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Tumendemberel O, Hendricks SA, Hohenlohe PA, Sullivan J, Zedrosser A, Saebø M, Proctor MF, Koprowski JL, Waits LP. Range-wide evolutionary relationships and historical demography of brown bears (Ursus arctos) revealed by whole-genome sequencing of isolated central Asian populations. Mol Ecol 2023; 32:5156-5169. [PMID: 37528604 DOI: 10.1111/mec.17091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 07/02/2023] [Accepted: 07/19/2023] [Indexed: 08/03/2023]
Abstract
Phylogeographic studies uncover hidden pathways of divergence and inform conservation. Brown bears (Ursus arctos) have one of the broadest distributions of all land mammals, ranging from Eurasia to North America, and are an important model for evolutionary studies. Although several whole genomes were available for individuals from North America, Europe and Asia, limited whole-genome data were available from Central Asia, including the highly imperilled brown bears in the Gobi Desert. To fill this knowledge gap, we sequenced whole genomes from nine Asian brown bears from the Gobi Desert of Mongolia, Northern Mongolia and the Himalayas of Pakistan. We combined these data with published brown bear sequences from Europe, Asia and North America, as well as other bear species. Our goals were to determine the evolutionary relationships among brown bear populations worldwide, their genetic diversity and their historical demography. Our analyses revealed five major lineages of brown bears based on a filtered set of 684,081 single nucleotide polymorphisms. We found distinct evolutionary lineages of brown bears in the Gobi, Himalayas, northern Mongolia, Europe and North America. The lowest level of genetic diversity and the highest level of inbreeding were found in Pakistan, the Gobi Desert and Central Italy. Furthermore, the effective population size (Ne ) for all brown bears decreased over the last 70,000 years. Our results confirm the genetic distinctiveness and ancient lineage of brown bear subspecies in the Gobi Desert of Mongolia and the Himalayas of Pakistan and highlight their importance for conservation.
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Affiliation(s)
- Odbayar Tumendemberel
- Haub School of Environment and Natural Resources, University of Wyoming, Laramie, Wyoming, USA
- Department of Natural Science and Environmental Health, University of South-Eastern Norway, Bø i Telemark, Norway
| | - Sarah A Hendricks
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
| | - Paul A Hohenlohe
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Jack Sullivan
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Andreas Zedrosser
- Department of Natural Science and Environmental Health, University of South-Eastern Norway, Bø i Telemark, Norway
| | - Mona Saebø
- Department of Natural Science and Environmental Health, University of South-Eastern Norway, Bø i Telemark, Norway
| | | | - John L Koprowski
- Haub School of Environment and Natural Resources, University of Wyoming, Laramie, Wyoming, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, Idaho, USA
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2
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da Silva Coelho FA, Gill S, Tomlin CM, Papavassiliou M, Farley SD, Cook JA, Sonsthagen SA, Sage GK, Heaton TH, Talbot SL, Lindqvist C. Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska. Mol Ecol 2023. [PMID: 37096383 DOI: 10.1111/mec.16960] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/28/2023] [Accepted: 04/12/2023] [Indexed: 04/26/2023]
Abstract
During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still questions about whether ice-free refugia were present in the Alexander Archipelago along the Southeast (SE) Alaska coast during the last glacial maximum (LGM). Numerous subfossils have been recovered from caves in SE Alaska, including American black (Ursus americanus) and brown (U. arctos) bears, which today are found in the Alexander Archipelago but are genetically distinct from mainland bear populations. Hence, these bear species offer an ideal system to investigate long-term occupation, potential refugial survival and lineage turnover. Here, we present genetic analyses based on 99 new complete mitochondrial genomes from ancient and modern brown and black bears spanning the last ~45,000 years. Black bears form two SE Alaskan subclades, one preglacial and another postglacial, that diverged >100,000 years ago. All postglacial ancient brown bears are closely related to modern brown bears in the archipelago, while a single preglacial brown bear is found in a distantly related clade. A hiatus in the bear subfossil record around the LGM and the deep split of their pre- and postglacial subclades fail to support a hypothesis of continuous occupancy in SE Alaska throughout the LGM for either species. Our results are consistent with an absence of refugia along the SE Alaska coast, but indicate that vegetation quickly expanded after deglaciation, allowing bears to recolonize the area after a short-lived LGM peak.
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Affiliation(s)
| | - Stephanie Gill
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | - Crystal M Tomlin
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | | | - Sean D Farley
- Alaska Department of Fish and Game, Anchorage, Alaska, USA
| | - Joseph A Cook
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Sarah A Sonsthagen
- U.S. Geological Survey, Nebraska Cooperative Fish and Wildlife Research Unit, University of Nebraska-Lincoln, School of Natural Resources, Lincoln, Nebraska, USA
| | - George K Sage
- Far Northwestern Institute of Art and Science, Anchorage, Alaska, USA
| | - Timothy H Heaton
- Department of Earth Sciences, University of South Dakota, Vermillion, South Dakota, USA
| | - Sandra L Talbot
- Far Northwestern Institute of Art and Science, Anchorage, Alaska, USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
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3
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Hu L, Long J, Lin Y, Gu Z, Su H, Dong X, Lin Z, Xiao Q, Batbayar N, Bold B, Deutschová L, Ganusevich S, Sokolov V, Sokolov A, Patel HR, Waters PD, Graves JAM, Dixon A, Pan S, Zhan X. Arctic introgression and chromatin regulation facilitated rapid Qinghai-Tibet Plateau colonization by an avian predator. Nat Commun 2022; 13:6413. [PMID: 36302769 PMCID: PMC9613686 DOI: 10.1038/s41467-022-34138-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
The Qinghai-Tibet Plateau (QTP), possesses a climate as cold as that of the Arctic, and also presents uniquely low oxygen concentrations and intense ultraviolet (UV) radiation. QTP animals have adapted to these extreme conditions, but whether they obtained genetic variations from the Arctic during cold adaptation, and how genomic mutations in non-coding regions regulate gene expression under hypoxia and intense UV environment, remain largely unknown. Here, we assemble a high-quality saker falcon genome and resequence populations across Eurasia. We identify female-biased hybridization with Arctic gyrfalcons in the last glacial maximum, that endowed eastern sakers with alleles conveying larger body size and changes in fat metabolism, predisposing their QTP cold adaptation. We discover that QTP hypoxia and UV adaptations mainly involve independent changes in non-coding genomic variants. Our study highlights key roles of gene flow from Arctic relatives during QTP hypothermia adaptation, and cis-regulatory elements during hypoxic response and UV protection.
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Affiliation(s)
- Li Hu
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Juan Long
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Yi Lin
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Zhongru Gu
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Han Su
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Xuemin Dong
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Zhenzhen Lin
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Qian Xiao
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China ,grid.20513.350000 0004 1789 9964Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, 100875 Beijing, China
| | - Nyambayar Batbayar
- Wildlife Science and Conservation Center, Union Building B-802, Ulaanbaatar, 14210 Mongolia
| | - Batbayar Bold
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China ,Wildlife Science and Conservation Center, Union Building B-802, Ulaanbaatar, 14210 Mongolia
| | - Lucia Deutschová
- grid.455051.0Raptor Protection of Slovakia, Trhová 54, SK-841 01, Bratislava, Slovakia
| | - Sergey Ganusevich
- Wild Animal Rescue Centre, Krasnostudencheskiy pr., 21-45, Moscow, 125422 Russia
| | - Vasiliy Sokolov
- grid.426536.00000 0004 1760 306XInstitute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, 202-8 Marta Street, Ekaterinburg, 620144 Russia
| | - Aleksandr Sokolov
- Arctic Research Station of the Institute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, 21 Zelenaya Gorka, Labytnangi, Yamalo-Nenetski District 629400 Russia
| | - Hardip R. Patel
- grid.1001.00000 0001 2180 7477The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601 Australia
| | - Paul D. Waters
- grid.1005.40000 0004 4902 0432School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW Sydney, Sydney, NSW 2052 Australia
| | | | - Andrew Dixon
- Emirates Falconers’ Club, Al Mamoura Building (A), P.O. Box 47716, Muroor Road, Abu Dhabi, UAE ,grid.511767.30000 0004 5895 0922International Wildlife Consultants, P.O. Box 19, Carmarthen, SA33 5YL UK
| | - Shengkai Pan
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Xiangjiang Zhan
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China ,grid.9227.e0000000119573309Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223 China
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4
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Chetri M. First camera-trap confirmation of Tibetan Brown Bear Ursus arctos pruinosus Blyth, 1854 (Mammalia: Carnivora: Ursidae) with a review of its distribution and status in Nepal. JOURNAL OF THREATENED TAXA 2022. [DOI: 10.11609/jott.7797.14.9.21797-21804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The Tibetan Brown Bear Ursus arctos pruinosus is a large mammalian carnivore of high-altitude environments that is closely associated with the pastoral landscape. Limited information is available on this species, probably due to its rarity in the Himalaya. To date, scientific evidence of the presence of Tibetan Brown Bears has not been reported officially. The information presented here is based on data collected in the central Himalayan region of Nepal in 2003–2014 during biodiversity surveys and other research. Methods included random walks along livestock trails, transect surveys, opportunistic camera trapping, and herders’ reports & interviews. This is the first camera-trap confirmation of the Tibetan Brown Bear in the central Himalaya. The distribution map was updated based on direct observation, signs and field reports gathered from reliable sources. The presence of signs (diggings, footprints, and feces) and direct observation in the Annapurna-Manaslu landscape reveal that bears are closely associated with Himalayan marmots and other small rodents. Local folklore, legends, and cultural beliefs have played important roles in Brown Bear conservation in the central Himalaya.
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5
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Hennelly LM, Habib B, Modi S, Rueness EK, Gaubert P, Sacks BN. Ancient divergence of Indian and Tibetan wolves revealed by recombination-aware phylogenomics. Mol Ecol 2021; 30:6687-6700. [PMID: 34398980 DOI: 10.1111/mec.16127] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/24/2021] [Accepted: 08/13/2021] [Indexed: 12/29/2022]
Abstract
The grey wolf (Canis lupus) expanded its range across Holarctic regions during the late Pleistocene. Consequently, most grey wolves share recent (<100,000 years ago) maternal origins corresponding to a widespread Holarctic clade. However, two deeply divergent (200,000-700,000 years ago) mitochondrial clades are restricted, respectively, to the Indian subcontinent and the Tibetan Plateau, where remaining wolves are endangered. No genome-wide analysis had previously included wolves corresponding to the mitochondrial Indian clade or attempted to parse gene flow and phylogeny. We sequenced four Indian and two Tibetan wolves and included 31 additional canid genomes to resolve the phylogenomic history of grey wolves. Genomic analyses revealed Indian and Tibetan wolves to be distinct from each other and from broadly distributed wolf populations corresponding to the mitochondrial Holarctic clade. Despite gene flow, which was reflected disproportionately in high-recombination regions of the genome, analyses revealed Indian and Tibetan wolves to be basal to Holarctic grey wolves, in agreement with the mitochondrial phylogeny. In contrast to mitochondrial DNA, however, genomic findings suggest the possibility that the Indian wolf could be basal to the Tibetan wolf, a discordance potentially reflecting selection on the mitochondrial genome. Together, these findings imply that southern regions of Asia have been important centers for grey wolf evolution and that Indian and Tibetan wolves represent evolutionary significant units (ESUs). Further study is needed to assess whether these ESUs warrant recognition as distinct species. This question is especially urgent regarding the Indian wolf, which represents one of the world's most endangered wolf populations.
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Affiliation(s)
- Lauren M Hennelly
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Bilal Habib
- Department of Animal Ecology and Conservation, Wildlife Institute of India, Dehradun, Uttarakhand, India
| | - Shrushti Modi
- Department of Animal Ecology and Conservation, Wildlife Institute of India, Dehradun, Uttarakhand, India
| | - Eli K Rueness
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique (EDB), CNRS/UPS/IRD, Université Toulouse III Paul Sabatier - Bâtiment 4R1, Toulouse cedex 9, France
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, California, USA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
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6
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Mengüllüoğlu D, Ambarlı H, Barlow A, Paijmans JLA, Sayar AO, Emir H, Kandemir İ, Hofer H, Fickel J, Förster DW. Mitogenome Phylogeny Including Data from Additional Subspecies Provides New Insights into the Historical Biogeography of the Eurasian lynx Lynx lynx. Genes (Basel) 2021; 12:genes12081216. [PMID: 34440390 PMCID: PMC8392285 DOI: 10.3390/genes12081216] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 11/16/2022] Open
Abstract
Previous molecular studies of the wide-ranging Eurasian lynx Lynx lynx focused mainly on its northern Palearctic populations, with the consequence that the reconstruction of this species’ evolutionary history did not include genetic variation present in its southern Palearctic distribution. We sampled a previously not considered Asian subspecies (L. l. dinniki), added published data from another Asian subspecies (L. l. isabellinus), and reassessed the Eurasian lynx mtDNA phylogeny along with previously published data from northern Palearctic populations. Our mitogenome-based analyses revealed the existence of three major clades (A: Central Asia, B: SE Europe/SW Asia, C: Europe and Northern Asia) and at least five lineages, with diversification in Lynx lynx commencing at least 28kyr earlier than hitherto estimated. The subspecies L. l. isabellinus harbors the most basal matriline, consistent with the origin of Lynx lynx in this subspecies’ current range. L. l. dinniki harbors the second most basal matriline, which is related to, and may be the source of, the mtDNA diversity of the critically endangered Balkan lynx L. l. balcanicus. Our results suggest that the Anatolian peninsula was a glacial refugium for Eurasian lynx, with previously unconsidered implications for the colonization of Europe by this species.
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Affiliation(s)
- Deniz Mengüllüoğlu
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (H.H.); (J.F.); (D.W.F.)
- Correspondence:
| | - Hüseyin Ambarlı
- Department of Wildlife Ecology and Management, Faculty of Forestry, Düzce University, Düzce 81620, Turkey;
| | - Axel Barlow
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK;
| | - Johanna L. A. Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany;
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Ali Onur Sayar
- Department of Game and Wildlife, Cankiri Karatekin University, Cankiri 18100, Turkey;
| | - Hasan Emir
- Wildlife Department of General Directorate of Nature Conservation and National Parks, Turkish Ministry of Agriculture and Forestry, Ankara 06000, Turkey;
| | - İrfan Kandemir
- Department of Biology, Ankara University, Ankara 06000, Turkey;
| | - Heribert Hofer
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (H.H.); (J.F.); (D.W.F.)
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, 10315 Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, 10315 Berlin, Germany
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (H.H.); (J.F.); (D.W.F.)
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany;
| | - Daniel W. Förster
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (H.H.); (J.F.); (D.W.F.)
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7
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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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8
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Nasanbat B, Ceacero F, Ravchig S. A small neighborhood well-organized: seasonal and daily activity patterns of the community of large and mid-sized mammals around waterholes in the Gobi Desert, Mongolia. Front Zool 2021; 18:25. [PMID: 34001162 PMCID: PMC8130113 DOI: 10.1186/s12983-021-00412-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/05/2021] [Indexed: 11/16/2022] Open
Abstract
Background Animal communities have complex patterns of ecological segregation at different levels according to food resources, habitats, behavior, and activity patterns. Understanding these patterns among the community is essential for the conservation of the whole ecosystem. However, these networks are difficult to study nowadays, due to anthropic disturbances and local extinctions, making it difficult to conclude if segregation patterns are natural or human-induced. We studied ecological segregation in a community of large and mid-sized mammals in the Great Gobi Desert, a remote arid area free from recent extinctions and human disturbances. Activity patterns of 10 sympatric mammal species were monitored around 6 waterholes through camera-trapping over a two-year period, and analyzed them primarily through circular statistics. Results Complex patterns of spatial, seasonal, and daily segregation were found. Overlap in seasonal activity was detected in only 3 of the 45 possible pairs of species. Four species used the waterholes all-year-round, while others peaked their activity during different periods. The Bactrian camel showed continuous daily activity, the grey wolf had bimodal activity, and the argali and Siberian ibex were diurnal, while the others had nocturnal peaks during different hours. Daily and spatial overlap were both detected in only 6 of the 45 pairs. Only one species pair (snow leopard and Eurasian lynx) showed an overlap at two levels: seasonal and daily. Climate and moon phase significantly affected the activity of certain species. Conclusions Altogether, the results showed complex patterns of ecological segregation at different levels in the use of the key resource in arid environments: waterholes. These results are important for understanding the biology of these species under natural conditions, as well as potential changes in altered ecosystems, and may help to design conservation strategies.
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Affiliation(s)
- Battogtokh Nasanbat
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czechia.,Institute of Biology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia.,School of Arts and Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Francisco Ceacero
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czechia.
| | - Samiya Ravchig
- School of Arts and Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
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9
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da Silva Coelho FA, Gill S, Tomlin CM, Heaton TH, Lindqvist C. An early dog from southeast Alaska supports a coastal route for the first dog migration into the Americas. Proc Biol Sci 2021; 288:20203103. [PMID: 33622130 PMCID: PMC7934960 DOI: 10.1098/rspb.2020.3103] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The oldest confirmed remains of domestic dogs in North America are from mid-continent archaeological sites dated approximately 9900 calibrated years before present (cal BP). Although this date suggests that dogs may not have arrived alongside the first Native Americans, the timing and routes for the entrance of New World dogs remain uncertain. Here, we present a complete mitochondrial genome of a dog from southeast Alaska, dated to 10 150 ± 260 cal BP. We compared this high-coverage genome with data from modern dog breeds, historical Arctic dogs and American precontact dogs (PCDs) from before European arrival. Our analyses demonstrate that the ancient dog belongs to the PCD lineage, which diverged from Siberian dogs around 16 700 years ago. This timing roughly coincides with the minimum suggested date for the opening of the North Pacific coastal (NPC) route along the Cordilleran Ice Sheet and genetic evidence for the initial peopling of the Americas. This ancient southeast Alaskan dog occupies an early branching position within the PCD clade, indicating it represents a close relative of the earliest PCDs that were brought alongside people migrating from eastern Beringia southward along the NPC to the rest of the Americas. The stable isotope δ13C value of this early dog indicates a marine diet, different from the younger mid-continent PCDs' terrestrial diet. Although PCDs were largely replaced by modern European dog breeds, our results indicate that their population decline started approximately 2000 years BP, coinciding with the expansion of Inuit peoples, who are associated with traditional sled-dog culture. Our findings suggest that dogs formed part of the initial human habitation of the New World, and provide insights into their replacement by both Arctic and European lineages.
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Affiliation(s)
| | - Stephanie Gill
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Crystal M Tomlin
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Timothy H Heaton
- Department of Earth Sciences, University of South Dakota, Vermillion, SD 57069, USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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10
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Dar SA, Singh SK, Wan HY, Kumar V, Cushman SA, Sathyakumar S. Projected climate change threatens Himalayan brown bear habitat more than human land use. Anim Conserv 2021. [DOI: 10.1111/acv.12671] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- S. A. Dar
- Wildlife Institute of India Dehradun India
| | | | - H. Y. Wan
- Department of Wildlife Humboldt State University Arcata CA USA
| | - V. Kumar
- Wildlife Institute of India Dehradun India
| | - S. A. Cushman
- USDA Forest Service Rocky Mountain Research Station Flagstaff AZ USA
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11
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Bit A, Thakur M, Singh SK, Joshi BD, Singh VK, Sharma LK, Tripathy B, Chandra K. Assembling mitogenome of Himalayan Black Bear (U. t. laniger) from low depth reads and its application in drawing phylogenetic inferences. Sci Rep 2021; 11:730. [PMID: 33436634 PMCID: PMC7803731 DOI: 10.1038/s41598-020-76872-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 11/04/2020] [Indexed: 12/01/2022] Open
Abstract
The complete mitogenome of Himalayan black bear (Ursus thibetanus laniger) from Indian Himalayan region was assembled following the modified approach of mitochondrial baiting and mapping using the next-generation sequencing reads. The complete mitogenome was of 16,556 bp long, consisted of 37 genes that contained 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 1 control region. The complete base composition was 31.33% A, 15.24% G, 25.45%C, and 27.98%T and gene arrangement was similar to the other sub-species of Asiatic black bear. The relative synonymous codon usage analysis revealed the maximum abundance of Isoleucine, Tyrosine, Leucine and Threonine. The assembled mitogenome of U. t. laniger exhibited 99% similarity with the mitogenomes of Himalayan black bear available from Nepal and Tibetan Plateau-Himalaya region. The findings of the present study has proven low depth sequencing data, adequate and highly efficient in rapid recovering the mitochondrial genome by overcoming the conventional strategies of obtaining long-range PCR and subsequently drawing phylogenetic inferences.
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Affiliation(s)
- Amrita Bit
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India
| | - Mukesh Thakur
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India.
| | - Sujeet Kumar Singh
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India
| | - Bheem Dutt Joshi
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India
| | - Vinay Kumar Singh
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India
| | - Lalit Kumar Sharma
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India
| | - Basudev Tripathy
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India
| | - Kailash Chandra
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India
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12
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Sheremetyeva IN. Comparison of Ancient Haplotypes with Modern Island Reed Vole Populations. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420070145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Phylogenetic analysis of marginal Asiatic black bears reveals a recent Iranian–Himalayan divergence and has implications for taxonomy and conservation. Mamm Biol 2020. [DOI: 10.1007/s42991-020-00044-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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14
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Zhu C, Xu W, Li J, Liu C, Hu M, Yuan Y, Yuan K, Zhang Y, Song X, Han J, Cui X. Draft Genome Assembly for the Tibetan Black Bear ( Ursus thibetanus thibetanus). Front Genet 2020; 11:231. [PMID: 32300354 PMCID: PMC7142260 DOI: 10.3389/fgene.2020.00231] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/26/2020] [Indexed: 12/17/2022] Open
Affiliation(s)
- Chenglong Zhu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Wenjie Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Jianchuan Li
- Department of Animal Resources, Tibet Plateau Institute of Biology, Lhasa, China
| | - Chang Liu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Mingliang Hu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yuan Yuan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Ke Yuan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yijiuling Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Xingzhi Song
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Jin Han
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Xinxin Cui
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
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15
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Sharief A, Joshi BD, Kumar V, Kumar M, Dutta R, Sharma CM, Thapa A, Rana HS, Mukherjee T, Singh A, Thakur M, Sharma LK, Chandra K. Identifying Himalayan brown bear (Ursus arctos isabellinus) conservation areas in Lahaul Valley, Himachal Pradesh. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2019.e00900] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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16
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Sun S, Wu Y, Ge X, Jakovlić I, Zhu J, Mahboob S, Al-Ghanim KA, Al-Misned F, Fu H. Disentangling the interplay of positive and negative selection forces that shaped mitochondrial genomes of Gammarus pisinnus and Gammarus lacustris. ROYAL SOCIETY OPEN SCIENCE 2020; 7:190669. [PMID: 32218929 PMCID: PMC7029888 DOI: 10.1098/rsos.190669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 11/29/2019] [Indexed: 05/16/2023]
Abstract
We hypothesized that the mitogenome of Gammarus lacustris (GL), native to the Qinghai-Tibet Plateau, might exhibit genetic adaptations to the extreme environmental conditions associated with high altitudes (greater than 3000 m). To test this, we also sequenced the mitogenome of Gammarus pisinnus (GP), whose native range is close to the Tibetan plateau, but at a much lower altitude (200-1500 m). The two mitogenomes exhibited conserved mitochondrial architecture, but low identity between genes (55% atp8 to 76.1% cox1). Standard (homogeneous) phylogenetic models resolved Gammaridae as paraphyletic, but 'heterogeneous' CAT-GTR model as monophyletic. In indirect support of our working hypothesis, GL, GP and Gammarus fossarum exhibit evidence of episodic diversifying selection within the studied Gammaroidea dataset. The mitogenome of GL generally evolves under a strong purifying selection, whereas GP evolves under directional (especially pronounced in atp8) and/or relaxed selection. This is surprising, as GP does not inhabit a unique ecological niche compared to other gammarids. We propose that this rapid evolution of the GP mitogenome may be a reflection of its relatively recent speciation and heightened non-adaptive (putatively metabolic rate-driven) mutational pressures. To test these hypotheses, we urge sequencing mitogenomes of remaining Gammarus species populating the same geographical range as GP.
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Affiliation(s)
- Shengming Sun
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, People's Republic of China
| | - Ying Wu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, People's Republic of China
| | - Xianping Ge
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, People's Republic of China
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, People's Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan, People's Republic of China
| | - Jian Zhu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, People's Republic of China
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, People's Republic of China
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh-11451, Riyadh, Saudi Arabia
- Department of Zoology, GC University, Faisalabad, Pakistan
| | - Khalid Abdullah Al-Ghanim
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh-11451, Riyadh, Saudi Arabia
| | - Fahad Al-Misned
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh-11451, Riyadh, Saudi Arabia
| | - Hongtuo Fu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, People's Republic of China
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17
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Tumendemberel O, Zedrosser A, Proctor MF, Reynolds HV, Adams JR, Sullivan JM, Jacobs SJ, Khorloojav T, Tserenbataa T, Batmunkh M, Swenson JE, Waits LP. Phylogeography, genetic diversity, and connectivity of brown bear populations in Central Asia. PLoS One 2019; 14:e0220746. [PMID: 31408475 PMCID: PMC6692007 DOI: 10.1371/journal.pone.0220746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/22/2019] [Indexed: 11/28/2022] Open
Abstract
Knowledge of genetic diversity and population structure is critical for conservation and management planning at the population level within a species' range. Many brown bear populations in Central Asia are small and geographically isolated, yet their phylogeographic relationships, genetic diversity, and contemporary connectivity are poorly understood. To address this knowledge gap, we collected brown bear samples from the Gobi Desert (n = 2360), Altai, Sayan, Khentii, and Ikh Khyangan mountains of Mongolia (n = 79), and Deosai National Park in the Himalayan Mountain Range of Pakistan (n = 5) and generated 927 base pairs of mitochondrial DNA (mtDNA) sequence data and genotypes at 13 nuclear DNA microsatellite loci. We documented high levels of mtDNA and nDNA diversity in the brown bear populations of northern Mongolia (Altai, Sayan, Buteeliin nuruu and Khentii), but substantially lower diversity in brown bear populations in the Gobi Desert and Himalayas of Pakistan. We detected 3 brown bear mtDNA phylogeographic groups among bears of the region, with clade 3a1 in Sayan, Khentii, and Buteeliin nuruu mountains, clade 3b in Altai, Sayan, Buteeliin nuruu, Khentii, and Ikh Khyangan, and clade 6 in Gobi and Pakistan. Our results also clarified the phylogenetic relationships and divergence times with other brown bear mtDNA clades around the world. The nDNA genetic structure analyses revealed distinctiveness of Gobi bears and different population subdivisions compared to mtDNA results. For example, genetic distance for nDNA microsatellite loci between the bears in Gobi and Altai (FST = 0.147) was less than that of the Gobi and Pakistan (FST = 0.308) suggesting more recent male-mediated nuclear gene flow between Gobi and Altai than between Gobi and the Pakistan bears. Our results provide valuable information for conservation and management of bears in this understudied region of Central Asia and highlight the need for special protection and additional research on Gobi brown bears.
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Affiliation(s)
- Odbayar Tumendemberel
- Department of Natural Science and Environmental Health, University of South-Eastern Norway, Bø i Telemark, Norway
| | - Andreas Zedrosser
- Department of Natural Science and Environmental Health, University of South-Eastern Norway, Bø i Telemark, Norway
| | | | | | - Jennifer R. Adams
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Jack M. Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Sarah J. Jacobs
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Tumennasan Khorloojav
- Genetics Laboratory, Institute of General and Experimental Biology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia
| | - Tuya Tserenbataa
- Sunshine Village Complex, Bayanzurkh District, Ulaanbaatar, Mongolia
| | - Mijiddorj Batmunkh
- Mongolian-Chinese Joint Molecular Biology Laboratory, Ulaanbaatar, Mongolia
| | - Jon E. Swenson
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, Idaho, United States of America
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18
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Zhang D, Zou H, Hua CJ, Li WX, Mahboob S, Al-Ghanim KA, Al-Misned F, Jakovlić I, Wang GT. Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda. Genome Biol Evol 2019; 11:1797-1812. [PMID: 31192351 PMCID: PMC6601869 DOI: 10.1093/gbe/evz121] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2019] [Indexed: 01/04/2023] Open
Abstract
The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different data sets (morphological, nuclear, mitochondrial) often producing starkly incongruent phylogenetic hypotheses. We hypothesized that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different data sets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artifacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artifacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements might produce major compositional biases even on relatively short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.
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Affiliation(s)
- Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Cong-Jie Hua
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Wen-Xiang Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Zoology, GC University, Faisalabad, Pakistan
| | | | - Fahad Al-Misned
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
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19
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Rey-Iglesia A, García-Vázquez A, Treadaway EC, van der Plicht J, Baryshnikov GF, Szpak P, Bocherens H, Boeskorov GG, Lorenzen ED. Evolutionary history and palaeoecology of brown bear in North-East Siberia re-examined using ancient DNA and stable isotopes from skeletal remains. Sci Rep 2019; 9:4462. [PMID: 30872771 PMCID: PMC6418263 DOI: 10.1038/s41598-019-40168-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 02/04/2019] [Indexed: 12/24/2022] Open
Abstract
Over 60% of the modern distribution range of brown bears falls within Russia, yet palaeoecological data from the region remain scarce. Complete modern Russian brown bear mitogenomes are abundant in the published literature, yet examples of their ancient counterparts are absent. Similarly, there is only limited stable isotopic data of prehistoric brown bears from the region. We used ancient DNA and stable carbon (δ13C) and nitrogen (δ15N) isotopes retrieved from five Pleistocene Yakutian brown bears (one Middle Pleistocene and four Late Pleistocene), to elucidate the evolutionary history and palaeoecology of the species in the region. We were able to reconstruct the complete mitogenome of one of the Late Pleistocene specimens, but we were unable to assign it to any of the previously published brown bear mitogenome clades. A subsequent analysis of published mtDNA control region sequences, which included sequences of extinct clades from other geographic regions, assigned the ancient Yakutian bear to the extinct clade 3c; a clade previously identified from Late Quaternary specimens from Eastern Beringia and Northern Spain. Our analyses of stable isotopes showed relatively high δ15N values in the Pleistocene Yakutian brown bears, suggesting a more carnivorous diet than contemporary brown bears from Eastern Beringia.
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Affiliation(s)
- Alba Rey-Iglesia
- Natural History Museum of Denmark, University of Copenhagen, DK-1350, Copenhagen K, Denmark.
| | - Ana García-Vázquez
- Instituto de Xeoloxía Isidro Parga Pondal, ESCI, Campus de Elviña, Universidade da Coruña, 15071A, Coruña, Spain
| | - Eve C Treadaway
- Natural History Museum of Denmark, University of Copenhagen, DK-1350, Copenhagen K, Denmark
| | | | | | - Paul Szpak
- Department of Anthropology, Trent University, Peterborough, Ontario, K9L 0G2, Canada
| | - Hervé Bocherens
- Department of Geosciences, Tübingen University, 72074, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, 72074, Tübingen, Germany
| | - Gennady G Boeskorov
- Diamond and Precious Metals Geology Institute, Siberian Branch of Russian Academy of Sciences, 677980, Yakutsk, Russia
| | - Eline D Lorenzen
- Natural History Museum of Denmark, University of Copenhagen, DK-1350, Copenhagen K, Denmark.
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20
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Kadariya R, Shimozuru M, Maldonado JE, Moustafa MAM, Sashika M, Tsubota T. High genetic diversity and distinct ancient lineage of Asiatic black bears revealed by non-invasive surveys in the Annapurna Conservation Area, Nepal. PLoS One 2018; 13:e0207662. [PMID: 30517155 PMCID: PMC6281213 DOI: 10.1371/journal.pone.0207662] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/05/2018] [Indexed: 11/19/2022] Open
Abstract
Asiatic black bears (Ursus thibetanus) have a widespread distribution in mountain landscapes, and are considered vulnerable globally, but are low-priority species for conservation in Nepal. Habitat fragmentation, illegal hunting, and human-bear conflict are the major threats to Asiatic black bears across their global range. Having an adequate level of genetic variation in a population helps with adapting to rapidly changing environments, and thus is important for the long-term health of bear populations. Accordingly, we conducted non-invasive surveys of bear populations in the Annapurna Conservation Area (ACA) to elucidate genetic diversity, genetic structure, and the phylogenetic relationship of Asiatic black bears from this region of Nepal to other subspecies. To assess levels of genetic diversity and population genetic structure, we genotyped eight microsatellite loci using 147 samples, identifying 60 individuals in an area of approximately 525 km2. We found that the Asiatic black bear population in the ACA has maintained high levels of genetic diversity (HE = 0.76) as compared to other bear populations from range countries. We did not detect a signature of population substructure among sampling localities and this suggests that animals are moving freely across the landscape within the ACA. We also detected a moderate population size that may increase with the availability of suitable habitat in the ACA, so bear-related conflict should be addressed to ensure the long-term viability of this expanding bear populations. Primers specific to bears were designed to amplify a 675 bp fragment of the mitochondrial control region from the collected samples. Three haplotypes were observed from the entire conservation area. The complete mitochondrial genome (16,771 bp), the first obtained from wild populations of the Himalayan black bear (U. t. laniger), was also sequenced to resolve the phylogenetic relationships of closely related subspecies of Asiatic black bears. The resulting phylogeny indicated that Himalayan black bear populations in Nepal are evolutionary distinct from other known subspecies of Asiatic black bears.
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Affiliation(s)
- Rabin Kadariya
- Laboratory of Wildlife Biology and Medicine, Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- National Trust for Nature Conservation, Khumaltar, Lalitpur, Nepal
| | - Michito Shimozuru
- Laboratory of Wildlife Biology and Medicine, Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Jesús E. Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States of America
| | - Mohamed Abdallah Mohamed Moustafa
- Laboratory of Wildlife Biology and Medicine, Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- Department of Animal Medicine, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Mariko Sashika
- Laboratory of Wildlife Biology and Medicine, Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Toshio Tsubota
- Laboratory of Wildlife Biology and Medicine, Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- * E-mail:
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21
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Zou H, Jakovlić I, Zhang D, Chen R, Mahboob S, Al-Ghanim KA, Al-Misned F, Li WX, Wang GT. The complete mitochondrial genome of Cymothoa indica has a highly rearranged gene order and clusters at the very base of the Isopoda clade. PLoS One 2018; 13:e0203089. [PMID: 30180209 PMCID: PMC6122833 DOI: 10.1371/journal.pone.0203089] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/14/2018] [Indexed: 11/18/2022] Open
Abstract
As a result of great diversity in life histories and a large number of described species, taxonomic and phylogenetic uncertainty permeates the entire crustacean order of Isopoda. Large molecular datasets capable of providing sufficiently high phylogenetic resolution, such as mitochondrial genomes (mitogenomes), are needed to infer their evolutionary history with confidence, but isopod mitogenomes remain remarkably poorly represented in public databases. We sequenced the complete mitogenome of Cymothoa indica, a species belonging to a family from which no mitochondrial genome was sequenced yet, Cymothoidae. The mitogenome (circular, 14484 bp, A+T = 63.8%) is highly compact, appears to be missing two tRNA genes (trnI and trnE), and exhibits a unique gene order with a large number of rearrangements. High compactness and the existence of palindromes indicate that the mechanism behind these rearrangements might be associated with linearization events in its evolutionary history, similar to those proposed for isopods from the Armadillidium genus (Oniscidea). Isopods might present an important model system to study the proposed discontinuity in the dynamics of mitochondrial genomic architecture evolution. Phylogenetic analyses (Bayesian Inference and Maximum Likelihood) conducted using nucleotide sequences of all mitochondrial genes resolved Oniscidea and Cymothoida suborders as paraphyletic. Cymothoa indica was resolved as a sister group (basal) to all remaining isopods, which challenges the accepted isopod phylogeny, where Cymothoida are the most derived, and Phreatoicidea the most basal isopod group. There is growing evidence that Cymothoida suborder might be split into two evolutionary distant clades, with parasitic species being the most basal split in the Isopoda clade, but a much larger amount of molecular resources carrying a high phylogenetic resolution will be needed to infer the remarkably complex evolutionary history of this group of animals with confidence.
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Affiliation(s)
- Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | | | - Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Rong Chen
- Bio-Transduction Lab, Biolake, Wuhan, P. R. China
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Zoology, GC University, Faisalabad, Pakistan
| | | | - Fahad Al-Misned
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Wen-Xiang Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
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