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Pacheco C, Stronen AV, Jędrzejewska B, Plis K, Okhlopkov IM, Mamaev NV, Drovetski SV, Godinho R. Demography and evolutionary history of grey wolf populations around the Bering Strait. Mol Ecol 2022; 31:4851-4865. [PMID: 35822863 PMCID: PMC9545117 DOI: 10.1111/mec.16613] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 06/16/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022]
Abstract
Glacial and interglacial periods throughout the Pleistocene have been substantial drivers of change in species distributions. Earlier analyses suggested that modern grey wolves (Canis lupus) trace their origin to a single Late Pleistocene Beringian population that expanded east and westwards, starting c. 25,000 years ago (ya). Here, we examined the demographic and phylogeographic histories of extant populations around the Bering Strait with wolves from two inland regions of the Russian Far East (RFE) and one coastal and two inland regions of North‐western North America (NNA), genotyped for 91,327 single nucleotide polymorphisms. Our results indicated that RFE and NNA wolves had a common ancestry until c. 34,400 ya, suggesting that these populations started to diverge before the previously proposed expansion out of Beringia. Coastal and inland NNA populations diverged c. 16,000 ya, concordant with the minimum proposed date for the ecological viability of the migration route along the Pacific Northwest coast. Demographic reconstructions for inland RFE and NNA populations reveal spatial and temporal synchrony, with large historical effective population sizes that declined throughout the Pleistocene, possibly reflecting the influence of broadscale climatic changes across continents. In contrast, coastal NNA wolves displayed a consistently lower effective population size than the inland populations. Differences between the demographic history of inland and coastal wolves may have been driven by multiple ecological factors, including historical gene flow patterns, natural landscape fragmentation, and more recent anthropogenic disturbance.
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Affiliation(s)
- Carolina Pacheco
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Astrid Vik Stronen
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.,Department of Biotechnology and Life Sciences, Insubria University, Varese, Italy.,Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Kamila Plis
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Innokentiy M Okhlopkov
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Nikolay V Mamaev
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Sergei V Drovetski
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
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2
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Zdjelar N, Nagendran L, Kendall C, Ackermann RR, Schroeder L. The hybrid skull of the eastern coyote (Canis latrans var.): Nonmetric traits and craniomandibular shape. J Morphol 2021; 282:1745-1764. [PMID: 34609013 DOI: 10.1002/jmor.21417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/14/2021] [Accepted: 10/05/2021] [Indexed: 12/24/2022]
Abstract
The increasing awareness that hybridization, and resultant gene flow, plays a major role in animal diversification has led to a growing number of studies that have focused on assessing the morphological consequences of this process. Analyses of mammalian hybrids have identified skeletal effects of hybridization, including a suite of anomalous dental and sutural traits on the skull that are present at high frequencies in hybrid populations. These studies have also detected consistent patterns of morphological shape and size differences between hybrids and parental taxa across a wide variety of organisms. However, more research is required to understand the universality of these traits and shape/size differences. Building on these previous studies, a sample of genetically determined canid hybrids was examined, specifically the eastern coyote (Canis latrans var.), a hybrid between coyotes, wolves, and dogs, to test whether this group exhibits a comparable pattern of anomalous nonmetric characters, and to assess differences in craniomandibular shape and size. First, specimens of C. latrans var., C. latrans, and C. lupus were scored for anomalous traits, including supernumerary and rotated teeth, dental crowding, and sutural anomalies. Geometric morphometric analyses were then conducted on a subset of these individuals to explore craniomandibular size and shape variation, as well as allometry. The results are largely consistent with other studies, indicating that the incidence of dental anomalies, dental crowding, and sutural anomalies is significantly higher in hybrids. However, differences are not significant for supernumerary teeth. The exploration of morphometric variation identifies intermediate morphology in the hybrids, and some indication of greater morphological variability in the mandible. When these results are combined with previous studies, they suggest that skeletal signatures of hybridization are common to different mammalian taxa across multiple generations; however, some traits such as supernumerary teeth may be lost after a few generations.
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Affiliation(s)
- Natasa Zdjelar
- Department of Anthropology, University of Toronto, Toronto, Ontario, Canada
| | - Lavania Nagendran
- Department of Anthropology, University of Toronto, Toronto, Ontario, Canada
| | | | - Rebecca Rogers Ackermann
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa.,Department of Archaeology, University of Cape Town, Rondebosch, South Africa
| | - Lauren Schroeder
- Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa.,Department of Anthropology, University of Toronto Mississauga, Mississauga, Ontario, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
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4
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Sacks BN, Mitchell KJ, Quinn CB, Hennelly LM, Sinding MHS, Statham MJ, Preckler-Quisquater S, Fain SR, Kistler L, Vanderzwan SL, Meachen JA, Ostrander EA, Frantz LAF. Pleistocene origins, western ghost lineages, and the emerging phylogeographic history of the red wolf and coyote. Mol Ecol 2021; 30:4292-4304. [PMID: 34181791 DOI: 10.1111/mec.16048] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 06/18/2021] [Accepted: 06/24/2021] [Indexed: 11/29/2022]
Abstract
The red wolf (Canis rufus) of the eastern US was driven to near-extinction by colonial-era persecution and habitat conversion, which facilitated coyote (C. latrans) range expansion and widespread hybridization with red wolves. The observation of some grey wolf (C. lupus) ancestry within red wolves sparked controversy over whether it was historically a subspecies of grey wolf with its predominant "coyote-like" ancestry obtained from post-colonial coyote hybridization (2-species hypothesis) versus a distinct species closely related to the coyote that hybridized with grey wolf (3-species hypothesis). We analysed mitogenomes sourced from before the 20th century bottleneck and coyote invasion, along with hundreds of modern amplicons, which led us to reject the 2-species model and to investigate a broader phylogeographic 3-species model suggested by the fossil record. Our findings broadly support this model, in which red wolves ranged the width of the American continent prior to arrival of the grey wolf to the mid-continent 60-80 ka; red wolves subsequently disappeared from the mid-continent, relegated to California and the eastern forests, which ushered in emergence of the coyote in their place (50-30 ka); by the early Holocene (12-10 ka), coyotes had expanded into California, where they admixed with and phenotypically replaced western red wolves in a process analogous to the 20th century coyote invasion of the eastern forests. Findings indicate that the red wolf pre-dated not only European colonization but human, and possibly coyote, presence in North America. These findings highlight the urgency of expanding conservation efforts for the red wolf.
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Affiliation(s)
- Benjamin N Sacks
- Mammalian Ecology and Conservation Unit/Veterinary Genetics Laboratory and Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA (ACAD) and ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Cate B Quinn
- Mammalian Ecology and Conservation Unit/Veterinary Genetics Laboratory and Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Lauren M Hennelly
- Mammalian Ecology and Conservation Unit/Veterinary Genetics Laboratory and Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Mikkel-Holger S Sinding
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Mark J Statham
- Mammalian Ecology and Conservation Unit/Veterinary Genetics Laboratory and Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Sophie Preckler-Quisquater
- Mammalian Ecology and Conservation Unit/Veterinary Genetics Laboratory and Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Steven R Fain
- National Fish & Wildlife Forensic Laboratory, Ashland, OR, USA
| | - Logan Kistler
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Stevi L Vanderzwan
- Mammalian Ecology and Conservation Unit/Veterinary Genetics Laboratory and Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Julie A Meachen
- Anatomy Department, Des Moines University, Des Moines, IA, USA
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Laurent A F Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, Munich, Germany.,School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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5
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Perri AR, Mitchell KJ, Mouton A, Álvarez-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 MHS, Gilbert MTP, Stone AC, Shapiro B, Van Valkenburgh B, Wayne RK, Larson G, Cooper A, Frantz LAF. Dire wolves were the last of an ancient New World canid lineage. Nature 2021; 591:87-91. [PMID: 33442059 DOI: 10.1038/s41586-020-03082-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 11/12/2020] [Indexed: 11/09/2022]
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 Canidae2,3, 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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Affiliation(s)
- Angela R Perri
- Department of Archaeology, Durham University, Durham, UK.
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
| | - Alice Mouton
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | | | - Ardern Hulme-Beaman
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK.,School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| | - James Haile
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK
| | - Alexandra Jamieson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK
| | - Julie Meachen
- Department of Anatomy, Des Moines University, Des Moines, IA, USA
| | - Audrey T Lin
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK.,Department of Zoology, University of Oxford, Oxford, UK.,Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Blaine W Schubert
- Center of Excellence in Paleontology & Department of Geosciences, East Tennessee State University, Johnson City, TN, USA
| | - Carly Ameen
- Department of Archaeology, University of Exeter, Exeter, UK
| | | | - Pere Bover
- ARAID Foundation, Instituto Universitario de Investigación en Ciencias Ambientales (IUCA) - Aragosaurus Group, Universidad de Zaragoza, Zaragoza, Spain
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Alberto Carmagnini
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Christian Carøe
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK.,Department of Archaeology, University of Sydney, Sydney, New South Wales, Australia.,Department of Archaeology, University of Aberdeen, Aberdeen, UK.,Department of Archaeology, Simon Fraser University, Burnaby, Canada
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Allowen Evin
- Institut des Sciences de l'Evolution - Montpellier, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France
| | - Philippe Gaubert
- Laboratoire Evolution & Diversité Biologique, UPS/CNRS/IRD, Université Paul Sabatier, Toulouse, France
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Graham Gower
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Holly Heiniger
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Josh Kapp
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Pavel A Kosintsev
- Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of Sciences, Yekaterinburg, Russia.,Ural Federal University, Yekaterinburg, Russia
| | - Anna Linderholm
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK.,Department of Anthropology, Texas A&M University, College Station, TX, USA
| | - Andrew T Ozga
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, USA
| | | | - Alexander T Salis
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Nedda F Saremi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Colin Shew
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Katherine Skerry
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Dmitry E Taranenko
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Mary Thompson
- Idaho Museum of Natural History, Idaho State University, Pocatello, ID, USA
| | - Mikhail V Sablin
- Zoological Institute of the Russian Academy of Sciences, St Petersburg, Russia
| | - Yaroslav V Kuzmin
- Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Tomsk State University, Tomsk, Russia
| | - Matthew J Collins
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Mikkel-Holger S Sinding
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,NTNU University Museum, Trondheim, Norway
| | - Anne C Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Blaire Van Valkenburgh
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK
| | - Alan Cooper
- South Australian Museum, Adelaide, South Australia, Australia
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK. .,Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany.
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