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Mychajliw AM, Adams AJ, Brown KC, Campbell BT, Hardesty-Moore M, Welch ZS, Page HM, Southon JR, Cooper SD, Alagona PS. Coupled social and ecological change drove the historical extinction of the California grizzly bear ( Ursus arctos californicus). Proc Biol Sci 2024; 291:20230921. [PMID: 38196370 PMCID: PMC10777157 DOI: 10.1098/rspb.2023.0921] [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: 04/19/2023] [Accepted: 11/06/2023] [Indexed: 01/11/2024] Open
Abstract
Large carnivores (order Carnivora) are among the world's most threatened mammals due to a confluence of ecological and social forces that have unfolded over centuries. Combining specimens from natural history collections with documents from archival records, we reconstructed the factors surrounding the extinction of the California grizzly bear (Ursus arctos californicus), a once-abundant brown bear subspecies last seen in 1924. Historical documents portrayed California grizzlies as massive hypercarnivores that endangered public safety. Yet, morphological measurements on skulls and teeth generate smaller body size estimates in alignment with extant North American grizzly populations (approx. 200 kg). Stable isotope analysis (δ13C, δ15N) of pelts and bones (n = 57) revealed that grizzlies derived less than 10% of their nutrition from terrestrial animal sources and were therefore largely herbivorous for millennia prior to the first European arrival in this region in 1542. Later colonial land uses, beginning in 1769 with the Mission era, led grizzlies to moderately increase animal protein consumption (up to 26% of diet), but grizzlies still consumed far less livestock than otherwise claimed by contemporary accounts. We show how human activities can provoke short-term behavioural shifts, such as heightened levels of carnivory, that in turn can lead to exaggerated predation narratives and incentivize persecution, triggering rapid loss of an otherwise widespread and ecologically flexible animal.
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Affiliation(s)
- Alexis M. Mychajliw
- Department of Biology, Middlebury College, Middlebury, VT, USA
- Environmental Studies Program, Middlebury College, Middlebury, VT, USA
- La Brea Tar Pits & Museum, Los Angeles, CA, USA
| | - Andrea J. Adams
- Earth Research Institute, University of California, Santa Barbara, CA, USA
| | - Kevin C. Brown
- Environmental Studies Program, University of California, Santa Barbara, CA, USA
| | - Beau T. Campbell
- Dinosaur Institute, Natural History Museum of Los Angeles County, Los Angeles, CA, USA
| | - Molly Hardesty-Moore
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Zoë S. Welch
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Henry M. Page
- Marine Science Institute, University of California, Santa Barbara, CA, USA
| | - John R. Southon
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Scott D. Cooper
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Peter S. Alagona
- Environmental Studies Program, University of California, Santa Barbara, CA, USA
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2
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Zink RM, Klicka LB. The taxonomic basis of subspecies listed as threatened and endangered under the endangered species act. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.971280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
More than 170 subspecies are listed as threatened or endangered under the US Endangered Species Act. Most of these subspecies were described decades ago on the basis of geographical variation in morphology using relatively primitive taxonomic methods. The US Fish and Wildlife Service defaults to subspecies descriptions by taxonomists working with specific groups of organisms, but there is no single definition of subspecies across plants and animals. Valid tests today usually entail molecular analyses of variation within and among populations, although there is no reason that behavioral, ecological or molecular characters could not be used, and include tests for significant differences between samples of the putative endangered subspecies and its nearest geographic relatives. We evaluated data gathered since subspecies listed under the ESA were described finding about one-third are valid (distinct evolutionary taxa), one-third are not, and one-third have not been tested. Therefore, it should not be assumed that because a subspecies occurs in a checklist, it is taxonomically valid. If the US Fish and Wildlife Service intends to continue listing subspecies, we suggest that they convene taxonomic experts representing various groups of organisms to provide a minimal set of criteria for a subspecies to be listed under the ESA.
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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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4
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Puckett EE, Davis IS. Spatial patterns of genetic diversity in eight bear (Ursidae) species. URSUS 2021. [DOI: 10.2192/ursus-d-20-00029.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Emily E. Puckett
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
| | - Isis S. Davis
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
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5
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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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6
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Dueck LA. Genetic assessment of captive red pandas (Ailurus fulgens) in American zoos to address management separation by putative subspecies. Zoo Biol 2021; 40:238-251. [PMID: 33689172 DOI: 10.1002/zoo.21597] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 12/18/2020] [Accepted: 02/23/2021] [Indexed: 11/10/2022]
Abstract
Red pandas (Ailurus fulgens) are small charismatic mammals native across montane southern Asia, now endangered by human impacts. They are considered "living fossils" as the sole member of a distinct family, warranting higher conservation priority. Therefore, ex situ breeding programs were initiated to prevent extinction and act as genetic reservoirs for reintroduction, although complicated by apparent taxonomic subdivision. This study investigated whether the separation of captive red pandas in the North American Species Survival Plan® by putative subspecies was justified. A 383-bp segment of mitochondrial DNA control region was therefore sequenced from 67 members representing matriarchal lineages of both groups. A network analysis placed the 11 haplotypes found into separate but closely connected clusters, with one group more strongly related than the other. Statistical analyses and diversity indices corroborated differentiation between the two management units. Phylogenetic analyses employing multiple outgroups confirmed, although not robustly, reciprocal monophyly of the four- and seven-haplotype clades representing putative subspecies Ailurus fulgens fulgens and Ailurus fulgens styani, respectively. These empirical results are adequate to justify continued independent management of these zoo subpopulations, but cannot be definitive for taxonomic classification due to limited sampling from their native range. They will, however, be useful in evaluating long-term genetic diversity changes, focusing management efforts on newly revealed evolutionary limitations, and comparing with an assessment of wild red pandas to determine how representative zoo populations are for reintroduction purposes. Maintaining genetic diversity and population structure of endangered species is essential to protect evolutionary potential and adaptations for long-term sustainability.
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Affiliation(s)
- Lucy A Dueck
- Savannah River Ecology Laboratory, Aiken, South Carolina, USA
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7
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Glancy B, Kim Y, Katti P, Willingham TB. The Functional Impact of Mitochondrial Structure Across Subcellular Scales. Front Physiol 2020; 11:541040. [PMID: 33262702 PMCID: PMC7686514 DOI: 10.3389/fphys.2020.541040] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 10/20/2020] [Indexed: 12/12/2022] Open
Abstract
Mitochondria are key determinants of cellular health. However, the functional role of mitochondria varies from cell to cell depending on the relative demands for energy distribution, metabolite biosynthesis, and/or signaling. In order to support the specific needs of different cell types, mitochondrial functional capacity can be optimized in part by modulating mitochondrial structure across several different spatial scales. Here we discuss the functional implications of altering mitochondrial structure with an emphasis on the physiological trade-offs associated with different mitochondrial configurations. Within a mitochondrion, increasing the amount of cristae in the inner membrane improves capacity for energy conversion and free radical-mediated signaling but may come at the expense of matrix space where enzymes critical for metabolite biosynthesis and signaling reside. Electrically isolating individual cristae could provide a protective mechanism to limit the spread of dysfunction within a mitochondrion but may also slow the response time to an increase in cellular energy demand. For individual mitochondria, those with relatively greater surface areas can facilitate interactions with the cytosol or other organelles but may be more costly to remove through mitophagy due to the need for larger phagophore membranes. At the network scale, a large, stable mitochondrial reticulum can provide a structural pathway for energy distribution and communication across long distances yet also enable rapid spreading of localized dysfunction. Highly dynamic mitochondrial networks allow for frequent content mixing and communication but require constant cellular remodeling to accommodate the movement of mitochondria. The formation of contact sites between mitochondria and several other organelles provides a mechanism for specialized communication and direct content transfer between organelles. However, increasing the number of contact sites between mitochondria and any given organelle reduces the mitochondrial surface area available for contact sites with other organelles as well as for metabolite exchange with cytosol. Though the precise mechanisms guiding the coordinated multi-scale mitochondrial configurations observed in different cell types have yet to be elucidated, it is clear that mitochondrial structure is tailored at every level to optimize mitochondrial function to meet specific cellular demands.
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Affiliation(s)
- Brian Glancy
- Muscle Energetics Laboratory, NHLBI, National Institutes of Health, Bethesda, MD, United States
- NIAMS, National Institutes of Health, Bethesda, MD, United States
| | - Yuho Kim
- Muscle Energetics Laboratory, NHLBI, National Institutes of Health, Bethesda, MD, United States
- Department of Physical Therapy and Kinesiology, University of Massachusetts Lowell, Lowell, MA, United States
| | - Prasanna Katti
- Muscle Energetics Laboratory, NHLBI, National Institutes of Health, Bethesda, MD, United States
| | - T. Bradley Willingham
- Muscle Energetics Laboratory, NHLBI, National Institutes of Health, Bethesda, MD, United States
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8
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Mizumachi K, Gorbunov SV, Vasilevski AA, Amano T, Ono H, Kosintsev PA, Hirata D, Nishita Y, Masuda R. Phylogenetic relationships of ancient brown bears (Ursus arctos) on Sakhalin Island, revealed by APLP and PCR-direct sequencing analyses of mitochondrial DNA. MAMMAL RES 2020. [DOI: 10.1007/s13364-020-00542-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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9
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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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10
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Mizumachi K, Spassov N, Kostov D, Raichev EG, Peeva S, Hirata D, Nishita Y, Kaneko Y, Masuda R. Mitochondrial haplogrouping of the ancient brown bears (Ursus arctos) in Bulgaria, revealed by the APLP method. MAMMAL RES 2020. [DOI: 10.1007/s13364-020-00482-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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11
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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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12
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Matosiuk M, Śmietana W, Czajkowska M, Paule L, Štofik J, Krajmerová D, Bashta A, Jakimiuk S, Ratkiewicz M. Genetic differentiation and asymmetric gene flow among Carpathian brown bear ( Ursus arctos) populations-Implications for conservation of transboundary populations. Ecol Evol 2019; 9:1501-1511. [PMID: 30805177 PMCID: PMC6374679 DOI: 10.1002/ece3.4872] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 12/07/2018] [Indexed: 11/08/2022] Open
Abstract
The abundance and distribution of large carnivores in Europe have been historically reduced. Their recovery requires multilevel coordination, especially regarding transboundary populations. Here, we apply nuclear and mitochondrial genetic markers to test for admixture level and its impact on population genetic structure of contemporary brown bears (Ursus arctos) from the Eastern, Southern, and Western Carpathians. Carpathian Mountains (Europe). Nearly 400 noninvasive brown bear DNA samples from the Western (Poland) and Eastern Carpathians (Bieszczady Mountains in Poland, Slovakia, Ukraine) were collected. Together with DNA isolates from Slovakia and Romania, they were analyzed using the set of eight microsatellite loci and two mtDNA regions (control region and cytochrome b). A set of 113 individuals with complete genotypes was used to investigate genetic differentiation across national boundaries, genetic structuring within and between populations, and movement between populations. Transboundary brown bear subpopulations (Slovakia and Poland) did not show significant internal genetic structure, and thus were treated as cohesive units. All brown bears from the Western Carpathians carried mitochondrial haplotypes from the Eastern lineage, while the Western lineage prevailed in the brown bears from the Bieszczady Mountains. Despite similar levels of microsatellite variability, we documented significant differentiation among the studied populations for nuclear markers and mtDNA. We also detected male-biased and asymmetrical movement into the Bieszczady Mountains population from the Western Carpathians. Our findings suggest initial colonization of the Western Carpathians by brown bears possessing mtDNA from the Eastern lineage. Genetic structuring among populations at microsatellite loci could be a result of human-mediated alterations. Detected asymmetric gene flow suggests ongoing expansion from more abundant populations into the Bieszczady Mountains and thus supports a metapopulation model. The knowledge concerning this complex pattern can be implemented in a joint Carpathian brown bear management plan that should allow population mixing by dispersing males.
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Affiliation(s)
| | - Wojciech Śmietana
- Institute of Nature Conservation PASKrakówPoland
- Present address:
KRAMEKOKrakówPoland
| | | | | | | | | | - Andriy‐Taras Bashta
- Institute of Ecology of the CarpathiansNational Academy of Sciences of UkraineLvivUkraine
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The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis. Genes (Basel) 2018; 9:genes9120598. [PMID: 30513700 PMCID: PMC6315469 DOI: 10.3390/genes9120598] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/23/2018] [Accepted: 11/28/2018] [Indexed: 11/17/2022] Open
Abstract
The grizzly bear (Ursus arctos ssp. horribilis) represents the largest population of brown bears in North America. Its genome was sequenced using a microfluidic partitioning library construction technique, and these data were supplemented with sequencing from a nanopore-based long read platform. The final assembly was 2.33 Gb with a scaffold N50 of 36.7 Mb, and the genome is of comparable size to that of its close relative the polar bear (2.30 Gb). An analysis using 4104 highly conserved mammalian genes indicated that 96.1% were found to be complete within the assembly. An automated annotation of the genome identified 19,848 protein coding genes. Our study shows that the combination of the two sequencing modalities that we used is sufficient for the construction of highly contiguous reference quality mammalian genomes. The assembled genome sequence and the supporting raw sequence reads are available from the NCBI (National Center for Biotechnology Information) under the bioproject identifier PRJNA493656, and the assembly described in this paper is version QXTK01000000.
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14
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Dufresnes C, Miquel C, Remollino N, Biollaz F, Salamin N, Taberlet P, Fumagalli L. Howling from the past: historical phylogeography and diversity losses in European grey wolves. Proc Biol Sci 2018; 285:rspb.2018.1148. [PMID: 30068681 DOI: 10.1098/rspb.2018.1148] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/06/2018] [Indexed: 12/18/2022] Open
Abstract
Genetic bottlenecks resulting from human-induced population declines make alarming symbols for the irreversible loss of our natural legacy worldwide. The grey wolf (Canis lupus) is an iconic example of extreme declines driven by anthropogenic factors. Here, we assessed the genetic signatures of 150 years of wolf persecution throughout the Western Palaearctic by high-throughput mitochondrial DNA sequencing of historical specimens in an unprecedented spatio-temporal framework. Despite Late Pleistocene bottlenecks, we show that historical genetic variation had remained high throughout Europe until the last several hundred years. In Western Europe, where wolves nearly got fully exterminated, diversity dramatically collapsed at the turn of the twentieth century and recolonization from few homogeneous relict populations induced drastic shifts of genetic composition. By contrast, little genetic displacement and steady levels of diversity were maintained in Eastern European regions, where human persecution had lesser effects on wolf demography. By comparing prehistoric, historic and modern patterns of genetic diversity, our study hence traces the timeframe and the active human role in the decline of the grey wolf, an emblematic yet controversial animal which symbolizes the complex relationship between human societies and nature conservation.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.,Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Christian Miquel
- Laboratoire d'Écologie Alpine (LECA), UMR5553, BP53, 38041 Grenoble, Cedex 9, France
| | - Nadège Remollino
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - François Biollaz
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.,Route Pra de Louetse 32, 1968 Mase, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.,Department of Computational Biology University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Pierre Taberlet
- Laboratoire d'Écologie Alpine (LECA), UMR5553, BP53, 38041 Grenoble, Cedex 9, France
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
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15
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Salomashkina VV, Kholodova MV, Semenov UA, Muradov AS, Malkhasyan A. Genetic variability of brown bear (Ursus arctos L., 1758). RUSS J GENET+ 2017. [DOI: 10.1134/s1022795416120103] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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Ashrafzadeh MR, Kaboli M, Naghavi MR. Mitochondrial DNA analysis of Iranian brown bears (Ursus arctos) reveals new phylogeographic lineage. Mamm Biol 2016. [DOI: 10.1016/j.mambio.2015.09.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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17
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Çilingir FG, Akın Pekşen Ç, Ambarlı H, Beerli P, Bilgin CC. Exceptional maternal lineage diversity in brown bears (Ursus arctos) from Turkey. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12322] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- F. Gözde Çilingir
- Department of Biology; Middle East Technical University; Ankara Turkey
- Department of Biological Sciences; National University of Singapore; Singapore
| | - Çiğdem Akın Pekşen
- Department of Biology; Middle East Technical University; Ankara Turkey
- Deparment of Biology; Yüzüncüyıl University; Van Turkey
| | - Hüseyin Ambarlı
- Department of Biology; Middle East Technical University; Ankara Turkey
- Department of Wildlife Ecology and Management; Düzce University; Düzce Turkey
| | - Peter Beerli
- Department of Scientific Computing; Florida State University; Tallahassee FL USA
| | - C. Can Bilgin
- Department of Biology; Middle East Technical University; Ankara Turkey
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18
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Hassanin A. The role of Pleistocene glaciations in shaping the evolution of polar and brown bears. Evidence from a critical review of mitochondrial and nuclear genome analyses. C R Biol 2015; 338:494-501. [DOI: 10.1016/j.crvi.2015.04.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/17/2015] [Accepted: 04/18/2015] [Indexed: 11/25/2022]
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19
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Xenikoudakis G, Ersmark E, Tison JL, Waits L, Kindberg J, Swenson JE, Dalén L. Consequences of a demographic bottleneck on genetic structure and variation in the Scandinavian brown bear. Mol Ecol 2015; 24:3441-54. [PMID: 26042479 DOI: 10.1111/mec.13239] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 05/07/2015] [Accepted: 05/08/2015] [Indexed: 11/30/2022]
Abstract
The Scandinavian brown bear went through a major decline in population size approximately 100 years ago, due to intense hunting. After being protected, the population subsequently recovered and today numbers in the thousands. The genetic diversity in the contemporary population has been investigated in considerable detail, and it has been shown that the population consists of several subpopulations that display relatively high levels of genetic variation. However, previous studies have been unable to resolve the degree to which the demographic bottleneck impacted the contemporary genetic structure and diversity. In this study, we used mitochondrial and microsatellite DNA markers from pre- and postbottleneck Scandinavian brown bear samples to investigate the effect of the bottleneck. Simulation and multivariate analysis suggested the same genetic structure for the historical and modern samples, which are clustered into three subpopulations in southern, central and northern Scandinavia. However, the southern subpopulation appears to have gone through a marked change in allele frequencies. When comparing the mitochondrial DNA diversity in the whole population, we found a major decline in haplotype numbers across the bottleneck. However, the loss of autosomal genetic diversity was less pronounced, although a significant decline in allelic richness was observed in the southern subpopulation. Approximate Bayesian computations provided clear support for a decline in effective population size during the bottleneck, in both the southern and northern subpopulations. These results have implications for the future management of the Scandinavian brown bear because they indicate a recent loss in genetic diversity and also that the current genetic structure may have been caused by historical ecological processes rather than recent anthropogenic persecution.
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Affiliation(s)
- G Xenikoudakis
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden.,Department of Zoology, Stockholm University, SE-106 91, Stockholm, Sweden
| | - E Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden.,Department of Zoology, Stockholm University, SE-106 91, Stockholm, Sweden
| | - J-L Tison
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
| | - L Waits
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID, 83844, USA
| | - J Kindberg
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - J E Swenson
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, NO-1432, Ås, Norway.,Norwegian Institute for Nature Research, PO Box 5685 Sluppen, NO-7485, Trondheim, Norway
| | - L Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
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20
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Burrell AS, Disotell TR, Bergey CM. The use of museum specimens with high-throughput DNA sequencers. J Hum Evol 2015; 79:35-44. [PMID: 25532801 PMCID: PMC4312722 DOI: 10.1016/j.jhevol.2014.10.015] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/08/2014] [Accepted: 10/31/2014] [Indexed: 12/30/2022]
Abstract
Natural history collections have long been used by morphologists, anatomists, and taxonomists to probe the evolutionary process and describe biological diversity. These biological archives also offer great opportunities for genetic research in taxonomy, conservation, systematics, and population biology. They allow assays of past populations, including those of extinct species, giving context to present patterns of genetic variation and direct measures of evolutionary processes. Despite this potential, museum specimens are difficult to work with because natural postmortem processes and preservation methods fragment and damage DNA. These problems have restricted geneticists' ability to use natural history collections primarily by limiting how much of the genome can be surveyed. Recent advances in DNA sequencing technology, however, have radically changed this, making truly genomic studies from museum specimens possible. We review the opportunities and drawbacks of the use of museum specimens, and suggest how to best execute projects when incorporating such samples. Several high-throughput (HT) sequencing methodologies, including whole genome shotgun sequencing, sequence capture, and restriction digests (demonstrated here), can be used with archived biomaterials.
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Affiliation(s)
- Andrew S Burrell
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA.
| | - Todd R Disotell
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA; New York Consortium in Evolutionary Primatology, USA
| | - Christina M Bergey
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA; New York Consortium in Evolutionary Primatology, USA
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21
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Barnett R, Yamaguchi N, Shapiro B, Ho SYW, Barnes I, Sabin R, Werdelin L, Cuisin J, Larson G. Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis. BMC Evol Biol 2014; 14:70. [PMID: 24690312 PMCID: PMC3997813 DOI: 10.1186/1471-2148-14-70] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 03/13/2014] [Indexed: 11/15/2022] Open
Abstract
Background Understanding the demographic history of a population is critical to conservation and to our broader understanding of evolutionary processes. For many tropical large mammals, however, this aim is confounded by the absence of fossil material and by the misleading signal obtained from genetic data of recently fragmented and isolated populations. This is particularly true for the lion which as a consequence of millennia of human persecution, has large gaps in its natural distribution and several recently extinct populations. Results We sequenced mitochondrial DNA from museum-preserved individuals, including the extinct Barbary lion (Panthera leo leo) and Iranian lion (P. l. persica), as well as lions from West and Central Africa. We added these to a broader sample of lion sequences, resulting in a data set spanning the historical range of lions. Our Bayesian phylogeographical analyses provide evidence for highly supported, reciprocally monophyletic lion clades. Using a molecular clock, we estimated that recent lion lineages began to diverge in the Late Pleistocene. Expanding equatorial rainforest probably separated lions in South and East Africa from other populations. West African lions then expanded into Central Africa during periods of rainforest contraction. Lastly, we found evidence of two separate incursions into Asia from North Africa, first into India and later into the Middle East. Conclusions We have identified deep, well-supported splits within the mitochondrial phylogeny of African lions, arguing for recognition of some regional populations as worthy of independent conservation. More morphological and nuclear DNA data are now needed to test these subdivisions.
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Affiliation(s)
- Ross Barnett
- Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, Durham DH1 3LE, UK.
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22
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Salomashkina VV, Kholodova MV, Tuten’kov OY, Moskvitina NS, Erokhin NG. New data on the phylogeography and genetic diversity of the brown bear Ursus arctos Linnaeus, 1758 of Northeastern Eurasia (mtDNA control region polymorphism analysis). BIOL BULL+ 2014. [DOI: 10.1134/s1062359014010087] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Hirata D, Abramov AV, Baryshnikov GF, Masuda R. Mitochondrial DNA haplogrouping of the brown bear,Ursus arctos(Carnivora: Ursidae) in Asia, based on a newly developed APLP analysis. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daisuke Hirata
- Department of Natural History Sciences; Graduate School of Science; Hokkaido University; Sapporo 060-0810 Japan
| | - Alexei V. Abramov
- Laboratory of Mammalogy; Zoological Institute; Russian Academy of Sciences; St. Petersburg 199034 Russia
| | - Gennady F. Baryshnikov
- Laboratory of Mammalogy; Zoological Institute; Russian Academy of Sciences; St. Petersburg 199034 Russia
| | - Ryuichi Masuda
- Department of Natural History Sciences; Graduate School of Science; Hokkaido University; Sapporo 060-0810 Japan
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24
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Gus’kov VY, Sheremet’eva IN, Seredkin IV, Kryukov AP. Mitochondrial cytochrome b gene variation in brown bear (Ursus arctos Linnaeus, 1758) from southern part of Russian Far East. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413110070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Haponski AE, Stepien CA. Phylogenetic and biogeographical relationships of theSanderpikeperches (Percidae: Perciformes): patterns across North America and Eurasia. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12114] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amanda E. Haponski
- The Great Lakes Genetics/Genomics Laboratory; Lake Erie Center and the Department of Environmental Sciences; The University of Toledo; 6200 Bayshore Road; Toledo; OH; 43616; USA
| | - Carol A. Stepien
- The Great Lakes Genetics/Genomics Laboratory; Lake Erie Center and the Department of Environmental Sciences; The University of Toledo; 6200 Bayshore Road; Toledo; OH; 43616; USA
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26
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Hirata D, Mano T, Abramov AV, Baryshnikov GF, Kosintsev PA, Vorobiev AA, Raichev EG, Tsunoda H, Kaneko Y, Murata K, Fukui D, Masuda R. Molecular phylogeography of the brown bear (Ursus arctos) in Northeastern Asia based on analyses of complete mitochondrial DNA sequences. Mol Biol Evol 2013; 30:1644-52. [PMID: 23619144 DOI: 10.1093/molbev/mst077] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To further elucidate the migration history of the brown bears (Ursus arctos) on Hokkaido Island, Japan, we analyzed the complete mitochondrial DNA (mtDNA) sequences of 35 brown bears from Hokkaido, the southern Kuril Islands (Etorofu and Kunashiri), Sakhalin Island, and the Eurasian Continent (continental Russia, Bulgaria, and Tibet), and those of four polar bears. Based on these sequences, we reconstructed the maternal phylogeny of the brown bear and estimated divergence times to investigate the timing of brown bear migrations, especially in northeastern Eurasia. Our gene tree showed the mtDNA haplotypes of all 73 brown and polar bears to be divided into eight divergent lineages. The brown bear on Hokkaido was divided into three lineages (central, eastern, and southern). The Sakhalin brown bear grouped with eastern European and western Alaskan brown bears. Etorofu and Kunashiri brown bears were closely related to eastern Hokkaido brown bears and could have diverged from the eastern Hokkaido lineage after formation of the channel between Hokkaido and the southern Kuril Islands. Tibetan brown bears diverged early in the eastern lineage. Southern Hokkaido brown bears were closely related to North American brown bears.
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Affiliation(s)
- Daisuke Hirata
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, Japan
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27
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Bray SC, Austin JJ, Metcalf JL, Østbye K, Østbye E, Lauritzen SE, Aaris-Sørensen K, Valdiosera C, Adler CJ, Cooper A. Ancient DNA identifies post-glacial recolonisation, not recent bottlenecks, as the primary driver of contemporary mtDNA phylogeography and diversity in Scandinavian brown bears. DIVERS DISTRIB 2012. [DOI: 10.1111/j.1472-4642.2012.00923.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Sarah C.E. Bray
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences; University of Adelaide; Adelaide; SA; 5005; Australia
| | | | | | | | - Eivind Østbye
- Department of Biology; University of Oslo; PO Box 1066; Blindern, NO-0316; Oslo; Norway
| | - Stein-Erik Lauritzen
- Department of Earth Science; University of Bergen; Allegaten 41, NO-5007; Bergen; Norway
| | - Kim Aaris-Sørensen
- Centre for GeoGenetics, Natural History Museum of Copenhagen; University of Copenhagen; Universitetsparken 15, DK-2100; Copenhagen Ø; Denmark
| | - Cristina Valdiosera
- Centro Mixto; Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolucion y Comportamiento Humanos; c/Sinesio Delgado 4 Pabellon 14; 28029; Madrid; Spain
| | | | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences; University of Adelaide; Adelaide; SA; 5005; Australia
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28
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Koblmüller S, Wayne RK, Leonard JA. Impact of Quaternary climatic changes and interspecific competition on the demographic history of a highly mobile generalist carnivore, the coyote. Biol Lett 2012; 8:644-7. [PMID: 22491760 DOI: 10.1098/rsbl.2012.0162] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recurrent cycles of climatic change during the Quaternary period have dramatically affected the population genetic structure of many species. We reconstruct the recent demographic history of the coyote (Canis latrans) through the use of Bayesian techniques to examine the effects of Late Quaternary climatic perturbations on the genetic structure of a highly mobile generalist species. Our analysis reveals a lack of phylogeographic structure throughout the range but past population size changes correlated with climatic changes. We conclude that even generalist carnivorous species are very susceptible to environmental changes associated with climatic perturbations. This effect may be enhanced in coyotes by interspecific competition with larger carnivores.
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Affiliation(s)
- Stephan Koblmüller
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Avd. Américo Vespucio s/n, 41092 Seville, Spain
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29
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Abstract
Natural history museums around the world hold millions of animal and plant specimens that are potentially amenable to genetic analyses. With more and more populations and species becoming extinct, the importance of these specimens for phylogenetic and phylogeographic analyses is rapidly increasing. However, as most DNA extraction methods damage the specimens, nondestructive extraction methods are useful to balance the demands of molecular biologists, morphologists, and museum curators. Here, I describe a method for nondestructive DNA extraction from bony specimens (i.e., bones and teeth). In this method, the specimens are soaked in extraction buffer, and DNA is then purified from the soaking solution using adsorption to silica. The method reliably yields mitochondrial and often also nuclear DNA. The method has been adapted to DNA extraction from other types of specimens such as arthropods.
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Affiliation(s)
- Michael Hofreiter
- Department of Biology, The University of York, Wentworth Way, Heslington, York, YO10 5DD, UK.
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30
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MURTSKHVALADZE MARINE, GAVASHELISHVILI ALEXANDER, TARKHNISHVILI DAVID. Geographic and genetic boundaries of brown bear (Ursus arctos) population in the Caucasus. Mol Ecol 2010; 19:1829-41. [DOI: 10.1111/j.1365-294x.2010.04610.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Rohland N, Siedel H, Hofreiter M. A rapid column-based ancient DNA extraction method for increased sample throughput. Mol Ecol Resour 2009; 10:677-83. [PMID: 21565072 DOI: 10.1111/j.1755-0998.2009.02824.x] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Genetic analyses using museum specimens and ancient DNA from fossil samples are becoming increasingly important in phylogenetic and especially population genetic studies. Recent progress in ancient DNA sequencing technologies has substantially increased DNA sequence yields and, in combination with barcoding methods, has enabled large-scale studies using any type of DNA. Moreover, more and more studies now use nuclear DNA sequences in addition to mitochondrial ones. Unfortunately, nuclear DNA is, due to its much lower copy number in living cells compared to mitochondrial DNA, much more difficult to obtain from low-quality samples. Therefore, a DNA extraction method that optimizes DNA yields from low-quality samples and at the same time allows processing many samples within a short time frame is immediately required. In fact, the major bottleneck in the analysis process using samples containing low amounts of degraded DNA now lies in the extraction of samples, as column-based methods using commercial kits are fast but have proven to give very low yields, while more efficient methods are generally very time-consuming. Here, we present a method that combines the high DNA yield of batch-based silica extraction with the time-efficiency of column-based methods. Our results on Pleistocene cave bear samples show that DNA yields are quantitatively comparable, and in fact even slightly better than with silica batch extraction, while at the same time the number of samples that can conveniently be processed in parallel increases and both bench time and costs decrease using this method. Thus, this method is suited for harvesting the power of high-throughput sequencing using the DNA preserved in the millions of paleontological and museums specimens.
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Affiliation(s)
- Nadin Rohland
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA Department of Biology, University of York, YO10 5YW, York, UK
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32
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Calvignac S, Hughes S, Hänni C. Genetic diversity of endangered brown bear (Ursus arctos) populations at the crossroads of Europe, Asia and Africa. DIVERS DISTRIB 2009. [DOI: 10.1111/j.1472-4642.2009.00586.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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33
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McCarthy TM, Waits LP, Mijiddorj B. Status of the Gobi bear in Mongolia as determined by noninvasive genetic methods. URSUS 2009. [DOI: 10.2192/07gr013r.1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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KORSTEN MARJU, HO SIMONYW, DAVISON JOHN, PÄHN BERIT, VULLA EGLE, ROHT MARIS, TUMANOV IGORL, KOJOLA ILPO, ANDERSONE-LILLEY ZANETE, OZOLINS JANIS, PILOT MALGORZATA, MERTZANIS YORGOS, GIANNAKOPOULOS ALEXIOS, VOROBIEV ALEXA, MARKOV NIKOLAII, SAVELJEV ALEXANDERP, LYAPUNOVA ELENAA, ABRAMOV ALEXEIV, MÄNNIL PEEP, VALDMANN HARRI, PAZETNOV SERGEIV, PAZETNOV VALENTINS, RÕKOV ALEXANDERM, SAARMA URMAS. Sudden expansion of a single brown bear maternal lineage across northern continental Eurasia after the last ice age: a general demographic model for mammals? Mol Ecol 2009; 18:1963-79. [DOI: 10.1111/j.1365-294x.2009.04163.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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35
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Ohnishi N, Uno R, Ishibashi Y, Tamate HB, Oi T. The influence of climatic oscillations during the Quaternary Era on the genetic structure of Asian black bears in Japan. Heredity (Edinb) 2009; 102:579-89. [PMID: 19319151 DOI: 10.1038/hdy.2009.28] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The Asian black bear (Ursus thibetanus) inhabits two of the main islands, Honshu and Shikoku, in Japan. To determine how climatic oscillations during the Quaternary Era affected the genetic structure of the black bear populations in Japan, we examined their phylogeographic relationships and compared their genetic structure. We analysed an approximately 700-bp sequence in the D-loop region of mitochondrial DNA collected from 589 bears in this study with 108 bears from a previous study. We observed a total of 57 haplotypes and categorized them into three clusters (Eastern, Western and Southern) based on the spatial distribution of the haplotypes. All but 2 of the 41 haplotypes in the Eastern cluster were distributed locally. Genetic diversity was generally low in northern Japan and high in central Japan. Demographic tests rejected the expansion model in northern populations. Haplotypes of the Western and Southern clusters were unique to local populations. We conclude that the extant genetic structure of the Asian black bear populations arose as follows: first, populations became small and genetic drift decreased genetic diversity in the northern area during the last glacial period, whereas large continuous populations existed in the southern part of central Japan. These patterns were essentially maintained until the present time. In western and southern Japan, the effects of climatic oscillations were smaller, and thus, local structure was maintained.
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Affiliation(s)
- N Ohnishi
- Kansai Research Center, Forestry and Forest Products Research Institute, Nagaikyutaro, Kyoto, Japan.
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36
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37
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Calvignac S. [Climatic events and geographical patterns of the genetic diversity]. Med Sci (Paris) 2008; 24:686-8. [PMID: 18789209 DOI: 10.1051/medsci/20082489686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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38
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Gallo-Reynoso JP, Van Devender T, Reina-Guerrero AL, Egido-Villarreal J, Pfeiler E. Probable Occurrence of a Brown Bear (Ursus arctos) in Sonora, Mexico, in 1976. SOUTHWEST NAT 2008. [DOI: 10.1894/0038-4909(2008)53[256:pooabb]2.0.co;2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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39
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Nakagome S, Pecon-Slattery J, Masuda R. Unequal rates of Y chromosome gene divergence during speciation of the family Ursidae. Mol Biol Evol 2008; 25:1344-56. [PMID: 18400788 DOI: 10.1093/molbev/msn086] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Evolution of the bear family Ursidae is well investigated in terms of morphological, paleontological, and genetic features. However, several phylogenetic ambiguities occur within the subfamily Ursinae (the family Ursidae excluding the giant panda and spectacled bear), which may correlate with behavioral traits of female philopatry and male-biased dispersal which form the basis of the observed matriarchal population structure in these species. In the process of bear evolution, we investigate the premise that such behavioral traits may be reflected in patterns of variation among genes with different modes of inheritance: matrilineal mitochondrial DNA (mtDNA), patrilineal Y chromosome, biparentally inherited autosomes, and the X chromosome. In the present study, we sequenced 3 Y-linked genes (3,453 bp) and 4 X-linked genes (4,960 bp) and reanalyzed previously published sequences from autosome genes (2,347 bp) in ursid species to investigate differences in evolutionary rates associated with patterns of inheritance. The results describe topological incongruence between sex-linked genes and autosome genes and between nuclear DNA and mtDNA. In more ancestral branches within the bear phylogeny, Y-linked genes evolved faster than autosome and X-linked genes, consistent with expectations based on male-driven evolution. However, this pattern changes among branches leading to each species within the lineage of Ursinae whereby the evolutionary rates of Y-linked genes have fewer than expected substitutions. This inconsistency between more recent nodes of the bear phylogeny with more ancestral nodes may reflect the influences of sex-biased dispersal as well as molecular evolutionary characteristics of the Y chromosome, and stochastic events in species natural history, and phylogeography unique to ursine bears.
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Affiliation(s)
- Shigeki Nakagome
- Division of Biological Science, Graduate School of Science, Hokkaido University, Sapporo, Japan
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Zachos FE, Otto M, Unici R, Lorenzini R, Hartl GB. Evidence of a phylogeographic break in the Romanian brown bear (Ursus arctos) population from the Carpathians. Mamm Biol 2008. [DOI: 10.1016/j.mambio.2007.02.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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