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Ruiz-Puerta EJ, Keighley X, Desjardins SPA, Gotfredsen AB, Pan SE, Star B, Boessenkool S, Barrett JH, McCarthy ML, Andersen LW, Born EW, Howse LR, Szpak P, Pálsson S, Malmquist HJ, Rufolo S, Jordan PD, Olsen MT. Holocene deglaciation drove rapid genetic diversification of Atlantic walrus. Proc Biol Sci 2023; 290:20231349. [PMID: 37752842 PMCID: PMC10523089 DOI: 10.1098/rspb.2023.1349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 08/27/2023] [Indexed: 09/28/2023] Open
Abstract
Rapid global warming is severely impacting Arctic ecosystems and is predicted to transform the abundance, distribution and genetic diversity of Arctic species, though these linkages are poorly understood. We address this gap in knowledge using palaeogenomics to examine how earlier periods of global warming influenced the genetic diversity of Atlantic walrus (Odobenus rosmarus rosmarus), a species closely associated with sea ice and shallow-water habitats. We analysed 82 ancient and historical Atlantic walrus mitochondrial genomes (mitogenomes), including now-extinct populations in Iceland and the Canadian Maritimes, to reconstruct the Atlantic walrus' response to Arctic deglaciation. Our results demonstrate that the phylogeography and genetic diversity of Atlantic walrus populations was initially shaped by the last glacial maximum (LGM), surviving in distinct glacial refugia, and subsequently expanding rapidly in multiple migration waves during the late Pleistocene and early Holocene. The timing of diversification and establishment of distinct populations corresponds closely with the chronology of the glacial retreat, pointing to a strong link between walrus phylogeography and sea ice. Our results indicate that accelerated ice loss in the modern Arctic may trigger further dispersal events, likely increasing the connectivity of northern stocks while isolating more southerly stocks putatively caught in small pockets of suitable habitat.
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Affiliation(s)
- Emily J. Ruiz-Puerta
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
- Arctic Centre & Groningen Institute of Archaeology, Faculty of Arts, University of Groningen, PO Box 716, 9700 AS Groningen, The Netherlands
| | - Xénia Keighley
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
- The Bureau of Meteorology, The Treasury Building, Parkes Place West, Parkes, Australian Capital Territory 2600, Australia
| | - Sean P. A. Desjardins
- Arctic Centre & Groningen Institute of Archaeology, Faculty of Arts, University of Groningen, PO Box 716, 9700 AS Groningen, The Netherlands
- Palaeobiology Section, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario, Canada K1P 6P4
| | - Anne Birgitte Gotfredsen
- Section for GeoGenetics, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen Kobenhavn, Denmark
| | - Shyong En Pan
- Palaeobiology Section, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario, Canada K1P 6P4
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway
| | - James H. Barrett
- Department of Archaeology and Cultural History, NTNU University Museum, 7491 Trondheim, Norway
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
| | - Morgan L. McCarthy
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
| | - Liselotte W. Andersen
- Department of Ecoscience, Aarhus University, CF Møllers Allé 4-8, build. 1110, 8000 Aarhus C, Denmark
| | - Erik W. Born
- Greenland Institute of Natural Resources, PO Box 570, 3900 Nuuk, Greenland
| | - Lesley R. Howse
- Archaeology Centre, University of Toronto, 19 Ursula Franklin Street, Toronto, Ontario Canada M5S 2S2
| | - Paul Szpak
- Department of Anthropology, Trent University, 1600 West Bank Drive, Peterborough, Ontario, Canada K9L 0G2
| | - Snæbjörn Pálsson
- Faculty of Life and Environmental Sciences, University of Iceland, Askja, Sturlugata 7, 101 Reykjavik, Iceland
| | - Hilmar J. Malmquist
- Icelandic Museum of Natural History, Suðurlandsbraut 24, 108 Reykjavík, Iceland
| | - Scott Rufolo
- Palaeobiology Section, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario, Canada K1P 6P4
| | - Peter D. Jordan
- Department of Archaeology and Ancient History, Lund University, Helgonavägen 3, 223 62 Lund, Sweden
- Global Station for Indigenous Studies and Cultural Diversity (GSI), GI-CoRE, HokkaidoUniversity, Japan
| | - Morten Tange Olsen
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
- Natural History Museum of Denmark, University of Copenhagen, Denmark
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Loveridge AJ, Sousa LL, Cushman S, Kaszta Ż, Macdonald DW. Where have all the lions gone? Establishing realistic baselines to assess decline and recovery of African lions. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Andrew J. Loveridge
- Wildlife Conservation Research Unit, Recanati‐Kaplan Centre, Department of Zoology University of Oxford Oxford UK
| | - Lara L. Sousa
- Wildlife Conservation Research Unit, Recanati‐Kaplan Centre, Department of Zoology University of Oxford Oxford UK
| | - Samuel Cushman
- Wildlife Conservation Research Unit, Recanati‐Kaplan Centre, Department of Zoology University of Oxford Oxford UK
- US Forest Service, Rocky Mountain Research Station Flagstaff Arizona USA
| | - Żaneta Kaszta
- Wildlife Conservation Research Unit, Recanati‐Kaplan Centre, Department of Zoology University of Oxford Oxford UK
| | - David W. Macdonald
- Wildlife Conservation Research Unit, Recanati‐Kaplan Centre, Department of Zoology University of Oxford Oxford UK
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Bertola LD, Miller SM, Williams VL, Naude VN, Coals P, Dures SG, Henschel P, Chege M, Sogbohossou EA, Ndiaye A, Kiki M, Gaylard A, Ikanda DK, Becker MS, Lindsey P. Genetic guidelines for translocations: Maintaining intraspecific diversity in the lion ( Panthera leo). Evol Appl 2022; 15:22-39. [PMID: 35126646 PMCID: PMC8792481 DOI: 10.1111/eva.13318] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/26/2022] Open
Abstract
Conservation translocations have become an important management tool, particularly for large wildlife species such as the lion (Panthera leo). When planning translocations, the genetic background of populations needs to be taken into account; failure to do so risks disrupting existing patterns of genetic variation, ultimately leading to genetic homogenization, and thereby reducing resilience and adaptability of the species. We urge wildlife managers to include knowledge of the genetic background of source/target populations, as well as species-wide patterns, in any management intervention. We present a hierarchical decision-making tool in which we list 132 lion populations/lion conservation units and provide information on genetic assignment, uncertainty and suitability for translocation for each source/target combination. By including four levels of suitability, from 'first choice' to 'no option', we provide managers with a range of options. To illustrate the extent of international trade of lions, and the potential disruption of natural patterns of intraspecific diversity, we mined the CITES Trade Database for estimated trade quantities of live individuals imported into lion range states during the past 4 decades. We identified 1056 recorded individuals with a potential risk of interbreeding with wild lions, 772 being captive-sourced. Scoring each of the records with our decision-making tool illustrates that only 7% of the translocated individuals were 'first choice' and 73% were 'no option'. We acknowledge that other, nongenetic factors are important in the decision-making process, and hence a pragmatic approach is needed. A framework in which source/target populations are scored based on suitability is not only relevant to lion, but also to other species of wildlife that are frequently translocated. We hope that the presented overview supports managers to include genetics in future management decisions and contributes towards conservation of the lion in its full diversity.
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Affiliation(s)
- Laura D. Bertola
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- City College of New YorkNew YorkNew YorkUSA
| | - Susan M. Miller
- FitzPatrick Institute of African OrnithologyDSI‐NRF Centre of ExcellenceUniversity of Cape TownCape TownSouth Africa
- Institute for Communities and Wildlife in AfricaUniversity of Cape TownCape TownSouth Africa
| | - Vivienne L. Williams
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Vincent N. Naude
- Institute for Communities and Wildlife in AfricaUniversity of Cape TownCape TownSouth Africa
| | - Peter Coals
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Wildlife Conservation Research UnitUniversity of OxfordOxfordUK
| | | | | | - Monica Chege
- Institute of Environmental Sciences (CML)Leiden UniversityLeidenThe Netherlands
- Kenya Wildlife ServiceNairobiKenya
| | | | | | - Martial Kiki
- Département de Génie de l’EnvironnementUniversité d’Abomey‐CalaviCotonouBenin
| | - Angela Gaylard
- Conservation Development & Assurance DepartmentAfrican Parks NetworkJohannesburgSouth Africa
| | | | | | - Peter Lindsey
- Department of Zoology and EntomologyMammal Research InstituteUniversity of PretoriaPretoriaSouth Africa
- Environmental Futures Research InstituteGriffith UniversityNathanQueenslandAustralia
- Wildlife Conservation NetworkSan FranciscoCaliforniaUSA
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Mboumba JF, Hervé MR, Guyot V, Ysnel F. Small rodent communities (Muridae) in Gabonese savannas: species diversity and biogeographical affinities. MAMMALIA 2021. [DOI: 10.1515/mammalia-2020-0079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The study contributes to the knowledge of species composition and biogeographical affinities of savannas rodent in Gabon. Unlike small rodents in Gabonese forests, there is little data on the diversity of small rodents in Gabonese savannas. The diversity and distribution of rodent murid communities was studied in four different types of savanna in Gabon: Coastal Basin (South-West), Lopé/Okanda (in the Center), Batéké Plateaux (Southeastern) and Ngougnié/ N’yanga (in the South). A total of 428 individuals representing six species were captured over 11,920 trap nights. Trap success was highly variable (2.2–6.9 %). The most abundant species were Mus minutoides (69%) followed by Lemniscomys striatus (21.5%). Indices of species richness varied from 2 to 5 and diversity (Shannon and Weaver) was low in the four savannas with the highest value at Ngougnié/N’yanga (H′ = 1.2). Species distributions show that Gabonese savanna small rodents conform to four distribution types, with one species known from Zambesian savannas exhibiting austral affinities (Pelomys campanae: occurs in three southern savannas). This new information provides important insight into the biogeography of small rodents at a local and regional level. Moreover, the correspondence analysis highlighted an influence of local ecological factors on population abundance.
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Affiliation(s)
- Jean-François Mboumba
- Département de Biologie , Université des Sciences et Techniques de Masuku , Franceville B.P. 901 , Gabon
- EA 7462 GTUBE , Université de Rennes 1 , 35042 Rennes Cedex , France
| | - Maxime R. Hervé
- Université Rennes, Inra , IGEPP – UMR-A 1349 , F-35000 Rennes , France
| | - Véronique Guyot
- CNRS-UMR6552 EthoS , Université de Rennes 1 , 35042 Rennes Cedex , France
| | - Frederic Ysnel
- EA 7462 GTUBE , Université de Rennes 1 , 35042 Rennes Cedex , France
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Keighley X, Bro‐Jørgensen MH, Ahlgren H, Szpak P, Ciucani MM, Sánchez Barreiro F, Howse L, Gotfredsen AB, Glykou A, Jordan P, Lidén K, Olsen MT. Predicting sample success for large-scale ancient DNA studies on marine mammals. Mol Ecol Resour 2021; 21:1149-1166. [PMID: 33463014 PMCID: PMC8248401 DOI: 10.1111/1755-0998.13331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/03/2021] [Accepted: 01/11/2021] [Indexed: 11/29/2022]
Abstract
In recent years, nonhuman ancient DNA studies have begun to focus on larger sample sizes and whole genomes, offering the potential to reveal exciting and hitherto unknown answers to ongoing biological and archaeological questions. However, one major limitation to such studies is the substantial financial and time investments still required during sample screening, due to uncertainty regarding successful sample selection. This study investigates the effect of a wide range of sample properties including latitude, sample age, skeletal element, collagen preservation, and context on endogenous content and DNA damage profiles for 317 ancient and historic pinniped samples collected from across the North Atlantic and surrounding regions. Using generalised linear and mixed-effect models, we found that a range of factors affected DNA preservation within each of the species under consideration. The most important findings were that endogenous content varied significantly within species according to context, the type of skeletal element, the collagen content and collection year. There also appears to be an effect of the sample's geographic origin, with samples from the Arctic generally showing higher endogenous content and lower damage rates. Both latitude and sample age were found to have significant relationships with damage levels, but only for walrus samples. Sex, ontogenetic age and extraction material preparation were not found to have any significant relationship with DNA preservation. Overall, skeletal element and sample context were found to be the most influential factors and should therefore be considered when selecting samples for large-scale ancient genome studies.
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Affiliation(s)
- Xénia Keighley
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
- Arctic Centre/Groningen Institute of ArchaeologyFaculty of ArtsUniversity of GroningenAS GroningenThe Netherlands
| | - Maiken Hemme Bro‐Jørgensen
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Hans Ahlgren
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Paul Szpak
- Department of AnthropologyTrent UniversityPeterboroughOntarioCanada
| | - Marta Maria Ciucani
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
| | | | - Lesley Howse
- Archaeology CentreUniversity of TorontoTorontoOntarioCanada
| | | | - Aikaterini Glykou
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Peter Jordan
- Department of Archaeology and Ancient HistoryLund UniversityLundSweden
| | - Kerstin Lidén
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Morten Tange Olsen
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
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