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Segawa T, Rey-Iglesia A, Lorenzen ED, Westbury MV. The origins and diversification of Holarctic brown bear populations inferred from genomes of past and present populations. Proc Biol Sci 2024; 291:20232411. [PMID: 38264778 PMCID: PMC10806438 DOI: 10.1098/rspb.2023.2411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024] Open
Abstract
The brown bear (Ursus arctos) is one of the survivors of the Late Quaternary megafauna extinctions. However, despite being widely distributed across the Holarctic, brown bears have experienced extensive range reductions, and even extirpations in some geographical regions. Previous research efforts using genetic data have provided valuable insights into their evolutionary history. However, most studies have been limited to contemporary individuals or mitochondrial DNA, limiting insights into population processes that preceded the present. Here, we present genomic data from two Late Pleistocene brown bears from Honshu, Japan and eastern Siberia, and combine them with published contemporary and ancient genomes from across the Holarctic range of brown bears to investigate the evolutionary relationships among brown bear populations through time and space. By including genomic data from Late Pleistocene and Holocene individuals sampled outside the current distribution range, we uncover diversity not present in contemporary populations. Notably, although contemporary individuals display geographically structured populations most likely driven by isolation-by-distance, this pattern varies among the ancient samples across different regions. The inclusion of ancient brown bears in our analysis provides novel insights into the evolutionary history of brown bears and contributes to understanding the populations and diversity lost during the Late Quaternary.
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Affiliation(s)
- Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, Chuo, Yamanashi, Japan
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2
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Rey-Iglesia A, Wilson T, Routledge J, Skovrind M, Garde E, Heide-Jørgensen MP, Szpak P, Lorenzen ED. Combining δ13C and δ15N from bone and dentine in marine mammal palaeoecological research: insights from toothed whales. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2023; 59:66-77. [PMID: 36445837 DOI: 10.1080/10256016.2022.2145285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Stable carbon (δ13C) and nitrogen (δ15N) isotopic compositions of bone and dentine collagen extracted from museum specimens have been widely used to study the paleoecology of past populations. Due to possible systematic differences in stable isotope values between bone and dentine, dentine values need to be transformed into bone-collagen equivalent using a correction factor to allow comparisons between the two collagen sources. Here, we provide correction factors to transform dentine δ13C and δ15N values into bone-collagen equivalent for two toothed whales: narwhal and beluga. We sampled bone and dentine from the skulls of 11 narwhals and 26 belugas. In narwhals, dentine was sampled from tusk and embedded tooth; in belugas, dentine was sampled from tooth. δ13C and δ15N were measured, and intra-individual bone and dentine isotopic compositions were used to calculate correction factors for each species. We detected differences in δ13C and δ15N. In both narwhals and belugas, we found lower average δ13C and δ15N in bone compared with dentine. The correction factors provided by the study enable the combined analysis of stable isotope data from bone and dentine in these species.
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Affiliation(s)
| | | | | | - Mikkel Skovrind
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Eva Garde
- Greenland Institute of Natural Resources, Copenhagen, Denmark
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3
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de Jong MJ, Niamir A, Wolf M, Kitchener AC, Lecomte N, Seryodkin IV, Fain SR, Hagen SB, Saarma U, Janke A. Range-wide whole-genome resequencing of the brown bear reveals drivers of intraspecies divergence. Commun Biol 2023; 6:153. [PMID: 36746982 PMCID: PMC9902616 DOI: 10.1038/s42003-023-04514-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/20/2023] [Indexed: 02/08/2023] Open
Abstract
Population-genomic studies can shed new light on the effect of past demographic processes on contemporary population structure. We reassessed phylogeographical patterns of a classic model species of postglacial recolonisation, the brown bear (Ursus arctos), using a range-wide resequencing dataset of 128 nuclear genomes. In sharp contrast to the erratic geographical distribution of mtDNA and Y-chromosomal haplotypes, autosomal and X-chromosomal multi-locus datasets indicate that brown bear population structure is largely explained by recent population connectivity. Multispecies coalescent based analyses reveal cases where mtDNA haplotype sharing between distant populations, such as between Iberian and southern Scandinavian bears, likely results from incomplete lineage sorting, not from ancestral population structure (i.e., postglacial recolonisation). However, we also argue, using forward-in-time simulations, that gene flow and recombination can rapidly erase genomic evidence of former population structure (such as an ancestral population in Beringia), while this signal is retained by Y-chromosomal and mtDNA, albeit likely distorted. We further suggest that if gene flow is male-mediated, the information loss proceeds faster in autosomes than in X chromosomes. Our findings emphasise that contemporary autosomal genetic structure may reflect recent population dynamics rather than postglacial recolonisation routes, which could contribute to mtDNA and Y-chromosomal discordances.
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Affiliation(s)
- Menno J. de Jong
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325 Germany
| | - Aidin Niamir
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325 Germany
| | - Magnus Wolf
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325 Germany ,grid.7839.50000 0004 1936 9721Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse. 9, Frankfurt am Main, Germany
| | - Andrew C. Kitchener
- grid.422302.50000 0001 0943 6159Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh, EH1 1JF UK ,grid.4305.20000 0004 1936 7988School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh, EH8 9XP UK
| | - Nicolas Lecomte
- grid.265686.90000 0001 2175 1792Canada Research Chair in Polar and Boreal Ecology, Department of Biology, University of Moncton, Moncton, New Brunswick E1H1R2 Canada
| | - Ivan V. Seryodkin
- grid.465394.90000 0004 0611 5319Pacific Geographical Institute of the Far Eastern Branch of the Russian Academy of Sciences, 7 Radio St., Vladivostok, 690041 Russia
| | - Steven R. Fain
- National Fish & Wildlife Forensic Laboratory, Ashland, OR USA
| | - Snorre B. Hagen
- grid.454322.60000 0004 4910 9859Norwegian Institute of Bioeconomy Research, Division of Environment and Natural Resources, Svanhovd, N-9925 Svanvik, Norway
| | - Urmas Saarma
- grid.10939.320000 0001 0943 7661Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu, 50409 Estonia
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325 Germany ,grid.7839.50000 0004 1936 9721Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse. 9, Frankfurt am Main, Germany ,grid.511284.b0000 0004 8004 5574LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Strasse 14-16, Frankfurt am Main, Germany
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4
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Salis AT, Bray SCE, Lee MSY, Heiniger H, Barnett R, Burns JA, Doronichev V, Fedje D, Golovanova L, Harington CR, Hockett B, Kosintsev P, Lai X, Mackie Q, Vasiliev S, Weinstock J, Yamaguchi N, Meachen JA, Cooper A, Mitchell KJ. Lions and brown bears colonized North America in multiple synchronous waves of dispersal across the Bering Land Bridge. Mol Ecol 2022; 31:6407-6421. [PMID: 34748674 DOI: 10.1111/mec.16267] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 01/13/2023]
Abstract
The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far northeast Asia) and Eastern Beringia (northwest North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation and vegetation, impacting faunal community structure and demography. While these palaeoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyse mitochondrial genome data from ancient brown bears (Ursus arctos; n = 103) and lions (Panthera spp.; n = 39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underline the crucial biogeographical role of the Bering Land Bridge in the distribution, turnover and maintenance of megafaunal populations in North America.
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Affiliation(s)
- Alexander T Salis
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Sarah C E Bray
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Registry of Senior Australians (ROSA), South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
| | - Michael S Y Lee
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia.,South Australian Museum, Adelaide, South Australia, Australia
| | - Holly Heiniger
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Ross Barnett
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - James A Burns
- Curator Emeritus, Royal Alberta Museum, Edmonton, Alberta, Canada
| | | | - Daryl Fedje
- Department of Anthropology, University of Victoria, Victoria, B.C, Canada
| | | | - C Richard Harington
- Curator Emeritus and Research Associate, Research Division (Paleobiology), Canadian Museum of Nature, Ottawa, Canada
| | - Bryan Hockett
- US Department of Interior, Bureau of Land Management, Nevada State Office, Reno, Nevada, USA
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia.,Department of History, Ural Federal University, Yekaterinburg, Russia
| | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
| | - Quentin Mackie
- Department of Anthropology, University of Victoria, Victoria, B.C, Canada
| | - Sergei Vasiliev
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Russia
| | - Jacobo Weinstock
- Faculty of Humanities (Archaeology), University of Southampton, UK
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Julie A Meachen
- Anatomy Department, Des Moines University, Des Moines, Iowa, USA
| | - Alan Cooper
- South Australian Museum, Adelaide, South Australia, Australia
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Department of Zoology, Otago Palaeogenetics Laboratory, University of Otago, Dunedin, New Zealand
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5
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Boulygina E, Sharko F, Cheprasov M, Gladysheva-Azgari M, Slobodova N, Tsygankova S, Rastorguev S, Grigorieva L, Kopp M, Fernandes JMO, Novgorodov G, Boeskorov G, Protopopov A, Hwang WS, Tikhonov A, Nedoluzhko A. Ancient DNA Reveals Maternal Philopatry of the Northeast Eurasian Brown Bear ( Ursus arctos) Population during the Holocene. Genes (Basel) 2022; 13:1961. [PMID: 36360198 PMCID: PMC9689912 DOI: 10.3390/genes13111961] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/08/2022] [Accepted: 10/25/2022] [Indexed: 09/14/2023] Open
Abstract
Significant palaeoecological and paleoclimatic changes that took place during Late Pleistocene-Early Holocene transition are considered important factors that led to megafauna extinctions. Unlike many other species, the brown bear (Ursus arctos) has survived this geological time. Despite the fact that several mitochondrial DNA clades of brown bears became extinct at the end of the Pleistocene, this species is still widely distributed in Northeast Eurasia. Here, using the ancient DNA analysis of a brown bear individual that inhabited Northeast Asia in the Middle Holocene (3460 ± 40 years BP) and comparative phylogenetic analysis, we show a significant mitochondrial DNA similarity of the studied specimen with modern brown bears inhabiting Yakutia and Chukotka. In this study, we clearly demonstrate the maternal philopatry of the Northeastern Eurasian U. arctos population during the several thousand years of the Holocene.
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Affiliation(s)
- Eugenia Boulygina
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Fedor Sharko
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
- Limited Liability Company ELGENE, 109029 Moscow, Russia
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Maksim Cheprasov
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
| | - Maria Gladysheva-Azgari
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Natalia Slobodova
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Svetlana Tsygankova
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Sergey Rastorguev
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
- Limited Liability Company ELGENE, 109029 Moscow, Russia
| | - Lena Grigorieva
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
| | - Martina Kopp
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Jorge M. O. Fernandes
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Gavril Novgorodov
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
| | - Gennady Boeskorov
- Institute of Diamond and Precious Metals Geology, Siberian Branch of Russian 5 Academy of Sciences, 677007 Yakutsk, Russia
| | - Albert Protopopov
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
- Academy of Sciences of Sakha (Yakutia), 677007 Yakutsk, Russia
| | - Woo-Suk Hwang
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
- UAE Biotech Research Center, Abu Dhabi 30310, United Arab Emirates
| | - Alexei Tikhonov
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
- Zoological Institute Russian Academy of Sciences, 190121 Saint-Petersburg, Russia
| | - Artem Nedoluzhko
- Limited Liability Company ELGENE, 109029 Moscow, Russia
- Paleogenomics Laboratory, European University at Saint Petersburg, 191187 Saint-Petersburg, Russia
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6
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Hyun JY, Kim TW, Pandey P, Kim KS, Jeong SJ, Kang JK, Kong DY, Jung SH, Jeong HK, Han SH, Han SH, Lee H. Molecular identification of archaic bones as a native Korean black bear: implications for the ongoing bear restoration program. Anim Cells Syst (Seoul) 2022; 26:214-222. [PMID: 36275447 PMCID: PMC9586619 DOI: 10.1080/19768354.2022.2112755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The genetic investigation of the archeological or museum samples, including endangered species, provides vital information necessary to plan, implement, and revisit conservation strategies. In South Korea, the Asian black bear went almost extinct in wild by 2002, without leaving any authentic specimens representing the native population. Recently researchers found a set of animal bones in a natural cave in Mt. Taebaek (South Korea), suspected to be of a bear. In the present study, we undertook a molecular investigation and radiocarbon dating to establish the species’ identity, phylogenetic position, and approximate age of the recovered specimen. The genetic investigation (CytB, COI, D-loop, SRY, and ZFX-ZFY) identified the sample as a male Asian black bear with close phylogenetic affinity with Northeast Asian bears. Radiocarbon dating estimated the bones to be aged 1800–1942 calAD. These findings indicate that the bone specimens found in the natural cave in Mt. Taebaek were from an individual that naturally inhabited South Korea long before the importing of farm bears (the 1980s) and initiation of wild population restoration (2004). The present study provides the first genetic information record of the native South Korean black bear. Our findings reaffirm the appropriateness of the ongoing bear restoration program in South Korea, with the reintroduction of individuals from North Korea and Russia.
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Affiliation(s)
- Jee Yun Hyun
- Conservation Genome Resource Bank for Korean Wildlife (CGRB) and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- National Institute of Biological Resources, Incheon, Republic of Korea
| | - Tae-Wook Kim
- Habitat Conservation Division, Korea National Park Research Institute, Korea National Park Service, Yeongju, Republic of Korea
| | - Puneet Pandey
- Conservation Genome Resource Bank for Korean Wildlife (CGRB) and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- ENPROTEC India Foundation, Uttar Pradesh, India
| | - Kyung Seok Kim
- Department of Pediatrics-Nutrition, Baylor College of Medicine, Houston, USA
| | | | - Jae-Ku Kang
- Korea National Park Service, Wonju, Republic of Korea
| | - Dal-Yong Kong
- International Cooperation Division, Cultural Heritage Administration, Daejeon, Republic of Korea
| | - Seung-Ho Jung
- National Research Institute of Cultural Heritage, Cultural Heritage Administration, Daejeon, Republic of Korea
| | - Ho-Kweon Jeong
- Ecosystem of the Korean Peninsula Research Institute, Jeongseon, Republic of Korea
| | - Sang-Hoon Han
- Inter-Korea Wildlife Institute, Inje, Republic of Korea
| | - Sang-Hyun Han
- Habitat Conservation Division, Korea National Park Research Institute, Korea National Park Service, Yeongju, Republic of Korea
| | - Hang Lee
- Conservation Genome Resource Bank for Korean Wildlife (CGRB) and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
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7
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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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8
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Molodtseva AS, Makunin AI, Salomashkina VV, Kichigin IG, Vorobieva NV, Vasiliev SK, Shunkov MV, Tishkin AA, Grushin SP, Anijalg P, Tammeleht E, Keis M, Boeskorov GG, Mamaev N, Okhlopkov IM, Kryukov AP, Lyapunova EA, Kholodova MV, Seryodkin IV, Saarma U, Trifonov VA, Graphodatsky AS. Phylogeography of ancient and modern brown bears from eastern Eurasia. Biol J Linn Soc Lond 2022; 135:722-733. [PMID: 35359699 PMCID: PMC8943912 DOI: 10.1093/biolinnean/blac009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 11/12/2022]
Abstract
The brown bear (Ursus arctos) is an iconic carnivoran species of the Northern Hemisphere. Its population history has been studied extensively using mitochondrial markers, which demonstrated signatures of multiple waves of migration, arguably connected with glaciation periods. Among Eurasian brown bears, Siberian populations remain understudied. We have sequenced complete mitochondrial genomes of four ancient (~4.5-40 kya) bears from South Siberia and 19 modern bears from South Siberia and the Russian Far East. Reconstruction of phylogenetic relationships between haplotypes and evaluation of modern population structure have demonstrated that all the studied samples belong to the most widespread Eurasian clade 3. One of the ancient haplotypes takes a basal position relative to the whole of clade 3; the second is basal to the haplogroup 3a (the most common subclade), and two others belong to clades 3a1 and 3b. Modern Siberian bears retain at least some of this diversity; apart from the most common haplogroup 3a, we demonstrate the presence of clade 3b, which was previously found mainly in mainland Eurasia and Northern Japan. Our findings highlight the importance of South Siberia as a refugium for northern Eurasian brown bears and further corroborate the hypothesis of several waves of migration in the Pleistocene.
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Affiliation(s)
- Anna S Molodtseva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey I Makunin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia,Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | - Ilya G Kichigin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nadezhda V Vorobieva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey K Vasiliev
- Institute of Archaeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Mikhail V Shunkov
- Institute of Archaeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | | | - Peeter Anijalg
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Egle Tammeleht
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Marju Keis
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Gennady G Boeskorov
- Geological Museum, Institute of Diamond and Precious Metals Geology, Siberian Branch of the Russian Academy of Sciences, Yakutsk, Russia
| | - Nikolai Mamaev
- Institute for Biological Problems of Cryolithozone, Siberian Branch of the Russian Academy of Sciences, Yakutsk, Russia
| | - Innokenty M Okhlopkov
- Institute for Biological Problems of Cryolithozone, Siberian Branch of the Russian Academy of Sciences, Yakutsk, Russia
| | - Alexey P Kryukov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Elena A Lyapunova
- N. K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Marina V Kholodova
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Ivan V Seryodkin
- Pacific Institute of Geography, Far East Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | | | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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9
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Segawa T, Yonezawa T, Mori H, Akiyoshi A, Allentoft ME, Kohno A, Tokanai F, Willerslev E, Kohno N, Nishihara H. Ancient DNA reveals multiple origins and migration waves of extinct Japanese brown bear lineages. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210518. [PMID: 34386259 PMCID: PMC8334828 DOI: 10.1098/rsos.210518] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Little is known about how mammalian biogeography on islands was affected by sea-level fluctuations. In the Japanese Archipelago, brown bears (Ursus arctos) currently inhabit only Hokkaido, the northern island, but Pleistocene fossils indicate a past distribution throughout Honshu, Japan's largest island. However, the difficulty of recovering ancient DNA from fossils in temperate East Asia has limited our understanding of their evolutionary history. Here, we analysed mitochondrial DNA from a 32 500-year-old brown bear fossil from Honshu. Our results show that this individual belonged to a previously unknown lineage that split approximately 160 Ka from its sister lineage, the southern Hokkaido clade. This divergence time and fossil record suggest that brown bears migrated from the Eurasian continent to Honshu at least twice; the first population was an early-diverging lineage (greater than 340 Ka), and the second migrated via Hokkaido after approximately 160 Ka, during the ice age. Thus, glacial-age sea-level falls might have facilitated migrations of large mammals more frequently than previously thought, which may have had a substantial impact on ecosystem dynamics in these isolated islands.
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Affiliation(s)
- Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, Japan
| | - Takahiro Yonezawa
- Tokyo University of Agriculture, 1737 Funako, Atsugi City, Kanagawa, Japan
| | - Hiroshi Mori
- National Institute of Genetics, Yata 1111, Mishima City, Shizuoka, Japan
| | - Ayumi Akiyoshi
- National Institute of Polar Research, Midori-cho 10-3, Tachikawa City, Tokyo, Japan
| | - Morten E. Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia 6102, Australia
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ayako Kohno
- Department of Geology and Paleontology, National Museum of Nature and Science, Tokyo, Amakubo, Tsukuba, Ibaraki, Japan
| | - Fuyuki Tokanai
- Faculty of Science, Yamagata University, Jonan 4-3-16, Yonezawa City, Yamagata 990-3101, Japan
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Naoki Kohno
- Department of Geology and Paleontology, National Museum of Nature and Science, Tokyo, Amakubo, Tsukuba, Ibaraki, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai, Tsukuba, Ibaraki, Japan
| | - Hidenori Nishihara
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-S2-17 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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Krylovich OA, Boeskorov GG, Shchelchkova MV, Savinetsky AB. The Trophic Position of Pleistocene and Modern Brown Bears (Ursus arctos) of Yakutia Based on Stable Isotope Analyses. BIOL BULL+ 2021. [DOI: 10.1134/s1062359020080087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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