are supported by the Russian Science Foundation (grant no. 16-18-10265-RNF and 21-18-00457-RNF). Y.V.K. was supported by the Russian Science Foundation (grant no. 20-17-00033). M.H. was supported by the European Research Council (consolidator grant GeneFlow no. 310763). M.L.-G. was supported by the Czech Science Foundation GAČR (grant no. 15-06446S) and institutional financing of the Moravian Museum from the Czech Ministry of Culture (IP DKRVO 2019-2023, MK000094862). L.S. is supported by the Sir Henry Wellcome fellowship (220457/Z/20/Z). We thank Staatliches Museum für Naturkunde Stuttgart for sample access. L.F. and G.L. were supported by European Research Council grants (ERC-2013-StG-337574-UNDEAD and ERC-2019-StG-853272-PALAEOFARM) and Natural Environmental Research Council grants (NE/K005243/1, NE/K003259/1, NE/S007067/1 and NE/S00078X/1). L.F. was also supported by the Wellcome Trust (210119/Z/18/Z). This research was funded in whole, or in part, by the Wellcome Trust (FC001595). For the purpose of open access, the author has applied a CC-BY public copyright licence to any author accepted manuscript version arising from this submission.

PY - 2022/7/14

Y1 - 2022/7/14

N2 - The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.

AB - The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.

KW - archaeology

KW - ecological genetics

KW - evolutionary genetics

KW - population genetics

KW - Animals

KW - Genome/genetics

KW - Europe

KW - Genomics

KW - Dogs

KW - Domestication

KW - Phylogeny

KW - Wolves/genetics

UR - http://www.scopus.com/inward/record.url?scp=85133199579&partnerID=8YFLogxK

U2 - 10.1038/s41586-022-04824-9

DO - 10.1038/s41586-022-04824-9

M3 - Article

C2 - 35768506

SN - 1476-4687

VL - 607

SP - 313

EP - 320

JO - Nature

JF - Nature

ER -

Grey wolf genomic history reveals a dual ancestry of dogs

Abstract

Bibliographical note

Data Availability Statement

Keywords

Access to Document

Other files and links

Fingerprint

Cite this