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Hernández‐Alonso G, Ramos‐Madrigal J, Sun X, Scharff‐Olsen CH, Sinding MS, Martins NF, Ciucani MM, Mak SST, Lanigan LT, Clausen CG, Bhak J, Jeon S, Kim C, Eo KY, Cho S, Boldgiv B, Gantulga G, Unudbayasgalan Z, Kosintsev PA, Stenøien HK, Gilbert MTP, Gopalakrishnan S. Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing. Ecol Evol 2023; 13:e10404. [PMID: 37546572 PMCID: PMC10401669 DOI: 10.1002/ece3.10404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/07/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023] Open
Abstract
The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage, Canis coreanus. To investigate the Korean wolf's genetic affiliations and taxonomic status, we sequenced and analysed the genomes of a Korean wolf dated to the beginning of the 20th century, and a captive wolf originally from the Pyongyang Central Zoo. Our results indicated that the Korean wolf bears similar genetic ancestry to other regional East Asian populations, therefore suggesting it is not a distinct taxonomic lineage. We identified regional patterns of wolf population structure and admixture in East Asia with potential conservation consequences in the Korean Peninsula and on a regional scale. We find that the Korean wolf has similar genomic diversity and inbreeding to other East Asian wolves. Finally, we show that, in contrast to the historical sample, the captive wolf is genetically more similar to wolves from the Tibetan Plateau; hence, Korean wolf conservation programmes might not benefit from the inclusion of this specimen.
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Affiliation(s)
- Germán Hernández‐Alonso
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Jazmín Ramos‐Madrigal
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Xin Sun
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | | | | | - Nuno F. Martins
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Marta Maria Ciucani
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Sarah S. T. Mak
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Liam Thomas Lanigan
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Cecilie G. Clausen
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Jong Bhak
- Clinomics Inc.UlsanKorea
- Korean Genomics CenterUlsan National Institute of Science and TechnologyUlsanKorea
- Department of Biomedical Engineering, College of Information‐Bio Convergence EngineeringUlsan National Institute of Science and TechnologyUlsanKorea
- Personal Genomics InstituteGenome Research FoundationOsongKorea
| | - Sungwon Jeon
- Clinomics Inc.UlsanKorea
- Korean Genomics CenterUlsan National Institute of Science and TechnologyUlsanKorea
| | | | - Kyung Yeon Eo
- Department of Animal Health & WelfareSemyung UniversityJecheonKorea
| | - Seong‐Ho Cho
- Natural History MuseumKyungpook National UniversityGunwiKorea
| | - Bazartseren Boldgiv
- Laboratory of Ecological and Evolutionary SynthesisNational University of MongoliaUlaanbaatarMongolia
| | | | | | - Pavel A. Kosintsev
- Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of SciencesYekaterinburgRussia
- Ural Federal UniversityEkaterinburgRussia
| | - Hans K. Stenøien
- NTNU University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - M. Thomas P. Gilbert
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Shyam Gopalakrishnan
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Bioinformatics, Department of Health TechnologyTechnical University of DenmarkLyngbyDenmark
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2
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Paleogenomics reveals independent and hybrid origins of two morphologically distinct wolf lineages endemic to Japan. Curr Biol 2022; 32:2494-2504.e5. [DOI: 10.1016/j.cub.2022.04.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 01/31/2022] [Accepted: 04/13/2022] [Indexed: 11/23/2022]
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Werhahn G, Senn H, Macdonald DW, Sillero-Zubiri C. The Diversity in the Genus Canis Challenges Conservation Biology: A Review of Available Data on Asian Wolves. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.782528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Taxa belonging to the Genus Canis can challenge taxonomists because species boundaries and distribution ranges are often gradual. Species delineation within Canis is currently not based on consistent criteria, and is hampered by geographical bias and lack of taxonomic research. But a consistent taxonomy is critical, given its importance for assigning legal protection, conservation priorities, and financial resources. We carried out a qualitative review of the major wolf lineages so far identified from Asia from historical to contemporary time and considered relevant morphological, ecological, and genetic evidence. We present full mitochondrial phylogenies and genetic distances between these lineages. This review aims to summarize the available data on contemporary Asian wolf lineages within the context of the larger phylogenetic Canis group and to work toward a taxonomy that is consistent within the Canidae. We found support for the presence and taxon eligibility of Holarctic gray, Himalayan/Tibetan, Indian, and Arabian wolves in Asia and recommend their recognition at the taxonomic levels consistent within the group.
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Matsumura S, Terai Y, Hongo H, Ishiguro N. Analysis of the Mitochondrial Genomes of Japanese Wolf Specimens in the Siebold Collection, Leiden. Zoolog Sci 2021; 38:60-66. [PMID: 33639719 DOI: 10.2108/zs200019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 08/21/2020] [Indexed: 11/17/2022]
Abstract
The taxonomic status of extinct Japanese or Honshu wolves (Canis lupus hodophilax) has been disputed since the name hodophilax was first proposed by Temminck in 1839 on the basis of specimens stored in Leiden, the Netherlands. Points of controversy include whether the type specimen of hodophilax (Jentink c: RMNH.MAM.39181) and the other two specimens from Leiden (Jentink a: RMNH.MAM.39182 and Jentink b: RMNH.MAM.39183) represent different varieties or subspecies of Japanese wolves or not. Two Japanese names, ookami and jamainu, used to describe wild Canis species, further complicate the issue. In this study, the taxonomic status of Japanese wolves was clarified using mitochondrial DNA of the three specimens stored at the Naturalis Biodiversity Center in Leiden, in addition to three Japanese wolf specimens stored at the Museum für Naturkunde in Berlin and five new samples from Japan. The mitochondrial genomes of the type specimen of hodophilax (Jentink c) and another sample from Leiden (Jentink b) as well as Berlin specimens were included in the cluster of Japanese wolves distinct from other grey wolves. However, the other sample from Leiden (Jentink a) was identified as a domestic dog. A mitochondrial genome analysis suggested that Japanese wolves could be categorized into two distinct clusters. Studies of nuclear genomes are needed to further clarify the taxonomic status, divergence time, and population genetic structure of Japanese wolves.
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Affiliation(s)
- Shuichi Matsumura
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan,
| | - Yohey Terai
- School of Advanced Sciences, SOKENDAI (Graduate University for Advanced Studies), Hayama 240-0193, Japan
| | - Hitomi Hongo
- School of Advanced Sciences, SOKENDAI (Graduate University for Advanced Studies), Hayama 240-0193, Japan
| | - Naotaka Ishiguro
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan.,School of Advanced Sciences, SOKENDAI (Graduate University for Advanced Studies), Hayama 240-0193, Japan
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Niemann J, Gopalakrishnan S, Yamaguchi N, Ramos-Madrigal J, Wales N, Gilbert MTP, Sinding MHS. Extended survival of Pleistocene Siberian wolves into the early 20th century on the island of Honshū. iScience 2021; 24:101904. [PMID: 33364590 PMCID: PMC7753132 DOI: 10.1016/j.isci.2020.101904] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/30/2020] [Accepted: 12/03/2020] [Indexed: 01/19/2023] Open
Abstract
The Japanese or Honshū wolf was one the most distinct gray wolf subspecies due to its small stature and endemicity to the islands of Honshū, Shikoku, and Kyūshū. Long revered as a guardian of farmers and travellers, it was persecuted from the 17th century following a rabies epidemic, which led to its extinction in the early 20th century. To better understand its evolutionary history, we sequenced the nuclear genome of a 19th century Honshū wolf specimen to an average depth of coverage of 3.7✕. We find Honshū wolves were closely related to a lineage of Siberian wolves that were previously believed to have gone extinct in the Late Pleistocene, thereby extending the survival of this ancient lineage until the early 20th century. We also detected significant gene flow between Japanese dogs and the Honshū wolf, corroborating previous reports on Honshū wolf dog interbreeding. Generated 3.7✕ nuclear genome of the extinct Honshu wolf The Honshū wolf belonged to the lineage of Siberian Pleistocene wolves There was gene flow between Honshū wolves and Japanese dogs
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Affiliation(s)
- Jonas Niemann
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- BioArch, Department of Archaeology, University of York, York, UK
- Corresponding author
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Jazmín Ramos-Madrigal
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Nathan Wales
- BioArch, Department of Archaeology, University of York, York, UK
| | - M. Thomas P. Gilbert
- 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, NTNU, Trondheim, Norway
| | - Mikkel-Holger S. Sinding
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Greenland Institute of Natural Resources, Nuuk, Greenland
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Corresponding author
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Matsubayashi J, Ohta T, Takahashi O, Tayasu I. Reconstruction of the extinct Ezo wolf's diet. J Zool (1987) 2017. [DOI: 10.1111/jzo.12436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - T. Ohta
- Research Institute for Humanity and Nature Kyoto Japan
| | - O. Takahashi
- Chitose Archaeological Operations Center Chitose Board of Education Chitose Hokkaido Japan
| | - I. Tayasu
- Research Institute for Humanity and Nature Kyoto Japan
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Ishiguro N, Inoshima Y, Yanai T, Sasaki M, Matsui A, Kikuchi H, Maruyama M, Hongo H, Vostretsov YE, Gasilin V, Kosintsev PA, Quanjia C, Chunxue W. Japanese Wolves are Genetically Divided into Two Groups Based on an 8-Nucleotide Insertion/Deletion within the mtDNA Control Region. Zoolog Sci 2016; 33:44-9. [PMID: 26853868 DOI: 10.2108/zs150110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The mitochondrial DNA (mtDNA) control region (198- to 598-bp) of four ancient Canis specimens (two Canis mandibles, a cranium, and a first phalanx) was examined, and each specimen was genetically identified as Japanese wolf. Two unique nucleotide substitutions, the 78-C insertion and the 482-G deletion, both of which are specific for Japanese wolf, were observed in each sample. Based on the mtDNA sequences analyzed, these four specimens and 10 additional Japanese wolf samples could be classified into two groups- Group A (10 samples) and Group B (4 samples)-which contain or lack an 8-bp insertion/deletion (indel), respectively. Interestingly, three dogs (Akita-b, Kishu 25, and S-husky 102) that each contained Japanese wolf-specific features were also classified into Group A or B based on the 8-bp indel. To determine the origin or ancestor of the Japanese wolf, mtDNA control regions of ancient continental Canis specimens were examined; 84 specimens were from Russia, and 29 were from China. However, none of these 113 specimens contained Japanese wolf-specific sequences. Moreover, none of 426 Japanese modern hunting dogs examined contained these Japanese wolf-specific mtDNA sequences. The mtDNA control region sequences of Groups A and B appeared to be unique to grey wolf and dog populations.
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Affiliation(s)
| | | | - Tokuma Yanai
- 2 Laboratory of Veterinary Pathology, Veterinary Medicine, Faculty of Applied and Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Motoki Sasaki
- 3 Laboratory of Veterinary Anatomy, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Japan
| | - Akira Matsui
- 4 Nara National Culture Properties Research Institute, Nara 630-8577, Japan
| | - Hiroki Kikuchi
- 5 Institute for Research in Humanities, Kyoto University, Yoshidahonmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masashi Maruyama
- 6 Department of Maritime Civilizations, School of Marine and Technology, Tokai University, Shizuoka 424-8610, Japan
| | - Hitomi Hongo
- 7 Department of Advanced Sciences, Graduate University for Advanced Studies, Hayama 240-0193, Kanagawa, Japan
| | - Yuri E Vostretsov
- 8 Laboratory of Human Paleoecology, Russian Academy of Science, Far Eastern Division, Institute of History, Archaeology and Ethnology, 89, Pushkinskaya, St. Vladivostok, 690600, Russia
| | - Viatcheslav Gasilin
- 9 Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, 620144, Russia
| | - Pavel A Kosintsev
- 9 Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, 620144, Russia
| | - Chen Quanjia
- 10 Research Center of Chinese Frontier Archaeology of Jilin University, Changchun, 130012, China
| | - Wang Chunxue
- 10 Research Center of Chinese Frontier Archaeology of Jilin University, Changchun, 130012, China
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8
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Lee EJ, Merriwether DA, Kasparov AK, Nikolskiy PA, Sotnikova MV, Pavlova EY, Pitulko VV. Ancient DNA analysis of the oldest canid species from the Siberian Arctic and genetic contribution to the domestic dog. PLoS One 2015; 10:e0125759. [PMID: 26018528 PMCID: PMC4446326 DOI: 10.1371/journal.pone.0125759] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/26/2015] [Indexed: 11/18/2022] Open
Abstract
Modern Arctic Siberia provides a wealth of resources for archaeological, geological, and paleontological research to investigate the population dynamics of faunal communities from the Pleistocene, particularly as the faunal material coming from permafrost has proven suitable for genetic studies. In order to examine the history of the Canid species in the Siberian Arctic, we carried out genetic analysis of fourteen canid remains from various sites, including the well-documented Upper Paleolithic Yana RHS and Early Holocene Zhokhov Island sites. Estimated age of samples range from as recent as 1,700 years before present (YBP) to at least 360,000 YBP for the remains of the extinct wolf, Canis cf. variabilis. In order to examine the genetic affinities of ancient Siberian canids species to the domestic dog and modern wolves, we obtained mitochondrial DNA control region sequences and compared them to published ancient and modern canid sequences. The older canid specimens illustrate affinities with pre-domestic dog/wolf lineages while others appear in the major phylogenetic clades of domestic dogs. Our results suggest a European origin of domestic dog may not be conclusive and illustrates an emerging complexity of genetic contribution of regional wolf breeds to the modern Canis gene pool.
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Affiliation(s)
- Esther J. Lee
- Department of Anthropology, Binghamton University, Binghamton, NY, United States of America
- Department of Sociology, Anthropology, and Social Work, Texas Tech University, Lubbock, TX, United States of America
- * E-mail:
| | - D. Andrew Merriwether
- Department of Anthropology, Binghamton University, Binghamton, NY, United States of America
| | - Alexei K. Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | | | | | | | - Vladimir V. Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
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Reconstructing the colonization history of lost wolf lineages by the analysis of the mitochondrial genome. Mol Phylogenet Evol 2014; 80:105-12. [PMID: 25132126 DOI: 10.1016/j.ympev.2014.08.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 07/29/2014] [Accepted: 08/03/2014] [Indexed: 11/27/2022]
Abstract
The grey wolves (Canis lupus) originally inhabited major parts of the Northern hemisphere, but many local populations became extinct. Two lineages of wolves in Japan, namely, Japanese or Honshu (C. l. hodophilax) and Ezo or Hokkaido (C. l. hattai) wolves, rapidly went extinct between 100 and 120years ago. Here we analyse the complete mitochondrial genome sequences from ancient specimens and reconstruct the colonization history of the two extinct subspecies. We show a unique status of Japanese wolves in wolf phylogeny, suggesting their long time separation from other grey wolf populations. Japanese wolves appeared to have colonized the Japanese archipelago in the Late Pleistocene (ca. 25,000-125,000years ago). By contrast, Ezo wolves, which are clearly separated from Japanese wolves in phylogeny, are likely to have arrived at Japan relatively recently (<14,000years ago). Interestingly, their colonization history to Japan tallies well with the dynamics of wolf populations in Europe and America during the last several millennia. Our analyses suggest that at least several thousands of wolves once inhabited in the Japanese archipelago. Our analyses also show that an enigmatic clade of domestic dogs is likely to have originated from rare admixture events between male dogs and female Japanese wolves.
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