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Gossé KJ, Gonedelé‐Bi S, Dufour S, Danquah E, Gaubert P. Conservation genetics of the white-bellied pangolin in West Africa: A story of lineage admixture, declining demography, and wide sourcing by urban bushmeat markets. Ecol Evol 2024; 14:e11031. [PMID: 38435007 PMCID: PMC10905243 DOI: 10.1002/ece3.11031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 03/05/2024] Open
Abstract
During the last 40 years, the volumes of African pangolins feeding the illegal wildlife trade have dramatically increased. We conducted a conservation genetics survey of the most traded African species, the white bellied pangolin (WBP; Phataginus tricuspis), across three West African countries including Guinea, Côte d'Ivoire, and Ghana. Our study combining mitochondrial DNA sequencing and microsatellite genotyping is the first to reveal a wide pattern of admixture between two of the six mitochondrial lineages as previously delimited within WBP. We found a signature of isolation by distance but a lack of population genetic structuring, supporting the idea that WBP may have underestimated dispersal abilities. Levels of genetic diversity were low in West African lineages (WAfr and Gha) compared to Central Africa, reinforcing the picture of genetic pauperization shared by West African WBP. We observed a 85%-98% decline in the effective population size of WBP occurring c. 3200 to 400 ya, with current numbers (520-590) at the lower end of the conservative thresholds for minimum viable population size. The microsatellite markers were powerful enough to differentiate between individuals and identify replicated samples, confirming the utility of this approach in tracing the pangolin trade. Genetic diversity estimates confirmed that Yopougon, the main bushmeat market from Abidjan (Côte d'Ivoire), was fed by a large trade network as confirmed by vendors reporting 10 different sources situated 62-459 km away from the market. We conclude that WBP distributed in the Upper Guinean Block should be considered a single management unit of high conservation concern, as impacted by genetic diversity erosion, drastic decline in effective population size, and wide range sourcing for feeding urban bushmeat markets. Given the genetic admixture pattern detected within WBP from West Africa, we advocate for a multi-locus strategy to trace the international trade of the species.
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Affiliation(s)
- Koffi Jules Gossé
- Laboratoire de Biotechnologie, Agriculture et Valorisation des Ressources Biologiques, UFR BiosciencesUniversité Félix Houphouët‐BoignyAbidjanCôte d'Ivoire
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INPUniversité Toulouse 3 – Paul Sabatier (UT3)ToulouseFrance
| | - Sery Gonedelé‐Bi
- Laboratoire de Biotechnologie, Agriculture et Valorisation des Ressources Biologiques, UFR BiosciencesUniversité Félix Houphouët‐BoignyAbidjanCôte d'Ivoire
| | | | - Emmanuel Danquah
- Department of Wildlife and Range Management, Faculty of Renewable Natural ResourcesKwame Nkrumah University of Science and TechnologyKumasiGhana
| | - Philippe Gaubert
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INPUniversité Toulouse 3 – Paul Sabatier (UT3)ToulouseFrance
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR)Universidade do Porto, Terminal de Cruzeiros do Porto de LeixõesPortoPortugal
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Clements HS, Do Linh San E, Hempson G, Linden B, Maritz B, Monadjem A, Reynolds C, Siebert F, Stevens N, Biggs R, De Vos A, Blanchard R, Child M, Esler KJ, Hamann M, Loft T, Reyers B, Selomane O, Skowno AL, Tshoke T, Abdoulaye D, Aebischer T, Aguirre-Gutiérrez J, Alexander GJ, Ali AH, Allan DG, Amoako EE, Angedakin S, Aruna E, Avenant NL, Badjedjea G, Bakayoko A, Bamba-Kaya A, Bates MF, Bates PJJ, Belmain SR, Bennitt E, Bradley J, Brewster CA, Brown MB, Brown M, Bryja J, Butynski TM, Carvalho F, Channing A, Chapman CA, Cohen C, Cords M, Cramer JD, Cronk N, Cunneyworth PMK, Dalerum F, Danquah E, Davies-Mostert HT, de Blocq AD, De Jong YA, Demos TC, Denys C, Djagoun CAMS, Doherty-Bone TM, Drouilly M, du Toit JT, Ehlers Smith DA, Ehlers Smith YC, Eiseb SJ, Fashing PJ, Ferguson AW, Fernández-García JM, Finckh M, Fischer C, Gandiwa E, Gaubert P, Gaugris JY, Gibbs DJ, Gilchrist JS, Gil-Sánchez JM, Githitho AN, Goodman PS, Granjon L, Grobler JP, Gumbi BC, Gvozdik V, Harvey J, Hauptfleisch M, Hayder F, Hema EM, Herbst M, Houngbédji M, Huntley BJ, Hutterer R, Ivande ST, Jackson K, Jongsma GFM, Juste J, Kadjo B, Kaleme PK, Kamugisha E, Kaplin BA, Kato HN, Kiffner C, Kimuyu DM, Kityo RM, Kouamé NG, Kouete T M, le Roux A, Lee ATK, Lötter MC, Lykke AM, MacFadyen DN, Macharia GP, Madikiza ZJK, Mahlaba TAM, Mallon D, Mamba ML, Mande C, Marchant RA, Maritz RA, Markotter W, McIntyre T, Measey J, Mekonnen A, Meller P, Melville HI, Mganga KZ, Mills MGL, Minnie L, Missoup AD, Mohammad A, Moinde NN, Moise BFE, Monterroso P, Moore JF, Musila S, Nago SGA, Namoto MW, Niang F, Nicolas V, Nkenku JB, Nkrumah EE, Nono GL, Norbert MM, Nowak K, Obitte BC, Okoni-Williams AD, Onongo J, O'Riain MJ, Osinubi ST, Parker DM, Parrini F, Peel MJS, Penner J, Pietersen DW, Plumptre AJ, Ponsonby DW, Porembski S, Power RJ, Radloff FGT, Rambau RV, Ramesh T, Richards LR, Rödel MO, Rollinson DP, Rovero F, Saleh MA, Schmiedel U, Schoeman MC, Scholte P, Serfass TL, Shapiro JT, Shema S, Siebert SJ, Slingsby JA, Sliwa A, Smit-Robinson HA, Sogbohossou EA, Somers MJ, Spawls S, Streicher JP, Swanepoel L, Tanshi I, Taylor PJ, Taylor WA, Te Beest M, Telfer PT, Thompson DI, Tobi E, Tolley KA, Turner AA, Twine W, Van Cakenberghe V, Van de Perre F, van der Merwe H, van Niekerk CJG, van Wyk PCV, Venter JA, Verburgt L, Veron G, Vetter S, Vorontsova MS, Wagner TC, Webala PW, Weber N, Weier SM, White PA, Whitecross MA, Wigley BJ, Willems FJ, Winterbach CW, Woodhouse GM. The bii4africa dataset of faunal and floral population intactness estimates across Africa's major land uses. Sci Data 2024; 11:191. [PMID: 38346970 PMCID: PMC10861571 DOI: 10.1038/s41597-023-02832-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/07/2023] [Indexed: 02/15/2024] Open
Abstract
Sub-Saharan Africa is under-represented in global biodiversity datasets, particularly regarding the impact of land use on species' population abundances. Drawing on recent advances in expert elicitation to ensure data consistency, 200 experts were convened using a modified-Delphi process to estimate 'intactness scores': the remaining proportion of an 'intact' reference population of a species group in a particular land use, on a scale from 0 (no remaining individuals) to 1 (same abundance as the reference) and, in rare cases, to 2 (populations that thrive in human-modified landscapes). The resulting bii4africa dataset contains intactness scores representing terrestrial vertebrates (tetrapods: ±5,400 amphibians, reptiles, birds, mammals) and vascular plants (±45,000 forbs, graminoids, trees, shrubs) in sub-Saharan Africa across the region's major land uses (urban, cropland, rangeland, plantation, protected, etc.) and intensities (e.g., large-scale vs smallholder cropland). This dataset was co-produced as part of the Biodiversity Intactness Index for Africa Project. Additional uses include assessing ecosystem condition; rectifying geographic/taxonomic biases in global biodiversity indicators and maps; and informing the Red List of Ecosystems.
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Affiliation(s)
- Hayley S Clements
- Centre for Sustainability Transitions, Stellenbosch University, Stellenbosch, South Africa.
- Helsinki Lab of Interdisciplinary Conservation Science, University of Helsinki, Helsinki, Finland.
| | - Emmanuel Do Linh San
- Department of Zoology and Entomology, University of Fort Hare, Alice, South Africa
| | - Gareth Hempson
- Centre for African Ecology, School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Institute of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Birthe Linden
- Chair in Biodiversity Value & Change, Faculty of Science, Engineering & Agriculture, University of Venda, Thohoyandou, South Africa
| | - Bryan Maritz
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Bellville, South Africa
| | - Ara Monadjem
- Biological Sciences, University of Eswatini, Kwaluseni, Eswatini
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Chevonne Reynolds
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Frances Siebert
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Nicola Stevens
- Environmental Change Institute, University of Oxford, Oxford, United Kingdom
| | - Reinette Biggs
- Centre for Sustainability Transitions, Stellenbosch University, Stellenbosch, South Africa
- Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden
| | - Alta De Vos
- Centre for Sustainability Transitions, Stellenbosch University, Stellenbosch, South Africa
- Department of Environmental Sciences, Rhodes University, Makhanda, South Africa
| | - Ryan Blanchard
- Centre for Sustainability Transitions, Stellenbosch University, Stellenbosch, South Africa
- Fynbos Node of the South African Environmental Observation Network, Cape Town, South Africa
| | - Matthew Child
- South African National Biodiversity Institute, Cape Town, South Africa
| | - Karen J Esler
- Department of Conservation Ecology & Entomology, Stellenbosch University, Stellenbosch, South Africa
| | - Maike Hamann
- Centre for Sustainability Transitions, Stellenbosch University, Stellenbosch, South Africa
- Centre for Geography and Environmental Science, University of Exeter, Penryn, Cornwall, United Kingdom
| | - Ty Loft
- School of Geography and the Environment, Environmental Change Institute, University of Oxford, Oxford, United Kingdom
| | - Belinda Reyers
- Centre for Environmental Studies, University of Pretoria, Pretoria, South Africa
| | - Odirilwe Selomane
- Centre for Sustainability Transitions, Stellenbosch University, Stellenbosch, South Africa
- Department of Agricultural Economics, Extension and Rural Development, University of Pretoria, Pretoria, South Africa
| | - Andrew L Skowno
- South African National Biodiversity Institute, Cape Town, South Africa
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | - Tshegofatso Tshoke
- Centre for Sustainability Transitions, Stellenbosch University, Stellenbosch, South Africa
- Department of Conservation Ecology & Entomology, Stellenbosch University, Stellenbosch, South Africa
| | | | | | - Jesús Aguirre-Gutiérrez
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
| | - Graham J Alexander
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - David G Allan
- Bird Department, Durban Natural Science Museum, Durban, South Africa
| | - Esther E Amoako
- Department of Environment and Sustainability Sciences, University for Development Studies, Tamale, Ghana
| | - Samuel Angedakin
- Department of Environmental Management, Makerere University, Kampala, Uganda
| | - Edward Aruna
- Biodiversity Conservation, Reptile and Amphibian Program - Sierra Leone, Freetown, Sierra Leone
| | - Nico L Avenant
- Department of Mammalogy, National Museum, Bloemfontein, South Africa
- Centre for Environmental Management, University of the Free State, Bloemfontein, South Africa
| | - Gabriel Badjedjea
- Aquatic Ecology, University of Kisangani/Biodiversity Monitoring Center, Kisangani, Democratic Republic of the Congo
| | - Adama Bakayoko
- UFR Sciences de la Nature, Universite NanguiI Abrogoua, Abidjan, Côte d'Ivoire
| | - Abraham Bamba-Kaya
- Institut de Recherches Agronomiques et Forestières (IRAF), Centre National de la Recherche Scientifique et Technologique (CENAREST), Libreville, Gabon
| | - Michael F Bates
- Department of Animal and Plant Systematics, National Museum, Bloemfontein, South Africa
- Department of Zoology & Entomology, University of the Free State, Bloemfontein, South Africa
| | | | - Steven R Belmain
- Agriculture, Health and Environment, Natural Resources Institute, University of Greenwich, Chatham, Maritime, United Kingdom
| | - Emily Bennitt
- Okavango Research Institute, University of Botswana, Maun, Botswana
| | - James Bradley
- Kalahari Research and Conservation, Botswana, Botswana
| | | | | | - Michelle Brown
- Department of Anthropology, University of Minnesota - Twin Cities, Minneapolis, MN, USA
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Thomas M Butynski
- Eastern Africa Primate Diversity and Conservation Program, Nanyuki, Kenya
| | - Filipe Carvalho
- Department of Zoology and Entomology, University of Fort Hare, Alice, South Africa
- BIOPOLIS-CIBIO/InBIO, University of Porto, Porto, Portugal
| | - Alan Channing
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | | | - Callan Cohen
- FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch, South Africa
| | - Marina Cords
- Department of Ecology, Evolution & Environmental Biology, Columbia University, New York, NY, USA
| | | | - Nadine Cronk
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Fredrik Dalerum
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- Biodiversity Research Institute (CSIC-UO-PA), Mieres, Spain
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Emmanuel Danquah
- Department of Wildlife and Range Management, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Harriet T Davies-Mostert
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- Conserve Global, London, United Kingdom
| | | | - Yvonne A De Jong
- Eastern Africa Primate Diversity and Conservation Program, Nanyuki, Kenya
| | - Terrence C Demos
- Negaunee Integrative Research Center, The Field Museum, Chicago, United States of America
| | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Chabi A M S Djagoun
- Faculty of Agronomic Sciences, Laboratory of Applied Ecology, University of Abomey Calavi, Cotonou, Benin
| | - Thomas M Doherty-Bone
- Conservation Programs, Royal Zoological Society of Scotland, Edinburgh, United Kingdom
| | - Marine Drouilly
- Institute for Communities and Wildlife in Africa (iCWild), University of Cape Town, Cape Town, South Africa
- Centre for Social Science Research (CSSR), University of Cape Town, Cape Town, South Africa
- Panthera, New York, USA
| | - Johan T du Toit
- Institute of Zoology, Zoological Society of London, London, United Kingdom
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - David A Ehlers Smith
- Centre for Functional Biodiversity, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Yvette C Ehlers Smith
- Centre for Functional Biodiversity, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Ezemvelo KZN Wildlife, Pietermaritzburg, South Africa
| | - Seth J Eiseb
- Department of Environmental Science, School of Science, University of Namibia, Windhoek, Namibia
| | - Peter J Fashing
- Anthropology Department & Environmental Studies Program, California State University Fullerton, Fullerton, United States of America
| | - Adam W Ferguson
- Gantz Family Collection Center, Field Museum of Natural History, Chicago, USA
| | | | - Manfred Finckh
- Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Claude Fischer
- Nature Management, University of Applied Sciences of Western Switzerland, Geneva, Jussy, Switzerland
| | - Edson Gandiwa
- Scientific Services, Zimbabwe Parks and Wildlife Management Authority, Harare, Zimbabwe
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique, IRD/CNRS/UPS, Université Toulouse III Paul Sabatier, Toulouse, cedex, 9, France
| | - Jerome Y Gaugris
- Flora Fauna & Man, Ecological Services Limited, Tortola, British Virgin Islands
| | | | - Jason S Gilchrist
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, Scotland, UK
| | | | | | | | - Laurent Granjon
- CBGP, IRD, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - J Paul Grobler
- Genetics, University of the Free State, Bloemfontein, South Africa
| | - Bonginkosi C Gumbi
- Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA, USA
| | - Vaclav Gvozdik
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Zoology, National Museum of the Czech Republic, Prague, Czech Republic
| | | | - Morgan Hauptfleisch
- Biodiversity Research Centre, Namibia University of Science and Technology, Windhoek, Namibia
| | - Firas Hayder
- Department of Zoology and Entomology, University of Fort Hare, Alice, South Africa
| | - Emmanuel M Hema
- Unité de Formation et de Recherche en Sciences Appliquées et Technologies (UFR-SAT), Université de Dédougou, Dédougou, Burkina Faso
| | - Marna Herbst
- Conservation Services, South African National Parks, Pretoria, South Africa
| | - Mariano Houngbédji
- Organisation pour le Développement Durable et la Biodiversité, Cotonou, Benin
| | - Brian J Huntley
- CIBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, University of Porto, Vairao, Portugal
| | | | - Samuel T Ivande
- A.P. Leventis Ornithological Research Institute (APLORI), University of Jos, Jos, Nigeria
| | - Kate Jackson
- Biology Department, Whitman College, Walla Walla, WA, USA
| | | | - Javier Juste
- Evolutionary Biology, Estación Biológica de Doñana (CSIC), Seville, Spain; CIBER, CIBERESP, Madrid, Spain
| | - Blaise Kadjo
- Natural habitats and biodiversity management, University Félix Houphouet-Boigny, Abidjan, Côte d'Ivoire
| | - Prince K Kaleme
- Department of Biology, CRSN/ LWIRO, DS Bukavu, DR Congo, Bukavu, Democratic Republic of the Congo
| | | | - Beth A Kaplin
- Center of Excellence in Biodiversity and Natural Resource Management, University of Rwanda, Huye, Rwanda
| | - Humphrey N Kato
- Biology, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Christian Kiffner
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, University of California, Los Angeles, USA
| | - Duncan M Kimuyu
- Department of Natural Resources, Karatina University, Karatina, Kenya
| | - Robert M Kityo
- Zoology, Entomology and Fisheries Sciences, Makerere University, Kampala, Uganda
| | - N'goran G Kouamé
- UFR Environnement, Laboratoire de Biodiversité et Ecologie Tropicale, Université Jean Lorougnon Guédé, Daloa, Côte d'Ivoire
| | - Marcel Kouete T
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, USA
| | - Aliza le Roux
- Zoology and Entomology, University of the Free State, Qwaqwa campus, Phuthaditjhaba, South Africa
| | - Alan T K Lee
- School of Life Sciences, University of KwaZulu-Natal, Scottsville, South Africa
| | - Mervyn C Lötter
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Duncan N MacFadyen
- Research and Conservation, Oppenheimer Generations, Parktown, Johannesburg, South Africa
| | | | - Zimkitha J K Madikiza
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - David Mallon
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Mnqobi L Mamba
- Biological Sciences, University of Eswatini, Kwaluseni, Eswatini
| | - Claude Mande
- Department of Ecology and Wildlife Management, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Rob A Marchant
- York institute for Tropical Ecosystems, University of York, York, United Kingdom
| | - Robin A Maritz
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Bellville, South Africa
- Conservation Alpha, Cape Town, South Africa
| | - Wanda Markotter
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
| | - Trevor McIntyre
- Department of Life and Consumer Sciences, University of South Africa, Roodepoort, South Africa
| | - John Measey
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
- Centre for Invasion Biology, Institute of Biodiversity, Yunnan University, Kunming, UMR7179, China
- MECADEV CNRS/MNHN, Département Adaptations du Vivant, Muséum National d'Histoire Naturelle, Bâtiment d'Anatomie Comparée, Paris, France
| | - Addisu Mekonnen
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Canada
| | - Paulina Meller
- Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Haemish I Melville
- Department of Environmental Sciences, University of South Africa, Florida, South Africa
| | - Kevin Z Mganga
- Copernicus Institute of Sustainable Development, Utrecht University, Utrecht, The Netherlands
| | - Michael G L Mills
- School of Biology and Environmental Science, University of Mpumalanga, Mbombela, South Africa
| | - Liaan Minnie
- School of Biology and Environmental Science, University of Mpumalanga, Mbombela, South Africa
- Centre for African Conservation Ecology, Nelson Mandela University, Gqeberha, South Africa
| | - Alain Didier Missoup
- Faculty of Science, Laboratory of Biology and Physiology of Animal Organisms, Zoology Unit, University of Douala, Douala, Cameroon
| | - Abubakr Mohammad
- Researcher, Conflict and Environmental Observatory, Manchester, United Kingdom
| | - Nancy N Moinde
- Conservation Biology, Institute of Primate Research-National Museums of Kenya, Nairobi, Kenya
| | | | - Pedro Monterroso
- Wildlife Conservation Ecology Research Group, CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairã, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- African Parks, Johannesburg, South Africa
| | | | - Simon Musila
- Mammalogy Section-Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Sedjro Gilles A Nago
- Laboratoire d'Ecologie, de Botanique et de Biologie végétale, University of Parakou, Parakou, Benin
| | - Maganizo W Namoto
- Indigenous Woodland Strategy Area, Forestry Research Institute of Malawi, Zomba, Malawi
| | - Fatimata Niang
- Institute of Environmental Sciences, Faculty of Technology and Sciences, University Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Jerry B Nkenku
- Departement of Biology, Faculty of Science, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Evans E Nkrumah
- Department of Wildlife and Range Management, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Gonwouo L Nono
- Department of Animal Biologie and Physiologie, University of Yaounde I, Yaounde, Cameroon
| | - Mulavwa M Norbert
- Primatology, Center for Research in Ecology and Forestry (CREF), Bikoro, Democratic Republic of the Congo
| | - Katarzyna Nowak
- Białowieża Geobotanical Station, Faculty of Biology, University of Warsaw, Białowieża, Poland
| | - Benneth C Obitte
- Small Mammal Conservation Organization, Benin City, Nigeria
- Biological Sciences, Texas Tech University, Lubbock, United States of America
| | | | | | - M Justin O'Riain
- Institute for Communities and Wildlife in Africa, University of Cape Town, Cape Town, South Africa
| | - Samuel T Osinubi
- Białowieża Geobotanical Station, Faculty of Biology, University of Warsaw, Białowieża, Poland
| | - Daniel M Parker
- School of Biology and Environmental Science, University of Mpumalanga, Mbombela, South Africa
| | - Francesca Parrini
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mike J S Peel
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Animal Production Institute, Rangeland Ecology, Agricultural Research Council, Pretoria, South Africa
- College of Agriculture and Environmental Sciences: Department of Environmental Sciences (ABEERU), University of South Africa, Pretoria, South Africa
| | - Johannes Penner
- Frogs & Friends, Berlin, Germany
- Chair of Wildlife Ecology & Management, University of Freiburg, Freiburg, Germany
| | - Darren W Pietersen
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Andrew J Plumptre
- KBA Secretariat, c/o BirdLife International, Cambridge, United Kingdom
| | - Damian W Ponsonby
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stefan Porembski
- Institute of Biosciences, Department of Botany, University of Rostock, Rostock, Germany
| | - R John Power
- Department of Economic Development, Environment, Conservation & Tourism, North West Provincial Government, Mahikeng, South Africa
| | - Frans G T Radloff
- Department of Conservation and Marine Sciences, Cape Peninsula University of Technology, Cape Town, South Africa
| | - Ramugondo V Rambau
- Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Tharmalingam Ramesh
- Division of Conservation Ecology, Sálim Ali Centre for Ornithology and Natural History, Coimbatore, India
| | - Leigh R Richards
- Mammalogy Department, Durban Natural Science Museum, Durban, South Africa
| | - Mark-Oliver Rödel
- Herpetology, Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Dominic P Rollinson
- FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch, South Africa
| | - Francesco Rovero
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | | | | | - M Corrie Schoeman
- School of Life Sciences, University of KwaZulu Natal, Durban, South Africa
| | - Paul Scholte
- Gesellschaft fuer Internationale Zusammenarbeit (GIZ), Addis Ababa, Ethiopia
| | - Thomas L Serfass
- Department of Biology and Natural Resources, Frostburg State University, Frostburg, USA
| | - Julie Teresa Shapiro
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Lyon, France
| | - Sidney Shema
- Ornithology Section, Zoology Department, National Museums of Kenya, Nairobi, Kenya
| | - Stefan J Siebert
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Jasper A Slingsby
- Fynbos Node of the South African Environmental Observation Network, Cape Town, South Africa
- Biological Sciences and Centre for Statistics in Ecology, Environment and Conservation, University of Cape Town, Cape Town, South Africa
| | | | - Hanneline A Smit-Robinson
- Conservation Division, BirdLife South Africa, Johannesburg, South Africa
- Applied Behavioural Ecological & Ecosystem Research Unit (ABEERU), University of South Africa, Florida, South Africa
| | | | - Michael J Somers
- Mammal Research Institute, Centre for Invasion Biology, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | | | - Jarryd P Streicher
- Centre for Functional Biodiversity, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Lourens Swanepoel
- Department of Biology, University of Venda, Thohoyandou, South Africa
| | - Iroro Tanshi
- Small Mammal Conservation Organization, Benin City, Nigeria
- Biology, University of Washington, Seattle, USA
| | - Peter J Taylor
- Zoology and Entomology, University of the Free State, Qwaqwa campus, Phuthaditjhaba, South Africa
| | | | - Mariska Te Beest
- Centre for African Conservation Ecology, Nelson Mandela University, Gqeberha, South Africa
- Grasslands-Forests-Wetlands Node of the South African Environmental Observation Network, Pietermaritzburg, South Africa
| | | | - Dave I Thompson
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Ndlovu Node of the South African Environmental Observation Network, Phalaborwa, South Africa
| | - Elie Tobi
- Gabon Biodiversity Program, Smithsonian National Zoo and Conservation Biology Institute, Center for Conservation and Sustainability, Gamba, Gabon
| | - Krystal A Tolley
- South African National Biodiversity Institute, Cape Town, South Africa
| | - Andrew A Turner
- Biodiversity Capabilities Directorate, CapeNature, Cape Town, South Africa
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Cape Town, South Africa
| | - Wayne Twine
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Victor Van Cakenberghe
- FunMorph Lab, Department of Biology, University of Antwerp, Antwerp, Belgium
- AfricanBats NPC, Centurion, South Africa
| | | | - Helga van der Merwe
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
- Arid Lands Node of the South African Environmental Observation Network, Kimberley, South Africa
| | - Chris J G van Niekerk
- NWU Botanical Garden, School of Biological Sciences, North-West University, Potchefstroom, South Africa
| | - Pieter C V van Wyk
- Richtersveld Desert Botanical Gardens, Richtersveld National Park, SANParks, Sendelingsdrift, South Africa
| | - Jan A Venter
- Department of Conservation Management, Nelson Mandela University, George, South Africa
| | - Luke Verburgt
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Geraldine Veron
- Institut de Systématique, Evolution, Biodiversité, Muséum National d'Histoire Naturelle, Paris, France
| | - Susanne Vetter
- Department of Botany, Rhodes University, Makhanda, South Africa
| | - Maria S Vorontsova
- Accelerated Taxonomy, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Thomas C Wagner
- Restoration Ecology, Technische Universität München, Freising, Germany
| | - Paul W Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya
| | - Natalie Weber
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Ecological Consultant, Fürth, Germany
| | - Sina M Weier
- SARChI (NRF-DST) Research Chair on Biodiversity Value and Change, University of Venda, Thohoyandou, South Africa
| | - Paula A White
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, USA
| | - Melissa A Whitecross
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Landscape Conservation Programme, BirdLife South Africa, Johannesburg, South Africa
| | - Benjamin J Wigley
- Plant Ecology, University of Bayreuth, Bayreuth, Germany
- School of Natural Resource Management, Nelson Mandela University, George, South Africa
- Scientific Services, South African National Parks, Skukuza, South Africa
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Balboa RF, Bertola LD, Brüniche-Olsen A, Rasmussen MS, Liu X, Besnard G, Salmona J, Santander CG, He S, Zinner D, Pedrono M, Muwanika V, Masembe C, Schubert M, Kuja J, Quinn L, Garcia-Erill G, Stæger FF, Rakotoarivony R, Henrique M, Lin L, Wang X, Heaton MP, Smith TPL, Hanghøj K, Sinding MHS, Atickem A, Chikhi L, Roos C, Gaubert P, Siegismund HR, Moltke I, Albrechtsen A, Heller R. African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival. Nat Commun 2024; 15:172. [PMID: 38172616 PMCID: PMC10764920 DOI: 10.1038/s41467-023-44105-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions, a perceived lack of interbreeding at contact, and putatively old divergence times, but historically, they were considered conspecific. Moreover, the presence of Malagasy bushpigs as the sole large terrestrial mammal shared with the African mainland raises intriguing questions about its origin and arrival in Madagascar. Analyses of 67 whole genomes revealed a genetic continuum between the two species, with putative signatures of historical gene flow, variable FST values, and a recent divergence time (<500,000 years). Thus, our study challenges key arguments for splitting Potamochoerus into two species and suggests their speciation might be incomplete. Our findings also indicate that Malagasy bushpigs diverged from southern African populations and underwent a limited bottleneck 1000-5000 years ago, concurrent with human arrival in Madagascar. These results shed light on the evolutionary history of an iconic and widespread African mammal and provide insight into the longstanding biogeographic puzzle surrounding the bushpig's presence in Madagascar.
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Affiliation(s)
- Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Guillaume Besnard
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
| | - Jordi Salmona
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shixu He
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Dietmar Zinner
- Cognitive Ecology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077, Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077, Göttingen, Germany
- Leibniz Science Campus Primate Cognition, 37077, Göttingen, Germany
| | - Miguel Pedrono
- UMR ASTRE, CIRAD, Campus International de Baillarguet, Montpellier, France
| | - Vincent Muwanika
- College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
| | - Charles Masembe
- College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Mikkel Schubert
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Anagaw Atickem
- Department of Zoological Sciences, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
| | - Lounès Chikhi
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077, Göttingen, Germany
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | | | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Chaber AL, Moloney GK, Renault V, Morrison-Lanjouw S, Garigliany M, Flandroy L, Pires D, Busoni V, Saegerman C, Gaubert P. Examining the international bushmeat traffic in Belgium: A threat to conservation and public health. One Health 2023; 17:100605. [PMID: 37577053 PMCID: PMC10416026 DOI: 10.1016/j.onehlt.2023.100605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/15/2023] Open
Abstract
The carriage of bushmeat into the European Union is an infringement of EU Animal Health and Wildlife Trade legislation and poses a threat to biodiversity and public health. To explore the nature and scale of the international bushmeat trade, seized leaking luggage and passengers arriving at Brussels Zaventem airport from sub-Saharan Africa between 2017 and 2018 were searched for "meat" (bushmeat and livestock) by border control authorities. Visual identification, radiography and genetic analysis were applied to derive information from seized specimens, including at least ten CITES-listed species. We estimate that an average of 3.9 t of bushmeat is smuggled monthly through Brussels. The average consignment of meat seized per passenger was 2.8 kg and 4 kg of bushmeat or domestic livestock meat, respectively. The international trafficking of bushmeat is evidently active, yet penalties are rarely enforced; hence we provide suggestions to simplify law enforcement procedures.
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Affiliation(s)
- Anne-Lise Chaber
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA, Australia
- Global One Health Alliance Pty Ltd, West Lakes Shore, SA 5021, Australia
| | - Georgia Kate Moloney
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA, Australia
- Global One Health Alliance Pty Ltd, West Lakes Shore, SA 5021, Australia
| | - Veronique Renault
- Faculty Veterinary Medicine of the University of Liège, Fundamental and Applied Research for Animals & Health, Avenue de Cureghem, 4000 Liège, Belgium
| | - Sandrella Morrison-Lanjouw
- University of Utrecht, Julius Center, Utrecht, The Netherlands
- Institute for Risk Assessment Sciences (IRAS), Utrecht, The Netherlands
| | - Mutien Garigliany
- Faculty Veterinary Medicine of the University of Liège, Fundamental and Applied Research for Animals & Health, Avenue de Cureghem, 4000 Liège, Belgium
| | - Lucette Flandroy
- Retired from the Belgian Federal Public Service Health, Food Chain Safety and Environment, DG Environment, Belgium
| | - Daniel Pires
- Faculty of Science, University of Porto, Rua do Campo Alegre 1021 1055, 4169-007 Porto, Portugal
- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal
| | - Valeria Busoni
- Faculty Veterinary Medicine of the University of Liège, Fundamental and Applied Research for Animals & Health, Avenue de Cureghem, 4000 Liège, Belgium
| | - Claude Saegerman
- Faculty Veterinary Medicine of the University of Liège, Fundamental and Applied Research for Animals & Health, Avenue de Cureghem, 4000 Liège, Belgium
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique, IRD/CNRS/UPS, Université Toulouse III Paul Sabatier – Bâtiment 4R1, 118 route de Narbonne, 31062 Toulouse cedex 9, France
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Heighton SP, Allio R, Murienne J, Salmona J, Meng H, Scornavacca C, Bastos ADS, Njiokou F, Pietersen DW, Tilak MK, Luo SJ, Delsuc F, Gaubert P. Pangolin Genomes Offer Key Insights and Resources for the World's Most Trafficked Wild Mammals. Mol Biol Evol 2023; 40:msad190. [PMID: 37794645 PMCID: PMC10551234 DOI: 10.1093/molbev/msad190] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023] Open
Abstract
Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and purported medicinal properties. Despite their conservation concern, knowledge of their evolution is limited by a paucity of genomic data. We aim to produce exhaustive genomic resources that include 3,238 orthologous genes and whole-genome polymorphisms to assess the evolution of all eight extant pangolin species. Robust orthologous gene-based phylogenies recovered the monophyly of the three genera and highlighted the existence of an undescribed species closely related to Southeast Asian pangolins. Signatures of middle Miocene admixture between an extinct, possibly European, lineage and the ancestor of Southeast Asian pangolins, provide new insights into the early evolutionary history of the group. Demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental versus island populations and species lineages, suggesting that conservation planning should consider intraspecific patterns. With the expected loss of genomic diversity from recent, extensive trafficking not yet realized in pangolins, we recommend that populations be genetically surveyed to anticipate any deleterious impact of the illegal trade. Finally, we produce a complete set of genomic resources that will be integral for future conservation management and forensic endeavors for pangolins, including tracing their illegal trade. These comprise the completion of whole-genomes for pangolins through the hybrid assembly of the first reference genome for the giant pangolin (Smutsia gigantea) and new draft genomes (∼43x-77x) for four additional species, as well as a database of orthologous genes with over 3.4 million polymorphic sites.
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Affiliation(s)
- Sean P Heighton
- Laboratoire Evolution et Diversité Biologique (EDB)— IRD-UPS-CNRS, Université Toulouse III, Toulouse, France
| | - Rémi Allio
- Institut des Sciences de l'Évolution de Montpellier (ISEM), Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité Biologique (EDB)— IRD-UPS-CNRS, Université Toulouse III, Toulouse, France
| | - Jordi Salmona
- Laboratoire Evolution et Diversité Biologique (EDB)— IRD-UPS-CNRS, Université Toulouse III, Toulouse, France
| | - Hao Meng
- The State Key Laboratory of Protein and Plant Gene Research of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Céline Scornavacca
- Institut des Sciences de l'Évolution de Montpellier (ISEM), Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Armanda D S Bastos
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Pretoria, South Africa
| | - Flobert Njiokou
- Laboratoire de Parasitologie et Ecologie, Faculté des Sciences, Université de Yaoundé I, Yaoundé, Cameroon
| | - Darren W Pietersen
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Pretoria, South Africa
| | - Marie-Ka Tilak
- Institut des Sciences de l'Évolution de Montpellier (ISEM), Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Frédéric Delsuc
- Institut des Sciences de l'Évolution de Montpellier (ISEM), Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique (EDB)— IRD-UPS-CNRS, Université Toulouse III, Toulouse, France
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade 16 do Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal
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6
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Gu TT, Wu H, Yang F, Gaubert P, Heighton SP, Fu Y, Liu K, Luo SJ, Zhang HR, Hu JY, Yu L. Genomic analysis reveals a cryptic pangolin species. Proc Natl Acad Sci U S A 2023; 120:e2304096120. [PMID: 37748052 PMCID: PMC10556634 DOI: 10.1073/pnas.2304096120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 07/26/2023] [Indexed: 09/27/2023] Open
Abstract
Eight extant species of pangolins are currently recognized. Recent studies found that two mitochondrial haplotypes identified in confiscations in Hong Kong could not be assigned to any known pangolin species, implying the existence of a species. Here, we report that two additional mitochondrial haplotypes identified in independent confiscations from Yunnan align with the putative species haplotypes supporting the existence of this mysterious species/population. To verify the new species scenario we performed a comprehensive analysis of scale characteristics and 138 whole genomes representing all recognized pangolin species and the cryptic new species, 98 of which were generated here. Our morphometric results clearly attributed this cryptic species to Asian pangolins (Manis sp.) and the genomic data provide robust and compelling evidence that it is a pangolin species distinct from those recognized previously, which separated from the Philippine pangolin and Malayan pangolin over 5 Mya. Our study provides a solid genomic basis for its formal recognition as the ninth pangolin species or the fifth Asian one, supporting a new taxonomic classification of pangolins. The effects of glacial climate changes and recent anthropogenic activities driven by illegal trade are inferred to have caused its population decline with the genomic signatures showing low genetic diversity, a high level of inbreeding, and high genetic load. Our finding greatly expands current knowledge of pangolin diversity and evolution and has vital implications for conservation efforts to prevent the extinction of this enigmatic and endangered species from the wild.
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Affiliation(s)
- Tong-Tong Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
| | - Hong Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
| | - Feng Yang
- Kadoorie Farm and Botanic Garden, Tai Po, Hong Kong Special Administrative Region999077, China
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique, Université Toulouse III–Paul Sabatier, 31062Toulouse Cedex 9, France
- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Porto4450-208, Portugal
| | - Sean P. Heighton
- Laboratoire Evolution et Diversité Biologique, Université Toulouse III–Paul Sabatier, 31062Toulouse Cedex 9, France
| | - Yeyizhou Fu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
| | - Ke Liu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
| | - Hua-Rong Zhang
- Kadoorie Farm and Botanic Garden, Tai Po, Hong Kong Special Administrative Region999077, China
| | - Jing-Yang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
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Gossé KJ, Gonedelé-Bi S, Justy F, Chaber AL, Kramoko B, Gaubert P. DNA-typing surveillance of the bushmeat in Côte d'Ivoire: a multi-faceted tool for wildlife trade management in West Africa. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01474-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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8
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Gonedelé Bi S, Kramoko B, Bené J, Koné I, Luiselli L, Gaubert P. Year-round longitudinal monitoring of a bushmeat market in central-western Côte d’Ivoire: implication for wildlife conservation. J Nat Conserv 2022. [DOI: 10.1016/j.jnc.2022.126297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Salmona J, Dayon J, Lecompte E, Karamanlidis AA, Aguilar A, Fernandez de Larrinoa P, Pires R, Mo G, Panou A, Agnesi S, Borrell A, Danyer E, Öztürk B, Tonay AM, Anestis AK, González LM, Dendrinos P, Gaubert P. The antique genetic plight of the Mediterranean monk seal ( Monachus monachus). Proc Biol Sci 2022; 289:20220846. [PMID: 36043283 PMCID: PMC9428542 DOI: 10.1098/rspb.2022.0846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 07/30/2022] [Indexed: 12/14/2022] Open
Abstract
Disentangling the impact of Late Quaternary climate change from human activities can have crucial implications on the conservation of endangered species. We investigated the population genetics and demography of the Mediterranean monk seal (Monachus monachus), one of the world's most endangered marine mammals, through an unprecedented dataset encompassing historical (extinct) and extant populations from the eastern North Atlantic to the entire Mediterranean Basin. We show that Cabo Blanco (Western Sahara/Mauritania), Madeira, Western Mediterranean (historical range) and Eastern Mediterranean regions segregate into four populations. This structure is probably the consequence of recent drift, combined with long-term isolation by distance (R2 = 0.7), resulting from prevailing short-distance (less than 500 km) and infrequent long-distance dispersal (less than 1500 km). All populations (Madeira especially), show high levels of inbreeding and low levels of genetic diversity, seemingly declining since historical time, but surprisingly not being impacted by the 1997 massive die-off in Cabo Blanco. Approximate Bayesian Computation analyses support scenarios combining local extinctions and a major effective population size decline in all populations during Antiquity. Our results suggest that the early densification of human populations around the Mediterranean Basin coupled with the development of seafaring techniques were the main drivers of the decline of Mediterranean monk seals.
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Affiliation(s)
- Jordi Salmona
- Laboratoire Évolution et Diversité Biologique, IRD-CNRS-UPS, Université Paul Sabatier, 118 route de Narbonne, Toulouse 31062, France
| | - Julia Dayon
- Laboratoire Évolution et Diversité Biologique, IRD-CNRS-UPS, Université Paul Sabatier, 118 route de Narbonne, Toulouse 31062, France
- CEFE, Université de Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - Emilie Lecompte
- Laboratoire Évolution et Diversité Biologique, IRD-CNRS-UPS, Université Paul Sabatier, 118 route de Narbonne, Toulouse 31062, France
| | - Alexandros A. Karamanlidis
- MOm/Hellenic Society for the Study and Protection of the Monk seal, Solomou Strasse 18, Athens 10682, Greece
| | - Alex Aguilar
- IRBio and Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain
| | | | - Rosa Pires
- Instituto das Florestas e Conservação da Natureza IP-RAM, Jardim Botânico da Madeira, Caminho do Meio, Bom Sucesso, Funchal, Madeira 9064-512, Portugal
| | - Giulia Mo
- Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Via Vitaliano Brancati 48, Rome 00144, Italy
| | - Aliki Panou
- Archipelagos - Environment and Development, Lourdata, Kefalonia 28100, Greece
| | - Sabrina Agnesi
- Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Via Vitaliano Brancati 48, Rome 00144, Italy
| | - Asunción Borrell
- IRBio and Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain
| | - Erdem Danyer
- Turkish Marine Research Foundation (TUDAV), PO Box 10, Beykoz, Istanbul, Turkey
| | - Bayram Öztürk
- Turkish Marine Research Foundation (TUDAV), PO Box 10, Beykoz, Istanbul, Turkey
- Faculty of Aquatic Sciences, Istanbul University, Kalenderhane Mah. Onaltı Mart Şehitleri Cad. No: 2 Fatih 34134 Istanbul, Turkey
| | - Arda M. Tonay
- Turkish Marine Research Foundation (TUDAV), PO Box 10, Beykoz, Istanbul, Turkey
- Faculty of Aquatic Sciences, Istanbul University, Kalenderhane Mah. Onaltı Mart Şehitleri Cad. No: 2 Fatih 34134 Istanbul, Turkey
| | | | - Luis M. González
- Subdirección General de Biodiversidad Terrestre y Marina, Ministerio para la Transición Ecológica y el Reto Demográfico, Pza. San Juan de la Cruz, 10, Madrid 28071, Spain
| | - Panagiotis Dendrinos
- MOm/Hellenic Society for the Study and Protection of the Monk seal, Solomou Strasse 18, Athens 10682, Greece
| | - Philippe Gaubert
- Laboratoire Évolution et Diversité Biologique, IRD-CNRS-UPS, Université Paul Sabatier, 118 route de Narbonne, Toulouse 31062, France
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10
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Garcia-Erill G, Jørgensen CHF, Muwanika VB, Wang X, Rasmussen MS, de Jong YA, Gaubert P, Olayemi A, Salmona J, Butynski TM, Bertola LD, Siegismund HR, Albrechtsen A, Heller R. Warthog Genomes Resolve an Evolutionary Conundrum and Reveal Introgression of Disease Resistance Genes. Mol Biol Evol 2022; 39:6627297. [PMID: 35779009 PMCID: PMC9250280 DOI: 10.1093/molbev/msac134] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
African wild pigs have a contentious evolutionary and biogeographic history. Until recently, desert warthog (Phacochoerus aethiopicus) and common warthog (P. africanus) were considered a single species. Molecular evidence surprisingly suggested they diverged at least 4.4 million years ago, and possibly outside of Africa. We sequenced the first whole-genomes of four desert warthogs and 35 common warthogs from throughout their range. We show that these two species diverged much later than previously estimated, 400,000–1,700,000 years ago depending on assumptions of gene flow. This brings it into agreement with the paleontological record. We found that the common warthog originated in western Africa and subsequently colonized eastern and southern Africa. During this range expansion, the common warthog interbred with the desert warthog, presumably in eastern Africa, underlining this region’s importance in African biogeography. We found that immune system–related genes may have adaptively introgressed into common warthogs, indicating that resistance to novel diseases was one of the most potent drivers of evolution as common warthogs expanded their range. Hence, we solve some of the key controversies surrounding warthog evolution and reveal a complex evolutionary history involving range expansion, introgression, and adaptation to new diseases.
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Affiliation(s)
- Genís Garcia-Erill
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Christian H F Jørgensen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Vincent B Muwanika
- Department of Environmental Management, Makerere University, PO Box 7062, Kampala, Uganda
| | - Xi Wang
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Malthe S Rasmussen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Yvonne A de Jong
- Eastern Africa Primate Diversity and Conservation Program & Lolldaiga Hills Research Programme, PO Box 149, Nanyuki 10400, Kenya
| | - Philippe Gaubert
- Laboratoire Évolution & Diversité Biologique, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, HO 220005 Ile Ife, Nigeria
| | - Jordi Salmona
- Laboratoire Évolution & Diversité Biologique, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Thomas M Butynski
- Eastern Africa Primate Diversity and Conservation Program & Lolldaiga Hills Research Programme, PO Box 149, Nanyuki 10400, Kenya
| | - Laura D Bertola
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Anders Albrechtsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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11
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Choo SW, Chong JL, Gaubert P, Hughes AC, O'Brien S, Chaber AL, Antunes A, Platto S, Sun NCM, Yu L, Koepfli KP, Suwal TL, Thakur M, Ntie S, Panjang E, Kumaran JV, Mahmood T, Heighton SP, Dorji D, Gonedelé BS, Nelson BR, Djagoun CAMS, Loh IH, Kaspal P, Pauklin S, Michelena T, Zhu H, Lipovich L, Tian X, Deng S, Mason CE, Hu J, White R, Jakubovics NS, Wee WY, Tan TK, Wong KT, Paterson S, Chen M, Zhang Y, Othman RY, Brown LC, Shen B, Shui G, Ang MY, Zhao Y, Li Y, Zhang B, Chong CT, Meng Y, Wong A, Su J, Omar H, Shen H, Tan CH, Xu H, Paterson IC, Wang M, Chan CK, Zhang S, Dutta A, Tee TS, Juvigny-Khenafou NPD, Mutha NVR, Aziz MA. A collective statement in support of saving pangolins. Sci Total Environ 2022; 824:153666. [PMID: 35176378 DOI: 10.1016/j.scitotenv.2022.153666] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Siew Woh Choo
- College of Science and Technology, Wenzhou-Kean University, Zhejiang Province, China; Zhejiang Bioinformatics International Science and Technology Cooperation Centre, Wenzhou-Kean University, Wenzhou, Zhejiang, China.
| | - Ju Lian Chong
- Faculty of Science & Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia; IUCN SSC Pangolin Specialist Group, C/O Zoological Society of London, Regents Park, London NW1 4RY, UK.
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique, IRD/CNRS/UPS, Université Paul Sabatier, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France
| | - Alice Catherine Hughes
- Biodiversity Conservation and Green Development Foundation (CBCGDF), Empark International Apartment, No. 69, Banding Road, Haidian District, Beijing, China
| | - Stephen O'Brien
- Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO University, St. Petersburg 197101, Russia; Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, Nova Southeastern University, 8000 North Ocean Drive, Ft Lauderdale, FL 33004, USA
| | - Anne-Lise Chaber
- School of Animal and Veterinary Science, Roseworthy campus, University of Adelaide, 5371 Roseworthy, South Australia, Australia
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Sara Platto
- Department of Biotechnology, College of Life Sciences, Jianghan University, Wuhan, Hubei, China
| | - Nick Ching-Min Sun
- Department of Entomology, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Klaus-Peter Koepfli
- Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO University, St. Petersburg 197101, Russia; Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA; Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC 20008, USA
| | - Tulshi Laxmi Suwal
- Small Mammal Conservation and Research Foundation, Balkhu Bandhudatta Marg, Kathmandu, Nepal
| | - Mukesh Thakur
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Stephan Ntie
- Laboratoire de Biologie Moléculaire et Cellulaire (LABMC), Département de Biologie, Université des Sciences et Techniques de Masuku (USTM), BP 941 Franceville, Gabon
| | - Elisa Panjang
- IUCN SSC Pangolin Specialist Group, C/O Zoological Society of London, Regents Park, London NW1 4RY, UK; Danau Girang Field Centre, Sabah, Malaysia; School of Biosciences, Cardiff University, UK
| | - Jayaraj Vijaya Kumaran
- Faculty of Earth Science, Universiti Malaysia Kelantan, UMK Jeli Campus, Jeli, Kelantan, Malaysia
| | - Tariq Mahmood
- IUCN SSC Pangolin Specialist Group, C/O Zoological Society of London, Regents Park, London NW1 4RY, UK; Department of Wildlife Management, PMAS Arid Agricultural University Rawalpindi, Pakistan
| | - Sean P Heighton
- Laboratoire Evolution et Diversité Biologique, IRD/CNRS/UPS, Université Paul Sabatier, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France
| | - Dago Dorji
- Division Forest Office, Sarpang Department of Forests and Park Services, Ministry of Agriculture and Forests, Bhutan
| | - Bi Sery Gonedelé
- Laboratory of Biotechnology, Agriculture and Valorization of Biological Resources, UFR Biosciences, University Félix Houphouët Boigny, Abidjan, Côte d'Ivoire
| | - Bryan Raveen Nelson
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | | | - Ing Hoe Loh
- School of Business and Management, RMIT University Vietnam, Handi Resco Building, 521 Kim Ma, Ba Dinh District, Hanoi, Viet Nam
| | - Prativa Kaspal
- Women for Conservation & Bhaktapur Multiple Campus, Nepal
| | - Siim Pauklin
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Oxford OX3 7LD, UK
| | - Toby Michelena
- College of Science and Technology, Wenzhou-Kean University, Zhejiang Province, China
| | - Hongxiang Zhu
- Bossco Institute of Ecological Environment, Guangxi University, Nanning 530004, China
| | - Leonard Lipovich
- Department of Basic Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Xuechen Tian
- College of Science and Technology, Wenzhou-Kean University, Zhejiang Province, China; Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Siwei Deng
- Botnar Research Centre, University of Oxford, Windmill Road, Oxford OX3 7LD, UK
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Ave., New York, NY 10021, USA
| | - Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Robert White
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing St, Cambridge CB2 3DY, UK
| | - Nicholas S Jakubovics
- School of Dental Sciences, Faculty of Medical Sciences, Framlington Place, Newcastle University, Newcastle-upon-Tyne NE2 4BW, UK
| | - Wei Yee Wee
- School of Science, Monash University Malaysia, 47500 Bandar Sunway, Malaysia
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Kum Thong Wong
- Department of Pathology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Steve Paterson
- Centre for Genomic Research, University of Liverpool, Liverpool L69 7ZB, UK
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou 310058, China
| | - Yixin Zhang
- Research Center of Cultural Landscape Protection and Ecological Restoration, The Sino-Portugal Joint Laboratory of Cultural Heritage Conservation Science Supported by the Belt and Road Initiative, Soochow University, Suzhou, Jiangsu 215123, China
| | - Rofina Yasmin Othman
- Centre for Research in Biotechnology for Agriculture, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Larry C Brown
- College of Science and Technology, Wenzhou-Kean University, Zhejiang Province, China
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Xinchuan Road 2222, Chengdu, Sichuan, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Mia Yang Ang
- Department of Clinical Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yunqi Zhao
- College of Science and Technology, Wenzhou-Kean University, Zhejiang Province, China
| | - Yongming Li
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, Wirral CH64 7TE, UK
| | - Bo Zhang
- College of Science and Technology, Wenzhou-Kean University, Zhejiang Province, China; Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Cheng Tung Chong
- China-UK Low Carbon College, Shanghai Jiao Tong University, Lingang, Shanghai 201306, China
| | - Yu Meng
- College of Science and Technology, Wenzhou-Kean University, Zhejiang Province, China
| | - Aloysius Wong
- College of Science and Technology, Wenzhou-Kean University, Zhejiang Province, China; Zhejiang Bioinformatics International Science and Technology Cooperation Centre, Wenzhou-Kean University, Wenzhou, Zhejiang, China
| | - Jianzhong Su
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Hasmahzaiti Omar
- Museum of Zoology (Block J14), Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia; Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Hua Shen
- College of Science and Technology, Wenzhou-Kean University, Zhejiang Province, China
| | - Choo Hock Tan
- Department of Pharmacology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Hongyu Xu
- College of Science and Technology, Wenzhou-Kean University, Zhejiang Province, China
| | - Ian C Paterson
- Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University Malaya, 50603 Kuala Lumpur, Malaysia
| | - Minyan Wang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Ren'ai Road, Suzhou 215123, China
| | - Chee-Kai Chan
- College of Science and Technology, Wenzhou-Kean University, Zhejiang Province, China
| | - Siyuan Zhang
- Pangolin Working Group, Biodiversity Conservation and Green Development Foundation (CBCGDF), Empark International Apartment, No. 69, Banding Road, Haidian District, Beijing, China
| | - Avirup Dutta
- Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia
| | - Tay Sun Tee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Noël P D Juvigny-Khenafou
- Quantitative Landscape Ecology, Institute for Environmental Sciences, University Koblenz-Landau, Fortstrasse 7, 76829 Landau in der Pfalz, Germany
| | - Naresh V R Mutha
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Muhamad Afiq Aziz
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
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12
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Marsh CJ, Sica YV, Burgin CJ, Dorman WA, Anderson RC, del Toro Mijares I, Vigneron JG, Barve V, Dombrowik VL, Duong M, Guralnick R, Hart JA, Maypole JK, McCall K, Ranipeta A, Schuerkmann A, Torselli MA, Lacher T, Mittermeier RA, Rylands AB, Sechrest W, Wilson DE, Abba AM, Aguirre LF, Arroyo‐Cabrales J, Astúa D, Baker AM, Braulik G, Braun JK, Brito J, Busher PE, Burneo SF, Camacho MA, Cavallini P, de Almeida Chiquito E, Cook JA, Cserkész T, Csorba G, Cuéllar Soto E, da Cunha Tavares V, Davenport TRB, Deméré T, Denys C, Dickman CR, Eldridge MDB, Fernandez‐Duque E, Francis CM, Frankham G, Franklin WL, Freitas T, Friend JA, Gadsby EL, Garbino GST, Gaubert P, Giannini N, Giarla T, Gilchrist JS, Gongora J, Goodman SM, Gursky‐Doyen S, Hackländer K, Hafner MS, Hawkins M, Helgen KM, Heritage S, Hinckley A, Hintsche S, Holden M, Holekamp KE, Honeycutt RL, Huffman BA, Humle T, Hutterer R, Ibáñez Ulargui C, Jackson SM, Janecka J, Janecka M, Jenkins P, Juškaitis R, Juste J, Kays R, Kilpatrick CW, Kingston T, Koprowski JL, Kryštufek B, Lavery T, Lee TE, Leite YLR, Novaes RLM, Lim BK, Lissovsky A, López‐Antoñanzas R, López‐Baucells A, MacLeod CD, Maisels FG, Mares MA, Marsh H, Mattioli S, Meijaard E, Monadjem A, Morton FB, Musser G, Nadler T, Norris RW, Ojeda A, Ordóñez‐Garza N, Pardiñas UFJ, Patterson BD, Pavan A, Pennay M, Pereira C, Prado J, Queiroz HL, Richardson M, Riley EP, Rossiter SJ, Rubenstein DI, Ruelas D, Salazar‐Bravo J, Schai‐Braun S, Schank CJ, Schwitzer C, Sheeran LK, Shekelle M, Shenbrot G, Soisook P, Solari S, Southgate R, Superina M, Taber AB, Talebi M, Taylor P, Vu Dinh T, Ting N, Tirira DG, Tsang S, Turvey ST, Valdez R, Van Cakenberghe V, Veron G, Wallis J, Wells R, Whittaker D, Williamson EA, Wittemyer G, Woinarski J, Zinner D, Upham NS, Jetz W. Expert range maps of global mammal distributions harmonised to three taxonomic authorities. J Biogeogr 2022; 49:979-992. [PMID: 35506011 PMCID: PMC9060555 DOI: 10.1111/jbi.14330] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 01/05/2022] [Accepted: 01/13/2022] [Indexed: 06/01/2023]
Abstract
AIM Comprehensive, global information on species' occurrences is an essential biodiversity variable and central to a range of applications in ecology, evolution, biogeography and conservation. Expert range maps often represent a species' only available distributional information and play an increasing role in conservation assessments and macroecology. We provide global range maps for the native ranges of all extant mammal species harmonised to the taxonomy of the Mammal Diversity Database (MDD) mobilised from two sources, the Handbook of the Mammals of the World (HMW) and the Illustrated Checklist of the Mammals of the World (CMW). LOCATION Global. TAXON All extant mammal species. METHODS Range maps were digitally interpreted, georeferenced, error-checked and subsequently taxonomically aligned between the HMW (6253 species), the CMW (6431 species) and the MDD taxonomies (6362 species). RESULTS Range maps can be evaluated and visualised in an online map browser at Map of Life (mol.org) and accessed for individual or batch download for non-commercial use. MAIN CONCLUSION Expert maps of species' global distributions are limited in their spatial detail and temporal specificity, but form a useful basis for broad-scale characterizations and model-based integration with other data. We provide georeferenced range maps for the native ranges of all extant mammal species as shapefiles, with species-level metadata and source information packaged together in geodatabase format. Across the three taxonomic sources our maps entail, there are 1784 taxonomic name differences compared to the maps currently available on the IUCN Red List website. The expert maps provided here are harmonised to the MDD taxonomic authority and linked to a community of online tools that will enable transparent future updates and version control.
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Affiliation(s)
- Charles J. Marsh
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Yanina V. Sica
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Connor J. Burgin
- Department of BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - Wendy A. Dorman
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Robert C. Anderson
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Isabel del Toro Mijares
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Jessica G. Vigneron
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Vijay Barve
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
| | - Victoria L. Dombrowik
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Michelle Duong
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Robert Guralnick
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
| | - Julie A. Hart
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
- New York Natural Heritage ProgramState University of New York College of Environmental Science and ForestryAlbanyNew YorkUSA
| | - J. Krish Maypole
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Kira McCall
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Ajay Ranipeta
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Anna Schuerkmann
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Michael A. Torselli
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Thomas Lacher
- Department of Ecology and Conservation BiologyTexas A&M UniversityCollege StationTexasUSA
- Re:wildAustinTexasUSA
| | | | | | | | - Don E. Wilson
- National Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of ColumbiaUSA
| | - Agustín M. Abba
- Centro de Estudios Parasitológicos y de Vectores (CEPAVE‐UNLP‐CONICET)La Plata, Buenos AiresArgentina
| | - Luis F. Aguirre
- Centro de Biodiversidad y GenéticaUniversidad Mayor de San SimónCochabambaBolivia
| | | | - Diego Astúa
- Departamento de ZoologiaUniversidade Federal de PernambucoRecifePernambucoBrazil
| | - Andrew M. Baker
- School of Biology and Environmental Science, Faculty of ScienceQueensland University of TechnologyBrisbaneQueenslandAustralia
- Biodiversity and Geosciences ProgramQueensland MuseumBrisbaneQueenslandAustralia
| | - Gill Braulik
- School of BiologyUniversity of St. AndrewsSt. Andrews, FifeUK
| | | | - Jorge Brito
- Instituto Nacional de Biodiversidad (INABIO)QuitoEcuador
| | - Peter E. Busher
- College of General StudiesBoston UniversityBostonMassachusettsUSA
| | - Santiago F. Burneo
- Sección Mastozoología, Museo de Zoología, Facultad de Ciencias Exactas y NaturalesPontificia Universidad Católica del EcuadorQuitoEcuador
| | - M. Alejandra Camacho
- Sección Mastozoología, Museo de Zoología, Facultad de Ciencias Exactas y NaturalesPontificia Universidad Católica del EcuadorQuitoEcuador
| | | | | | - Joseph A. Cook
- Museum of Southwestern Biology and Department of BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - Tamás Cserkész
- Department of ZoologyHungarian Natural History MuseumBudapestHungary
| | - Gábor Csorba
- Department of ZoologyHungarian Natural History MuseumBudapestHungary
| | | | - Valeria da Cunha Tavares
- Vale Technological InstituteBelémParáBrazil
- Laboratório de Mamíferos, Departamento de Sistemática e Ecologia, CCEN/DSEUniversidade Federal da ParaíbaJoão PessoaPBBrazil
| | - Tim R. B. Davenport
- Species Conservation & Science (Africa)Wildlife Conservation Society (WCS)ArushaTanzania
| | | | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB)Muséum national d'Histoire naturelle (CNRS)ParisFrance
| | - Christopher R. Dickman
- Desert Ecology Research Group, School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | - Mark D. B. Eldridge
- Australian Museum Research InstituteAustralian MuseumSydneyNew South WalesAustralia
| | - Eduardo Fernandez‐Duque
- Department of Anthropology and School of the EnvironmentYale UniversityNew HavenConnecticutUSA
| | - Charles M. Francis
- Canadian Wildlife ServiceEnvironment and Climate Change CanadaOttawaOntarioCanada
| | - Greta Frankham
- Australian Museum Research InstituteAustralian MuseumSydneyNew South WalesAustralia
| | - William L. Franklin
- Deparment of Natural Resource Ecology and EnvironmentIowa State UniversityAmesIowaUSA
| | - Thales Freitas
- Departamento de GenéticaUniversidade Federal do Rio Grande do SulPorto AlegreRio Grande do SulBrazil
| | - J. Anthony Friend
- Department of BiodiversityConservation and AttractionsAlbanyWestern AustraliaAustralia
| | | | | | - Philippe Gaubert
- Laboratoire Évolution & Diversité BiologiqueUniversité Toulouse III Paul SabatierToulouseFrance
| | - Norberto Giannini
- Unidad Ejecutora LilloCONICET ‐ Fundación Miguel LilloSan Miguel de Tucumán, TucumánArgentina
| | - Thomas Giarla
- Department of BiologySiena CollegeLoudonvilleNew YorkUSA
| | | | - Jaime Gongora
- Sydney School of Veterinary Science, Faculty of ScienceThe University of SydneySydneyNew South WalesAustralia
| | - Steven M. Goodman
- Negaunee Integrative Research Center, Field Museum of Natural HistoryChicagoIllinoisUSA
| | | | - Klaus Hackländer
- Institute of Wildlife Biology and Game ManagementUniversity of Natural Resources and Life SciencesWienAustria
| | - Mark S. Hafner
- Museum of Natural ScienceLouisiana State UniversityBaton RougeLouisianaUSA
| | - Melissa Hawkins
- National Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of ColumbiaUSA
| | - Kristofer M. Helgen
- Australian Museum Research InstituteAustralian MuseumSydneyNew South WalesAustralia
| | - Steven Heritage
- Duke Lemur Center, Museum of Natural HistoryDuke UniversityDurhamNorth CarolinaUSA
| | | | | | - Mary Holden
- Department of MammalogyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | - Kay E. Holekamp
- Department of Integrative BiologyMichigan State UniversityEast LansingMichiganUSA
| | | | | | - Tatyana Humle
- Durrell Institute of Conservation and EcologySchool of Anthropology and Conservation, University of KentCanterburyUK
| | | | | | | | - Jan Janecka
- Department of Biological SciencesDuquesne UniversityPittsburghPennsylvaniaUSA
| | - Mary Janecka
- Department of Biological SciencesUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Paula Jenkins
- Mammal Group, Vertebrates DivisionDepartment of Life Sciences, The Natural History MuseumLondonUK
| | | | | | - Roland Kays
- North Carolina Museum of Natural SciencesRaleighNorth CarolinaUSA
| | | | - Tigga Kingston
- Department of Biological SciencesTexas Tech UniversityLubbockTexasUSA
| | | | | | - Tyrone Lavery
- Fenner School of Environment and SocietyThe Australian National UniversityActonAustralian Capital TerritoryAustralia
| | - Thomas E. Lee
- Department of BiologyAbilene Christian UniversityAbileneTexasUSA
| | - Yuri L. R. Leite
- Departamento de Ciências BiológicasUniversidade Federal do Espírito SantoVitóriaEspiríto SantoBrazil
| | | | - Burton K. Lim
- Department of Natural HistoryRoyal Ontario MuseumTorontoOntarioCanada
| | | | - Raquel López‐Antoñanzas
- Institut des Sciences de l'Évolution de Montpellier (ISE‐M, UMR 5554, UM/CNRS/IRD/EPHE)MontpellierFrance
| | | | | | - Fiona G. Maisels
- Wildlife Conservation SocietyGlobal Conservation ProgramNew YorkNew YorkUSA
- Faculty of Natural SciencesUniversity of StirlingStirlingUK
| | | | - Helene Marsh
- Division of Tropical Environments and SocietiesCentre for Tropical Water and Aquatic Ecosystem Research, James Cook UniversityTownsvilleQueenslandAustralia
| | - Stefano Mattioli
- Research Unit of Behavioural Ecology, Ethology and Wildlife Management, Department of Life SciencesUniversity of SienaSienaItaly
| | - Erik Meijaard
- Borneo FuturesBandar Seri BegawanBABrunei Darussalam
| | - Ara Monadjem
- Department of Biological SciencesUniversity of EswatiniKwaluseniEswatini
- Department of Zoology & Entomology, Mammal Research InstituteUniversity of PretoriaPretoriaSouth Africa
| | | | - Grace Musser
- Jackson School of GeosciencesUniversity of Texas at AustinAustinTexasUSA
| | - Tilo Nadler
- Cuc Phuong CommuneNho Quan DistrictNinh BInh, ProvinceVietnam
| | - Ryan W. Norris
- Evolution, Ecology and Organismal BiologyThe Ohio State UniversityLimaOhioUSA
| | - Agustina Ojeda
- Instituto Argentino de Zonas Áridas (IADIZA)‐CCT Mendoza‐CONICETMendozaArgentina
| | | | | | - Bruce D. Patterson
- Negaunee Integrative Research Center, Field Museum of Natural HistoryChicagoIllinoisUSA
| | - Ana Pavan
- Universidade de São PauloSão PauloBrazil
| | - Michael Pennay
- NSW National Parks and Wildlife ServiceQueanbeyanNew South WalesAustralia
| | | | | | - Helder L. Queiroz
- Instituto de Desenvolvimento Sustentável Mamirauá – IDSMTeféAmazonasBrazil
| | | | - Erin P. Riley
- Department of AnthropologySan Diego State UniversitySan DiegoCaliforniaUSA
| | - Stephen J. Rossiter
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | - Daniel I. Rubenstein
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
| | - Dennisse Ruelas
- Museo de Historia NaturalUniversidad Nacional Mayor de San Marcos, LimaLimaPeru
- Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS‐IRD‐UM)Université de MontpellierMontpellier Cedex 5France
| | | | - Stéphanie Schai‐Braun
- Institute of Wildlife Biology and Game ManagementUniversity of Natural Resources and Life SciencesViennaAustria
| | - Cody J. Schank
- Re:wildAustinTexasUSA
- Department of Geography and the EnvironmentThe University of Texas at AustinAustinTexasUSA
| | | | - Lori K. Sheeran
- Department of Anthropology and Museum StudiesCentral Washington UniversityEllensburgWAUSA
| | - Myron Shekelle
- Department of AnthropologyWestern Washington UniversityBellinghamWAUSA
| | - Georgy Shenbrot
- Mitrani Department of Desert EcologyJacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevMidreshet Ben‐GurionIsrael
| | - Pipat Soisook
- Princess Maha Chakri Sirindhorn Natural History MuseumPrince of Songkhla UniversityHatyai, SongkhlaThailand
| | - Sergio Solari
- Instituto de BiologíaUniversidad de AntioquiaMedellínColombia
| | | | - Mariella Superina
- IMBECU, CCT CONICET Mendoza – UNCuyoParque Gral. San MartínMendozaArgentina
| | - Andrew B. Taber
- Forestry DivisionFood and Agriculture Organization of the United NationsRomeItaly
| | - Maurício Talebi
- Laboratório de Ecologia e Conservação da NaturezaDeptartamento de Ciências AmbientaisUniversidade Federal de São Paulo (UNIFESP) ‐ Campus Diadema, DiademaSão PauloBrazil
| | | | - Thong Vu Dinh
- Institute of Ecology and Biological ResourcesVietnam Academy of Science and TechnologyHanoiVietnam
| | - Nelson Ting
- Department of AnthropologyUniversity of OregonEugeneOregonUSA
| | | | - Susan Tsang
- Department of MammalogyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | | | - Raul Valdez
- Department of Fish, Wildlife, and Conservation EcologyNew Mexico State UniversityLas CrucesNew MexicoUSA
| | - Victor Van Cakenberghe
- Laboratory for Functional Morphology, Biology DepartmentUniversity of Antwerp, Campus Drie EikenAntwerpen (Wilrijk)Belgium
| | - Geraldine Veron
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRSSorbonne Université, EPHE, Université des AntillesParisFrance
| | | | - Rod Wells
- Biological Sciences, College of Science and EngineeringFlinders UniversityAdelaideSouth AustraliaAustralia
| | - Danielle Whittaker
- BEACON Center for the Study of Evolution in ActionMichigan State UniversityEast LansingMichiganUSA
| | | | - George Wittemyer
- Department of Fish, Wildlife and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - John Woinarski
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityCasuarinaNorthern TerritoryAustralia
| | - Dietmar Zinner
- German Primate Center (DPZ)Leibniz Institute for Primate ResearchGöttingenGermany
| | - Nathan S. Upham
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | - Walter Jetz
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
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Djagoun CAMS, Nago G, Azihou AF, Vodouhê F, Agli A, Zanvo S, Djossa B, Assogbadjo A, Sinsin B, Gaubert P. Assessing local knowledge on the diversity and abundance of bushmeat species and hunting pressure in the fragmented forest islands of southern Benin (Dahomey Gap). Afr J Ecol 2022. [DOI: 10.1111/aje.12955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chabi A. M. S. Djagoun
- Laboratory of Applied Ecology Faculty of Agronomic Sciences University of Abomey‐Calavi Cotonou Benin
| | - Gilles Nago
- Laboratoire d’Ecologie de Botanique et de Biologie végétale Faculté d’Agronomie Université de Parakou Parakou République du Bénin
| | - Akomian F. Azihou
- Laboratory of Applied Ecology Faculty of Agronomic Sciences University of Abomey‐Calavi Cotonou Benin
| | - Fifanou Vodouhê
- Laboratoire d’Ecologie de Botanique et de Biologie végétale Faculté d’Agronomie Université de Parakou Parakou République du Bénin
| | - Auriane Agli
- Laboratory of Applied Ecology Faculty of Agronomic Sciences University of Abomey‐Calavi Cotonou Benin
| | - Stanislas Zanvo
- Laboratory of Applied Ecology Faculty of Agronomic Sciences University of Abomey‐Calavi Cotonou Benin
- Unité de Recherche en Foresterie et Conservation des Bioressources (U/RFCBio) Université Nationale d'Agriculture de Porto‐Novo Porto‐Novo Benin
| | - Bruno Djossa
- Laboratory of Applied Ecology Faculty of Agronomic Sciences University of Abomey‐Calavi Cotonou Benin
- Laboratoire Evolution et Diversité Biologique UPS/CNRS/IRD Université Paul Sabatier Toulouse France
| | - Achile Assogbadjo
- Laboratory of Applied Ecology Faculty of Agronomic Sciences University of Abomey‐Calavi Cotonou Benin
| | - Brice Sinsin
- Laboratory of Applied Ecology Faculty of Agronomic Sciences University of Abomey‐Calavi Cotonou Benin
| | - Philippe Gaubert
- Unité de Recherche en Foresterie et Conservation des Bioressources (U/RFCBio) Université Nationale d'Agriculture de Porto‐Novo Porto‐Novo Benin
- CIIMAR Terminal de Cruzeiros Do Porto de Leixoes Avenida General Norton de Matos s/n Matosinhos Portugal
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14
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Zanvo S, Djagoun CAMS, Azihou AF, Djossa B, Afiademanyo K, Olayemi A, Agbangla C, Sinsin B, Gaubert P. Can DNA help trace the local trade of pangolins? Conservation genetics of white-bellied pangolins from the Dahomey Gap (West Africa). BMC Ecol Evol 2022; 22:16. [PMID: 35164675 PMCID: PMC8842964 DOI: 10.1186/s12862-022-01971-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/21/2022] [Indexed: 11/20/2022] Open
Abstract
Background African pangolins are currently experiencing unprecedented levels of harvesting, feeding both local demands and the illegal international trade. So far, the lack of knowledge on the population genetics of African pangolins has hampered any attempts at assessing their demographic status and tracing their trade at the local scale. We conducted a pioneer study on the genetic tracing of the African pangolin trade in the Dahomey Gap (DG). We sequenced and genotyped 189 white-bellied pangolins from 18 forests and 12 wildlife markets using one mitochondrial fragment and 20 microsatellite loci. Results Tree-based assignment procedure showed that the pangolin trade is endemic to the DG region, as it was strictly fed by the the Dahomey Gap lineage (DGL). DGL populations were characterized by low levels of genetic diversity, an overall absence of equilibrium, important inbreeding levels, and lack of geographic structure. We identified a 92–98% decline in DGL effective population size 200–500 ya—concomitant with major political transformations along the ‘Slave Coast’—leading to contemporaneous estimates being inferior to minimum viable population size (< 500). Genetic tracing suggested that wildlife markets from the DG sourced pangolins through the entire DGL range. Our loci provided the necessary power to distinguish among all the genotyped pangolins, tracing the dispatch of a same individual on the markets and within local communities. We developed an approach combining rarefaction analysis of private allele frequencies with cross-validation of observed data that traced five traded pangolins to their forest origin, c. 200–300 km away from the markets. Conclusions Although the genetic toolkit that we designed from traditional markers can prove helpful to trace the illegal trade in pangolins, our tracing ability was limited by the lack of population structure within the DGL. Given the deleterious combination of genetic, demographic, and trade-related factors affecting DGL populations, the conservation status of white-bellied pangolins in the DG should be urgently re-evaluated. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01971-5.
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15
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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: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Oates JF, Woodman N, Gaubert P, Sargis EJ, Wiafe ED, Lecompte E, Dowsett-Lemaire F, Dowsett RJ, Gonedelé Bi S, Ikemeh RA, Djagoun CAMS, Tomsett L, Bearder SK. A new species of tree hyrax (Procaviidae: Dendrohyrax) from West Africa and the significance of the Niger–Volta interfluvium in mammalian biogeography. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Abstract
Tree hyraxes (Dendrohyrax) are one of only three genera currently recognized in Procaviidae, the only extant family in the mammalian order Hyracoidea. Their taxonomy and natural history have received little attention in recent decades. All tree hyrax populations of Guineo-Congolian forests of Africa are currently treated as a single species, Dendrohyrax dorsalis, the western tree hyrax, but many other groups of mammals distributed across this large biome have been shown to consist of several different species, each restricted to a distinct biogeographical region. We analysed variation in loud-call structure, pelage colour, skull morphometrics and mitochondrial genomes in populations across much of the range of D. dorsalis. This integrative approach uncovered considerable cryptic variation. The population found between the Niger and Volta Rivers in West Africa is particularly distinctive, and we describe it herein as a new species. Our study highlights the need to revise the taxonomy of the genus Dendrohyrax in light of modern systematics and current understanding of its distribution. It also adds to a growing body of evidence that the Niger–Volta interfluvium has a distinct meso-mammal fauna. Unfortunately, the fauna of this region is under major threat and warrants much greater conservation attention.
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Affiliation(s)
- John F Oates
- Department of Anthropology, Hunter College CUNY, New York, NY 10065, USA
| | - Neal Woodman
- U. S. Geological Survey, Eastern Ecological Research Center, Laurel, MD 20708, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique, IRD/CNRS/UPS, Université Paul Sabatier, 31062 Toulouse, France
| | - Eric J Sargis
- Department of Anthropology, Yale University, New Haven, CT 06520, USA
- Divisions of Vertebrate Zoology and Vertebrate Paleontology, Yale Peabody Museum of Natural History, New Haven, CT 06520, USA
| | - Edward D Wiafe
- School of Natural and Environmental Sciences, University of Environment and Sustainable Development, Somanya, Ghana
| | - Emilie Lecompte
- Laboratoire Evolution et Diversité Biologique, IRD/CNRS/UPS, Université Paul Sabatier, 31062 Toulouse, France
| | | | | | - Sery Gonedelé Bi
- Département de Génétique, Université Félix Houphouët-Boigny, 01 BP V34 Abidjan, Ivory Coast
| | | | - Chabi A M S Djagoun
- Laboratoire d’Ecologie Appliquée, Faculté des Sciences Agronomiques, Université d’Abomey-Calavi, 01 B.P. 526 Cotonou, Benin
| | - Louise Tomsett
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Simon K Bearder
- School of Social Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
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Cordeiro-Estrela P, Feijó A, Gaubert P, Weksler M, Hautier L, Velazco PM, Teta P, Fabre PH, Veron G, Braun JK. The role and impact of Zootaxa in mammalogy in its first 20 years. Zootaxa 2021; 4979:7094. [PMID: 34187013 DOI: 10.11646/zootaxa.4979.1.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Indexed: 11/04/2022]
Abstract
Zootaxa came as a new and innovative publication medium for taxonomy, amidst a scenario of devaluation of this important biological science. After 20 years, it has ascertained itself as one of the main journals in animal taxonomy. However, the contribution of the journal to the taxonomy of Mammalia (mammals), one of the most studied groups of animals with a long-standing, dedicated spectrum of specialized journals (mammalogy), could have been expected as minor. All the current and former editors of the Mammalia section of Zootaxa analyzed the relative contribution of the journal to the description of new species of mammals since 2001. We also analyzed the contribution of Zootaxa by taxon, geographic origin of taxa, and geographic origin of first authors. The taxonomic methodology of authors in species description is described as well as the temporal trends in publications and publication subjects. We highlight the editors' picks and eventually, the challenges for the future. We found that Zootaxa has had a significant contribution to mammalogy, being the second journal (the first being Journal of Mammalogy) in terms of number of new species described (76; 10.6% of the new mammalian species described between 2001 and 2020). The majority of the new species were described following an integrative taxonomic approach with at least two sources of data (86%). The analysis of published taxa, their geographic origin, and the country of origin of first authors shows a wide coverage and exhaustive representation, except for the species from the Nearctic. We conclude that Zootaxa has likely responded to a repressed demand for an additional taxonomic journal in mammalogy, with as possible appeals the absence of publication fees and an established publication speed. With 246 articles published in the past 20 years, the Mammalia section of Zootaxa embraces a large spectrum of systematic subjects going beyond alpha taxonomy. The challenges for the future are to encourage publications of authors from the African continent, still poorly represented, and from the palaeontology community, as the journal has been open to palaeontology since its early days.
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Affiliation(s)
- Pedro Cordeiro-Estrela
- Laboratório de Mamíferos, Departamento de Sistemática e Ecologia, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, Campus I, João Pessoa, PB, Brazil..
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China..
| | - Philippe Gaubert
- Laboratoire volution Diversité Biologique, Université Toulouse III Paul Sabatier, 118 route de Narbonne Bât. 4R1, 31062 Toulouse cedex 9, France..
| | - Marcelo Weksler
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, 20940-040 Rio de Janeiro, RJ, Brazil..
| | - Lionel Hautier
- Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS-IRD-UM), Université de Montpellier, Place E. Bataillon - CC 064 - 34095, Montpellier Cedex 5, France. Mammal Section, Department of Life Sciences, The Natural History Museum, SW7 5DB London, United Kingdom.
| | - Paúl M Velazco
- Department of Mammalogy, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA. Department of Biology, Arcadia University, 450 S. Easton Road, Glenside, PA 19038, USA..
| | - Pablo Teta
- División Mastozoología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Avenida Ángel Gallardo 470, C1405DJR Buenos Aires, Argentina..
| | - Pierre-Henri Fabre
- Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS-IRD-UM), Université de Montpellier, Place E. Bataillon - CC 064 - 34095, Montpellier Cedex 5, France. Mammal Section, Department of Life Sciences, The Natural History Museum, SW7 5DB London, United Kingdom.
| | - Geraldine Veron
- Institut de Systématique, Evolution, Biodiversité,CNRS MNHN SU EPHE UA, Muséum National d'Histoire Naturelle, CP 51, 57 Rue Cuvier, 75231 Paris Cedex 05, France..
| | - Janet K Braun
- Sam Noble Oklahoma Museum of Natural History, 2401 Chautauqua Avenue, University of Oklahoma, Norman, OK 73072, USA..
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Zanvo S, Djagoun CA, Azihou AF, Sinsin B, Gaubert P. Preservative chemicals as a new health risk related to traditional medicine markets in western Africa. One Health 2021; 13:100268. [PMID: 34113707 PMCID: PMC8170156 DOI: 10.1016/j.onehlt.2021.100268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 11/18/2022] Open
Abstract
Health risks associated to the use of tropical wildlife have so far been envisioned through the lens of zoonotic pathogens spread by the bushmeat trade, putting aside the equally vibrant network of traditional medicine markets (TMMs). We collected information on the preservative techniques used for animal body parts from TMMs in Benin through a semi-structured questionnaire addressed to 45 sellers. We show that a recent shift from traditional preservative techniques using harmless treatments towards modern techniques –involving the recurrent use of hazardous chemicals (such as Sniper)– is likely to pose a serious health risk to practitioners and consumers of animal parts from TMMs in Benin. We conclude that the non-regulation of the TMM activities represents a critical risk to both biodiversity conservation and human health in western Africa.
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Affiliation(s)
- Stanislas Zanvo
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526 Cotonou, Benin
- Laboratoire Evolution et Diversité Biologique (EDB), CNRS/UPS/IRD, Université Toulouse III Paul Sabatier – Bâtiment 4R1, 118 route de Narbonne, 31062 Toulouse cedex 9, France
- Corresponding authors at: Laboratoire Evolution et Diversité Biologique (EDB), CNRS/UPS/IRD, Université Toulouse III Paul Sabatier – Bâtiment 4R1, 118 route de Narbonne, 31062 Toulouse cedex 9, France.
| | - Chabi A.M.S. Djagoun
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526 Cotonou, Benin
| | - Akomian F. Azihou
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526 Cotonou, Benin
| | - Brice Sinsin
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526 Cotonou, Benin
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique (EDB), CNRS/UPS/IRD, Université Toulouse III Paul Sabatier – Bâtiment 4R1, 118 route de Narbonne, 31062 Toulouse cedex 9, France
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal
- Corresponding authors at: Laboratoire Evolution et Diversité Biologique (EDB), CNRS/UPS/IRD, Université Toulouse III Paul Sabatier – Bâtiment 4R1, 118 route de Narbonne, 31062 Toulouse cedex 9, France.
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Zanvo S, Djagoun SCAM, Azihou FA, Djossa B, Sinsin B, Gaubert P. Ethnozoological and commercial drivers of the pangolin trade in Benin. J Ethnobiol Ethnomed 2021; 17:18. [PMID: 33757552 PMCID: PMC7985750 DOI: 10.1186/s13002-021-00446-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Pangolins are trafficked in unsustainable volumes to feed both local and global trade networks for their meat and the medicinal properties of their derivatives, including scales. We focus on a West African country (Benin) to assess the medicinal and spiritual values of pangolins among different ethnic groups and identify the cohort of buyers involved in the pangolin trade and related economic values along the chain, notably from local diasporas. METHODS We organised 54 focus groups in villages surrounding occurrence habitats of pangolins across Benin and conducted 35 individual interviews with vendors from five major traditional medicine markets (TMMs). Our questionnaire addressed the different uses of pangolins, the commercial value of pangolin items, the categories of clients and the related selling prices. RESULTS Pangolin meat was strictly consumed as food. Scales, head, bones, tongue, blood, heart and xiphisternum were the items used by local communities as part of medicinal (65% of the focus groups) and spiritual (37%) practices. Scales were the most frequently used item (use value index = 1.56). A total of 42 medicinal and spiritual uses, covering 15 International Classification of Diseases (ICD) categories, were recorded among ethnic groups. The ICD and spiritual categories-based analyses of similarity showed a partial overlapping of ethnozoological knowledge across Benin, although knowledge was significantly influenced by ethnicity and geographic location. The pricing of pangolins both varied with the category of stakeholders (local communities vs. stakeholders of TMMs) and clients (local and West African clients vs. Chinese community) and the type of items sold. The Chinese community was reported to only buy pangolins alive, and average selling prices were 3-8 times higher than those to West African clients. CONCLUSIONS Our results confirm that pangolins in Africa are valuable and versatile resources for consumption and medicinal / spiritual practices. The pangolin trade in Benin is based on an endogenous and complex network of actors that now appears influenced by the specific, high-valued demand from the Chinese diaspora. Further investigations are required to assess the growing impact of the Chinese demand on the African wildlife trade.
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Affiliation(s)
- Stanislas Zanvo
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526, Cotonou, Benin.
- Laboratoire Evolution et Diversité Biologique (EDB), CNRS/UPS/IRD, Université Toulouse III Paul Sabatier, Bâtiment 4R1, 118 route de Narbonne, 31062, Toulouse cedex 9, France.
| | - Sylvestre C A M Djagoun
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526, Cotonou, Benin
| | - Fortuné A Azihou
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526, Cotonou, Benin
| | - Bruno Djossa
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526, Cotonou, Benin
- Laboratoire de Foresterie et de Conservation des Bioressources (LaFCBio), Ecole de Foresterie Tropicale, Université Nationale d'Agriculture, Kétou, Benin
| | - Brice Sinsin
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526, Cotonou, Benin
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique (EDB), CNRS/UPS/IRD, Université Toulouse III Paul Sabatier, Bâtiment 4R1, 118 route de Narbonne, 31062, Toulouse cedex 9, France
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
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Perri AR, Mitchell KJ, Mouton A, Álvarez-Carretero S, Hulme-Beaman A, Haile J, Jamieson A, Meachen J, Lin AT, Schubert BW, Ameen C, Antipina EE, Bover P, Brace S, Carmagnini A, Carøe C, Samaniego Castruita JA, Chatters JC, Dobney K, Dos Reis M, Evin A, Gaubert P, Gopalakrishnan S, Gower G, Heiniger H, Helgen KM, Kapp J, Kosintsev PA, Linderholm A, Ozga AT, Presslee S, Salis AT, Saremi NF, Shew C, Skerry K, Taranenko DE, Thompson M, Sablin MV, Kuzmin YV, Collins MJ, Sinding MHS, Gilbert MTP, Stone AC, Shapiro B, Van Valkenburgh B, Wayne RK, Larson G, Cooper A, Frantz LAF. Dire wolves were the last of an ancient New World canid lineage. Nature 2021; 591:87-91. [PMID: 33442059 DOI: 10.1038/s41586-020-03082-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 11/12/2020] [Indexed: 11/09/2022]
Abstract
Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.
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Affiliation(s)
- Angela R Perri
- Department of Archaeology, Durham University, Durham, UK.
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
| | - Alice Mouton
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | | | - Ardern Hulme-Beaman
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK.,School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| | - James Haile
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK
| | - Alexandra Jamieson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK
| | - Julie Meachen
- Department of Anatomy, Des Moines University, Des Moines, IA, USA
| | - Audrey T Lin
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK.,Department of Zoology, University of Oxford, Oxford, UK.,Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Blaine W Schubert
- Center of Excellence in Paleontology & Department of Geosciences, East Tennessee State University, Johnson City, TN, USA
| | - Carly Ameen
- Department of Archaeology, University of Exeter, Exeter, UK
| | | | - Pere Bover
- ARAID Foundation, Instituto Universitario de Investigación en Ciencias Ambientales (IUCA) - Aragosaurus Group, Universidad de Zaragoza, Zaragoza, Spain
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Alberto Carmagnini
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Christian Carøe
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK.,Department of Archaeology, University of Sydney, Sydney, New South Wales, Australia.,Department of Archaeology, University of Aberdeen, Aberdeen, UK.,Department of Archaeology, Simon Fraser University, Burnaby, Canada
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Allowen Evin
- Institut des Sciences de l'Evolution - Montpellier, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France
| | - Philippe Gaubert
- Laboratoire Evolution & Diversité Biologique, UPS/CNRS/IRD, Université Paul Sabatier, Toulouse, France
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Graham Gower
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Holly Heiniger
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Josh Kapp
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Pavel A Kosintsev
- Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of Sciences, Yekaterinburg, Russia.,Ural Federal University, Yekaterinburg, Russia
| | - Anna Linderholm
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK.,Department of Anthropology, Texas A&M University, College Station, TX, USA
| | - Andrew T Ozga
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, USA
| | | | - Alexander T Salis
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Nedda F Saremi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Colin Shew
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Katherine Skerry
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Dmitry E Taranenko
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Mary Thompson
- Idaho Museum of Natural History, Idaho State University, Pocatello, ID, USA
| | - Mikhail V Sablin
- Zoological Institute of the Russian Academy of Sciences, St Petersburg, Russia
| | - Yaroslav V Kuzmin
- Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Tomsk State University, Tomsk, Russia
| | - Matthew J Collins
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Mikkel-Holger S Sinding
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,NTNU University Museum, Trondheim, Norway
| | - Anne C Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Blaire Van Valkenburgh
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK
| | - Alan Cooper
- South Australian Museum, Adelaide, South Australia, Australia
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK. .,Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany.
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Zanvo S, Gaubert P, Djagoun CA, Azihou AF, Djossa B, Sinsin B. Assessing the spatiotemporal dynamics of endangered mammals through local ecological knowledge combined with direct evidence: The case of pangolins in Benin (West Africa). Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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22
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Rey-Iglesia A, Gaubert P, Espregueira Themudo G, Pires R, de la Fuente C, Freitas L, Aguilar A, Borrell A, Krakhmalnaya T, Vasconcelos R, Campos PF. Mitogenomics of the endangered Mediterranean monk seal ( Monachus monachus) reveals dramatic loss of diversity and supports historical gene-flow between Atlantic and eastern Mediterranean populations. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa084] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The Mediterranean monk seal Monachus monachus is one of the most threatened marine mammals, with only 600–700 individuals restricted to three populations off the coast of Western Sahara and Madeira (North Atlantic) and between Greece and Turkey (eastern Mediterranean). Its original range was from the Black Sea (eastern Mediterranean) to Gambia (western African coast), but was drastically reduced by commercial hunting and human persecution since the early stages of marine exploitation.
We here analyse 42 mitogenomes of Mediterranean monk seals, from across their present and historical geographic ranges to assess the species population dynamics over time. Our data show a decrease in genetic diversity in the last 200 years. Extant individuals presented an almost four-fold reduction in genetic diversity when compared to historical specimens. We also detect, for the first time, a clear segregation between the two North Atlantic populations, Madeira and Cabo Blanco, regardless of their geographical proximity. Moreover, we show the presence of historical gene-flow between the two water basins, the Atlantic Ocean and the Mediterranean Sea, and the presence of at least one extinct maternal lineage in the Mediterranean. Our work demonstrates the advantages of using full mitogenomes in phylogeographic and conservation genomic studies of threatened species.
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Affiliation(s)
- Alba Rey-Iglesia
- Centre for Geogenetics, Natural History Museum Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique, UPS/CNRS/IRD, Université Paul Sabatier, Toulouse, France
- CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, Matosinhos, Portugal
| | - Gonçalo Espregueira Themudo
- CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, Matosinhos, Portugal
| | - Rosa Pires
- Instituto das Florestas e Conservação da Natureza, IP-RAM, Jardim Botânico da Madeira - Eng.º Rui Vieira, Caminho do Meio, Bom Sucesso, Funchal, Madeira, Portugal
| | - Constanza de la Fuente
- Centre for Geogenetics, Natural History Museum Denmark, University of Copenhagen, Copenhagen, Denmark
- Department of Human Genetics, University of Chicago, Chicago, USA
| | - Luís Freitas
- Museu da Baleia da Madeira, Rua da Pedra D’Eira, Caniçal, Madeira, Portugal
| | - Alex Aguilar
- IRBio and Department of Evolutive Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Asunción Borrell
- IRBio and Department of Evolutive Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Tatiana Krakhmalnaya
- National Museum of Natural History, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Raquel Vasconcelos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Paula F Campos
- Centre for Geogenetics, Natural History Museum Denmark, University of Copenhagen, Copenhagen, Denmark
- CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, Matosinhos, Portugal
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23
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Aguillon S, Din Dipita A, Lecompte E, Missoup AD, Tindo M, Gaubert P. Development and characterization of 20 polymorphic microsatellite markers for the white-bellied pangolin Phataginus tricuspis (Mammalia, Pholidota). Mol Biol Rep 2020; 47:4827-4833. [PMID: 32419053 PMCID: PMC7230135 DOI: 10.1007/s11033-020-05511-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/08/2020] [Indexed: 11/16/2022]
Abstract
Pangolins, or scaly anteaters, have recently been flagshiped as one of the most illegally traded mammals, and as a corollary, as potential intermediate hosts at the origin of the COVID-19 pandemic. In order to improve the traceability of their trade, we developed 20 polymorphic microsatellite loci for the white-bellied pangolin (Phataginus tricuspis), the species most frequently found on African bushmeat markets. We genotyped 24 white-bellied pangolins from the Douala market, Cameroon, originating from the Ebo forest c. 75 km north-east of Douala. The number of alleles per locus ranged from 4 to 12 (mean = 6.95), and mean observed and expected heterozygosities were 0.592 (0.208-0.875) and 0.671 (0.469-0.836), respectively. Genetic diversity was higher than that cross-estimated from microsatellite loci developed for other species of pangolins. Two loci deviated from Hardy-Weinberg equilibrium and two loci showed linkage disequilibrium. Genetic variance (PCoA) was increased with the addition of 13 pangolins of unknown origin, possibly suggesting that the Douala market is fed from differentiated source populations of white-bellied pangolins. Each of the 37 individuals had a unique multilocus genotype. The unbiased probability of identity (uPI) and the probability of identity among siblings (PIsibs) were both very low (uPI = 8.443 e-21; PIsibs = 1.011 e-07). Only five microsatellite loci were needed to reach the conservative value of PIsibs < 0.01, overall indicating a powerful discriminating power of our combined loci. These 20 newly developed microsatellite loci might prove useful in tracing the local-to-global trade of the white-bellied pangolin, and will hopefully contribute to the DNA-assisted implementation of future conservation strategies at reasonable costs.
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Affiliation(s)
- Samantha Aguillon
- Laboratoire Evolution et Diversité Biologique (EDB), CNRS/UPS/IRD, Université Toulouse III Paul Sabatier - Bâtiment 4R1, 118 route de Narbonne, 31062, Toulouse Cedex 9, France
| | - Alain Din Dipita
- Unité de Zoologie, Laboratoire de Biologie et Physiologie des Organismes Animaux, Faculté des Sciences, Université de Douala, BP 24157, Douala, Cameroon
| | - Emilie Lecompte
- Laboratoire Evolution et Diversité Biologique (EDB), CNRS/UPS/IRD, Université Toulouse III Paul Sabatier - Bâtiment 4R1, 118 route de Narbonne, 31062, Toulouse Cedex 9, France
| | - Alain Didier Missoup
- Unité de Zoologie, Laboratoire de Biologie et Physiologie des Organismes Animaux, Faculté des Sciences, Université de Douala, BP 24157, Douala, Cameroon
| | - Maurice Tindo
- Unité de Zoologie, Laboratoire de Biologie et Physiologie des Organismes Animaux, Faculté des Sciences, Université de Douala, BP 24157, Douala, Cameroon
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique (EDB), CNRS/UPS/IRD, Université Toulouse III Paul Sabatier - Bâtiment 4R1, 118 route de Narbonne, 31062, Toulouse Cedex 9, France.
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24
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Gopalakrishnan S, Sinding MHS, Ramos-Madrigal J, Niemann J, Samaniego Castruita JA, Vieira FG, Carøe C, de Manuel Montero M, Kuderna L, Serres A, González-Basallote VM, Liu YH, Wang GD, Marques-Bonet T, Mirarab S, Fernandes C, Gaubert P, Koepfli KP, Budd J, Rueness EK, Sillero C, Heide-Jørgensen MP, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig Ø, Hansen AJ, Gilbert MTP. Interspecific Gene Flow Shaped the Evolution of the Genus Canis. Curr Biol 2019; 29:4152. [PMID: 31794747 PMCID: PMC6892301 DOI: 10.1016/j.cub.2019.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Ferreira-Cardoso S, Billet G, Gaubert P, Delsuc F, Hautier L. Skull shape variation in extant pangolins (Pholidota: Manidae): allometric patterns and systematic implications. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Pangolins are among the most endangered groups of mammals, comprising eight extant species delineated into three genera. Despite several studies dedicated to their skeletal anatomy, the potential taxonomic insight from cranial morphological variation in extant Pholidota is yet to be assessed with modern geometric morphometric methods. We present the first comprehensive study on the cranial morphology of extant pangolins and discuss its implications for the taxonomy and evolution of the group. We performed landmark-based morphometric analyses on 241 museum specimens to describe the variation in skull shape in seven of the eight extant species. Our analyses revealed genus- and species-level morphological discrimination, with Asian species (Manis spp.) being grouped together, whereas African pangolins present distinct skull shapes between small (Phataginus spp.) and large (Smutsia spp.) species. Analyses of allometry also identified a set of traits whose allometric trajectories distinguish Asian from African specimens. Finally, we uncovered intraspecific variation in skull shape in white-bellied pangolins (Phataginus tricuspis) that partly corroborates recent DNA-based differentiation among biogeographically distinct populations. Overall, our results shed light on the morphological diversity of the skull of these enigmatic myrmecophagous mammals and confirm the genus-level classification and cryptic diversity within the white-bellied pangolin revealed by molecular phylogenetics.
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Affiliation(s)
| | - Guillaume Billet
- Centre de Recherche en Paléontologie Paris (CR2P), UMR CNRS 7207, MNHN, CNRS, SU, Muséum National d’Histoire Naturelle, Paris, France
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique (EDB), Université Paul Sabatier, Toulouse, France
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal
| | - Frédéric Delsuc
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Lionel Hautier
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
- Mammal Section, Life Sciences, Vertebrate Division, The Natural History Museum, London, UK
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26
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Gopalakrishnan S, Sinding MHS, Ramos-Madrigal J, Niemann J, Samaniego Castruita JA, Vieira FG, Carøe C, Montero MDM, Kuderna L, Serres A, González-Basallote VM, Liu YH, Wang GD, Marques-Bonet T, Mirarab S, Fernandes C, Gaubert P, Koepfli KP, Budd J, Rueness EK, Sillero C, Heide-Jørgensen MP, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig Ø, Hansen AJ, Gilbert MTP. Interspecific Gene Flow Shaped the Evolution of the Genus Canis. Curr Biol 2018; 28:3441-3449.e5. [PMID: 30344120 PMCID: PMC6224481 DOI: 10.1016/j.cub.2018.08.041] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 04/30/2018] [Accepted: 08/16/2018] [Indexed: 12/30/2022]
Abstract
The evolutionary history of the wolf-like canids of the genus Canis has been heavily debated, especially regarding the number of distinct species and their relationships at the population and species level [1-6]. We assembled a dataset of 48 resequenced genomes spanning all members of the genus Canis except the black-backed and side-striped jackals, encompassing the global diversity of seven extant canid lineages. This includes eight new genomes, including the first resequenced Ethiopian wolf (Canis simensis), one dhole (Cuon alpinus), two East African hunting dogs (Lycaon pictus), two Eurasian golden jackals (Canis aureus), and two Middle Eastern gray wolves (Canis lupus). The relationships between the Ethiopian wolf, African golden wolf, and golden jackal were resolved. We highlight the role of interspecific hybridization in the evolution of this charismatic group. Specifically, we find gene flow between the ancestors of the dhole and African hunting dog and admixture between the gray wolf, coyote (Canis latrans), golden jackal, and African golden wolf. Additionally, we report gene flow from gray and Ethiopian wolves to the African golden wolf, suggesting that the African golden wolf originated through hybridization between these species. Finally, we hypothesize that coyotes and gray wolves carry genetic material derived from a "ghost" basal canid lineage.
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Affiliation(s)
- Shyam Gopalakrishnan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Mikkel-Holger S Sinding
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; Natural History Museum, University of Oslo, Oslo, Norway; The Qimmeq Project, University of Greenland, Nuussuaq, Greenland; University of Greenland, Manuutoq 1, Nuuk, Greenland
| | - Jazmín Ramos-Madrigal
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Niemann
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jose A Samaniego Castruita
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Lukas Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | - Aitor Serres
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | | | - Yan-Hu Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan, China
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA, USA
| | - Carlos Fernandes
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Philippe Gaubert
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UM-CNRS-IRD-EPHE, Université de Montpellier, Montpellier, France
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA; Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 41A Sredniy Prospekt, St. Petersburg 199034, Russia
| | - Jane Budd
- Breeding Centre for Endangered Arabian Wildlife, Sharjah, United Arab Emirates
| | - Eli Knispel Rueness
- Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Claudio Sillero
- Wildlife Conservation Research Unit, Zoology, University of Oxford, Tubney House, Tubney OX13 5QL, UK; IUCN SSC Canid Specialist Group, Oxford, UK
| | - Mads Peter Heide-Jørgensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | - Bent Petersen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Thomas Sicheritz-Ponten
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Lutz Bachmann
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Øystein Wiig
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Anders J Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; The Qimmeq Project, University of Greenland, Nuussuaq, Greenland; University of Greenland, Manuutoq 1, Nuuk, Greenland
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; Norwegian University of Science and Technology, University Museum, Trondheim, Norway
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27
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Fabre PH, Tilak MK, Denys C, Gaubert P, Nicolas V, Douzery EJP, Marivaux L. Flightless scaly-tailed squirrels never learned how to fly: A reappraisal of Anomaluridae phylogeny. ZOOL SCR 2018. [DOI: 10.1111/zsc.12286] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Pierre-Henri Fabre
- Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE); c.c. 064; Université de Montpellier; Montpellier France
- National Museum of Natural History; Smithsonian Institution; Washington DC USA
| | - Marie-Ka Tilak
- Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE); c.c. 064; Université de Montpellier; Montpellier France
| | - Christiane Denys
- Institut de Systématique, Évolution, Biodiversité; ISYEB - UMR 7205, CNRS, MNHN, UPMC, EPHE; Muséum National d’Histoire Naturelle; Sorbonne Universités; Paris France
| | - Philippe Gaubert
- Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE); c.c. 064; Université de Montpellier; Montpellier France
- Laboratoire Evolution et Diversité Biologique (EDB) - UPS-CNRS- IRD; Université Paul Sabatier; Toulouse France
| | - Violaine Nicolas
- Institut de Systématique, Évolution, Biodiversité; ISYEB - UMR 7205, CNRS, MNHN, UPMC, EPHE; Muséum National d’Histoire Naturelle; Sorbonne Universités; Paris France
| | - Emmanuel J. P. Douzery
- Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE); c.c. 064; Université de Montpellier; Montpellier France
| | - Laurent Marivaux
- Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE); c.c. 064; Université de Montpellier; Montpellier France
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Gaubert P, Antunes A, Meng H, Miao L, Peigné S, Justy F, Njiokou F, Dufour S, Danquah E, Alahakoon J, Verheyen E, Stanley WT, O’Brien SJ, Johnson WE, Luo SJ. The Complete Phylogeny of Pangolins: Scaling Up Resources for the Molecular Tracing of the Most Trafficked Mammals on Earth. J Hered 2017; 109:347-359. [DOI: 10.1093/jhered/esx097] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/02/2017] [Indexed: 01/08/2023] Open
Affiliation(s)
- Philippe Gaubert
- Institut des Sciences de l’Evolution de Montpellier (ISEM)—UM-CNRS-IRD-EPHE, Université, France
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Portugal
| | - Hao Meng
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, China
| | - Lin Miao
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, China
| | - Stéphane Peigné
- Centre de recherche sur la paléobiodiversité et les paléoenvironnements (CR2P)—UMR 7207 MNHN/CNRS/UPMC, Muséum national d’Histoire naturelle—CP38, France
| | - Fabienne Justy
- Institut des Sciences de l’Evolution de Montpellier (ISEM)—UM-CNRS-IRD-EPHE, Université, France
| | - Flobert Njiokou
- Laboratoire de Parasitologie et Ecologie, Université de Yaoundé I, Faculté des Sciences, Cameroon
| | | | - Emmanuel Danquah
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, Ghana
| | | | - Erik Verheyen
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Belgium
- Evolutionary Ecology Group, University of Antwerp, Belgium
| | | | - Stephen J O’Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia
- Oceanographic Center, Dania Beach, FL
- Nova Southeastern University, Ft Lauderdale, FL
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA
| | - Shu-Jin Luo
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, China
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29
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Liu YH, Wang L, Xu T, Guo X, Li Y, Yin TT, Yang HC, Hu Y, Adeola AC, Sanke OJ, Otecko NO, Wang M, Ma Y, Charles OS, Sinding MHS, Gopalakrishnan S, Alfredo Samaniego J, Hansen AJ, Fernandes C, Gaubert P, Budd J, Dawuda PM, Knispel Rueness E, Jiang L, Zhai W, Gilbert MTP, Peng MS, Qi X, Wang GD, Zhang YP. Whole-Genome Sequencing of African Dogs Provides Insights into Adaptations against Tropical Parasites. Mol Biol Evol 2017; 35:287-298. [DOI: 10.1093/molbev/msx258] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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30
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Gaubert P, Patel RP, Veron G, Goodman SM, Willsch M, Vasconcelos R, Lourenço A, Sigaud M, Justy F, Joshi BD, Fickel J, Wilting A. Phylogeography of the Small Indian Civet and Origin of Introductions to Western Indian Ocean Islands. J Hered 2017; 108:270-279. [PMID: 27940474 DOI: 10.1093/jhered/esw085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 12/01/2016] [Indexed: 11/14/2022] Open
Abstract
The biogeographic dynamics affecting the Indian subcontinent, East and Southeast Asia during the Plio-Pleistocene has generated complex biodiversity patterns. We assessed the molecular biogeography of the small Indian civet (Viverricula indica) through mitogenome and cytochrome b + control region sequencing of 89 historical and modern samples to (1) establish a time-calibrated phylogeography across the species' native range and (2) test introduction scenarios to western Indian Ocean islands. Bayesian phylogenetic analyses identified 3 geographic lineages (East Asia, sister-group to Southeast Asia and the Indian subcontinent + northern Indochina) diverging 3.2-2.3 million years ago (Mya), with no clear signature of past demographic expansion. Within Southeast Asia, Balinese populations separated from the rest 2.6-1.3 Mya. Western Indian Ocean populations were assigned to the Indian subcontinent + northern Indochina lineage and had the lowest mitochondrial diversity. Approximate Bayesian computation did not distinguish between single versus multiple introduction scenarios. The early diversification of the small Indian civet was likely shaped by humid periods in the Late Pliocene-Early Pleistocene that created evergreen rainforest barriers, generating areas of intra-specific endemism in the Indian subcontinent, East, and Southeast Asia. Later, Pleistocene dispersals through drier conditions in South and Southeast Asia were likely, giving rise to the species' current natural distribution. Our molecular data supported the delineation of only 4 subspecies in V. indica, including an endemic Balinese lineage. Our study also highlighted the influence of prefirst millennium AD introductions to western Indian Ocean islands, with Indian and/or Arab traders probably introducing the species for its civet oil.
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Affiliation(s)
- Philippe Gaubert
- Institut des Sciences de l'Evolution de Montpellier (ISEM)-UM-CNRS-IRD-EPHE, Université de Montpellier, Place Eugène Bataillon-CC 64, Montpellier Cedex 05, France
| | - Riddhi P Patel
- Freie Universität Berlin, Berlin, Germany.,Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Géraldine Veron
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS MNHN UPMC EPHE, Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris, France
| | - Steven M Goodman
- Field Museum of Natural History, Chicago, IL, USA.,Association Vahatra, Antananarivo, Madagascar, East Africa
| | - Maraike Willsch
- Institut des Sciences de l'Evolution de Montpellier (ISEM)-UM-CNRS-IRD-EPHE, Université de Montpellier, Place Eugène Bataillon-CC 64, Montpellier Cedex 05, France.,Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, Berlin, Germany
| | - Raquel Vasconcelos
- Institute of Evolutionary Biology (CSIC-UPF), Passeig Marítim de la Barceloneta, Barcelona, Spain.,CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - André Lourenço
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia da Faculdade de Ciências da Universidade do Porto, Porto,Portugal
| | - Marie Sigaud
- Cellule Technique Océan Indien, Office National de la Chasse et de la Faune Sauvage (ONCFS), Saint-Denis, France
| | - Fabienne Justy
- Institut des Sciences de l'Evolution de Montpellier (ISEM)-UM-CNRS-IRD-EPHE, Université de Montpellier, Place Eugène Bataillon-CC 64, Montpellier Cedex 05, France
| | | | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Institute of Biochemistry & Biology, Potsdam University, Potsdam-Golm, Germany
| | - Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
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Gaubert P, Njiokou F, Ngua G, Afiademanyo K, Dufour S, Malekani J, Bi SG, Tougard C, Olayemi A, Danquah E, Djagoun CAMS, Kaleme P, Mololo CN, Stanley W, Luo SJ, Antunes A. Phylogeography of the heavily poached African common pangolin (Pholidota, Manis tricuspis) reveals six cryptic lineages as traceable signatures of Pleistocene diversification. Mol Ecol 2016; 25:5975-5993. [PMID: 27862533 DOI: 10.1111/mec.13886] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/24/2016] [Accepted: 09/27/2016] [Indexed: 01/03/2023]
Abstract
Knowledge on faunal diversification in African rainforests remains scarce. We used phylogeography to assess (i) the role of Pleistocene climatic oscillations in the diversification of the African common pangolin (Manis tricuspis) and (ii) the utility of our multilocus approach for taxonomic delineation and trade tracing of this heavily poached species. We sequenced 101 individuals for two mitochondrial DNA (mtDNA), two nuclear DNA and one Y-borne gene fragments (totalizing 2602 bp). We used a time-calibrated, Bayesian inference phylogenetic framework and conducted character-based, genetic and phylogenetic delineation of species hypotheses within African common pangolins. We identified six geographic lineages partitioned into western Africa, Ghana, the Dahomey Gap, western central Africa, Gabon and central Africa, all diverging during the Middle to Late Pleistocene. MtDNA (cytochrome b + control region) was the sole locus to provide diagnostic characters for each of the six lineages. Tree-based Bayesian delimitation methods using single- and multilocus approaches gave high support for 'species' level recognition of the six African common pangolin lineages. Although the diversification of African common pangolins occurred during Pleistocene cyclical glaciations, causative correlation with traditional rainforest refugia and riverine barriers in Africa was not straightforward. We conclude on the existence of six cryptic lineages within African common pangolins, which might be of major relevance for future conservation strategies. The high discriminative power of the mtDNA markers used in this study should allow an efficient molecular tracing of the regional origin of African common pangolin seizures.
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Affiliation(s)
- Philippe Gaubert
- Institut des Sciences de l'Evolution de Montpellier (ISEM) - UM-CNRS-IRD-EPHE-CIRAD, Université de Montpellier, Place Eugène Bataillon - CC 64, 34095, Montpellier Cedex 05, France.,CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
| | - Flobert Njiokou
- Laboratoire de Parasitologie et Ecologie, Faculté des Sciences, Université de Yaoundé I, BP 812, Yaoundé, Cameroon
| | - Gabriel Ngua
- Amigos de la Naturaleza y del Desarrollo de Guinea Ecuatorial (ANDEGE), Barrio Ukomba, S/N, Bata, Equatorial Guinea
| | - Komlan Afiademanyo
- Département de Zoologie et de Biologie Animale, Université de Lomé, BP 1515, Lomé, Togo
| | | | - Jean Malekani
- Department of Biology, University of Kinshasa, PO Box 218, Kinshasa XI, Democratic Republic of Congo
| | - Sery Gonedelé Bi
- Laboratoire de Génétique, Université Félix Houphouët Boigny d'Abidjan-Cocody, 22 BP 582, Abidjan 22, Côte d'Ivoire
| | - Christelle Tougard
- Institut des Sciences de l'Evolution de Montpellier (ISEM) - UM-CNRS-IRD-EPHE-CIRAD, Université de Montpellier, Place Eugène Bataillon - CC 64, 34095, Montpellier Cedex 05, France
| | - Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, HO 220005, Ile-Ife, Nigeria
| | - Emmanuel Danquah
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, University Post Office, Kumasi, Ghana
| | - Chabi A M S Djagoun
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526 LEA-FSA, Cotonou, Benin
| | - Prince Kaleme
- Laboratoire de Mammalogie, Département de Biologie, Centre de Recherches en Sciences Naturelles (CRSN) - Lwiro, DS (Dépêche Spéciale) Bukavu, Democratic Republic of Congo.,Department of Zoology, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa
| | - Casimir Nebesse Mololo
- Université de Kisangani, Faculté des Sciences, B.P. 2012, Kisangani, Democratic Republic of Congo
| | - William Stanley
- Science and Education, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA
| | - Shu-Jin Luo
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
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Barros T, Ferreira E, Rocha RG, Gaubert P, Bandeira V, Souto L, Mira A, Fonseca C. Genetic signature of the northward expansion of the Egyptian mongoose Herpestes ichneumon(Herpestidae) in the Iberian Peninsula. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12743] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tânia Barros
- Departamento de Biologia & Centros de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; 3810-193 Aveiro Portugal
| | - Eduardo Ferreira
- Departamento de Biologia & Centros de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; 3810-193 Aveiro Portugal
| | - Rita Gomes Rocha
- Departamento de Biologia & Centros de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; 3810-193 Aveiro Portugal
- Departamento de Ciências Biológicas; Centro de Ciências Humanas e Naturais; Universidade Federal do Espírito Santo; Av. Fernando Ferrari 514, Goiabeiras 29075-910 Vitória ES Brazil
| | - Philippe Gaubert
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UM-CNRS-IRD-CIRAD-EPHE; Université de Montpellier; Place Eugène Bataillon - CC 64; 34095 Montpellier, Cedex 05 France
| | - Victor Bandeira
- Departamento de Biologia & Centros de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; 3810-193 Aveiro Portugal
| | - Luis Souto
- Departamento de Biologia & Centros de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; 3810-193 Aveiro Portugal
| | - António Mira
- Unidade de Biologia da Conservação; Universidade de Évora; 7002-554 Évora Portugal
| | - Carlos Fonseca
- Departamento de Biologia & Centros de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; 3810-193 Aveiro Portugal
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Barros T, Gaubert P, Rocha RG, Bandeira V, Souto L, Mira A, Fonseca C. Mitochondrial demographic history of the Egyptian mongoose (Herpestes ichneumon), an expanding carnivore in the Iberian Peninsula. Mamm Biol 2016. [DOI: 10.1016/j.mambio.2015.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Cruz-Jofré F, Morales P, Vila I, Esquer-Garrigos Y, Hugueny B, Gaubert P, Poulin E, Méndez MA. Geographical isolation and genetic differentiation: the case ofOrestias ascotanensis(Teleostei: Cyprinodontidae), an Andean killifish inhabiting a highland salt pan. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12704] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Franco Cruz-Jofré
- Laboratorio de Genética y Evolución; Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425 Casilla 653 Ñuñoa Santiago Chile
- Escuela de Medicina Veterinaria; Facultad de Medicina Veterinaria y Recursos Naturales; Universidad Santo Tomás; Avenida Limonares 190 Viña del Mar Chile
| | - Pamela Morales
- Laboratorio de Genética y Evolución; Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425 Casilla 653 Ñuñoa Santiago Chile
| | - Irma Vila
- Laboratorio de Limnología; Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425, Casilla 653 Ñuñoa Santiago Chile
| | - Yareli Esquer-Garrigos
- UMR BOREA; Département Milieux et Peuplements Aquatiques; MNHN-CNRS 7208-IRD 207-UPMC; Muséum National d'Histoire Naturelle; 43 rue Cuvier 75231 Paris France
| | - Bernard Hugueny
- UMR BOREA; Département Milieux et Peuplements Aquatiques; MNHN-CNRS 7208-IRD 207-UPMC; Muséum National d'Histoire Naturelle; 43 rue Cuvier 75231 Paris France
| | - Philippe Gaubert
- UMR BOREA; Département Milieux et Peuplements Aquatiques; MNHN-CNRS 7208-IRD 207-UPMC; Muséum National d'Histoire Naturelle; 43 rue Cuvier 75231 Paris France
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UM2/CNRS/IRD; Université de Montpellier; Place Eugène Bataillon, CC 64 34095 Montpellier, Cedex 05 France
| | - Elie Poulin
- Laboratorio de Ecología Molecular; Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425, Casilla 653 Ñuñoa Santiago Chile
- Instituto de Ecología y Biodiversidad (IEB), Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425, Casilla 653 Ñuñoa Santiago Chile
| | - Marco A. Méndez
- Laboratorio de Genética y Evolución; Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425 Casilla 653 Ñuñoa Santiago Chile
- Instituto de Ecología y Biodiversidad (IEB), Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425, Casilla 653 Ñuñoa Santiago Chile
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Garrigos YE, Hugueny B, Koerner K, Ibañez C, Bonillo C, Pruvost P, Causse R, Cruaud C, Gaubert P. Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus Orestias (Teleostei: Cyprinodontidae). Zootaxa 2015; 3640:373-94. [PMID: 26000423 DOI: 10.11646/zootaxa.3640.3.3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Specimens stored in museum collections represent a crucial source of morphological and genetic information, notably for taxonomically problematic groups and extinct taxa. Although fluid-preserved specimens of groups such as teleosts may constitute an almost infinite source of DNA, few ancient DNA protocols have been applied to such material. In this study, we describe a non-invasive Guanidine-based (GuSCN) ancient DNA extraction protocol adapted to fluid-preserved specimens that we use to re-assess the systematics of the genus Orestias (Cyprinodontidae: Teleostei). The latter regroups pupfishes endemic to the inter-Andean basin that have been considered as a 'species flock', and for which the morphology-based taxonomic delimitations have been hotly debated. We extracted DNA from the type specimens of Orestias kept at the Muséum National d'Histoire Naturelle of Paris, France, including the extinct species O. cuvieri. We then built the first molecular (control region [CR] and rhodopsin [RH]) phylogeny including historical and recently collected representatives of all the Orestias complexes as recognized by Parenti (1984a): agassizii, cuvieri, gilsoni and mulleri. Our ancient DNA extraction protocol was validated after PCR amplification through an approach based on fragment-by-fragment chimera detection. After optimization, we were able to amplify < 200 bp fragments from both mitochondrial and nuclear DNA (CR and RH, respectively) from probably formalin-fixed type specimens bathed entirely in the extraction fluid. Most of the individuals exhibited few modifications of their external structures after GuSCN bath. Our approach combining type material and 'fresh' specimens allowed us to taxonomically delineate four clades recovered from the well-resolved CR tree into four redefined complexes: agassizii (sensu stricto, i.e. excluding luteus-like species), luteus, cuvieri and gilsoni. The mulleri complex is polyphyletic. Our phylogenetic analyses based on both mitochondrial and nuclear DNA revealed a main, deep dichotomy within the genus Orestias, separating the agassizii complex from a clade grouped under shallow dichotomies as (luteus, (cuvieri, gilsoni)). This 'deep and shallow' diversification pattern could fit within a scenario of ancient divergence between the agassizii complex and the rest of Orestias, followed by a recent diversification or adaptive radiation within each complex during the Pleistocene, in- and outside the Lake Titicaca. We could not recover the reciprocal monophyly of any of the 15 species or morphotypes that were considered in our analyses, possibly due to incomplete lineage sorting and/or hybridization events. As a consequence, our results starkly question the delineation of a series of diagnostic characters listed in the literature for Orestias. Although not included in our phylogenetic analysis, the syntype of O. jussiei could not be assigned to the agassizii complex as newly defined. The CR sequence of the extinct O. cuvieri was recovered within the cuvieri clade (same haplotype as one representative of O. pentlandii), so the mtDNA of the former species might still be represented in the wild.
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Affiliation(s)
- Yareli Esquer Garrigos
- UMR BOREA, Département Milieux et Peuplements Aquatiques MNHN - CNRS 7208 - IRD 207 - UPMC, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231 Paris, France.
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Gaubert P, Antunes A. What's behind these scales? Comments to "The complete mitochondrial genome of Temminck's ground pangolin (Smutsia temminckii; Smuts, 1832) and phylogenetic position of the Pholidota (Weber, 1904)". Gene 2015; 563:106-8. [PMID: 25796606 DOI: 10.1016/j.gene.2015.03.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 03/10/2015] [Accepted: 03/13/2015] [Indexed: 11/16/2022]
Affiliation(s)
- Philippe Gaubert
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UM2-CNRS-IRD, Université de Montpellier, Place Eugène Bataillon, CC 64, 34095 Montpellier Cedex 05, France.
| | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
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Papeş M, Cuzin F, Gaubert P. Niche dynamics in the European ranges of two African carnivores reflect their dispersal and demographic histories. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12477] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Monica Papeş
- Department of Zoology; Oklahoma State University; 501 Life Sciences West Stillwater OK 74078 USA
| | | | - Philippe Gaubert
- Institut des Sciences de l'Evolution de Montpellier (ISEM) - UM2-CNRS-IRD; Université Montpellier 2; Place Eugène Bataillon - CC 64 34095 Montpellier, Cedex 05 France
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Esquer-Garrigos Y, Hugueny B, Ibañez C, Zepita C, Koerner K, Lambourdière J, Couloux A, Gaubert P. Detecting natural hybridization between two vulnerable Andean pupfishes (Orestias agassizii and O. luteus) representative of the Altiplano endemic fisheries. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0695-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Gaubert P, Njiokou F, Olayemi A, Pagani P, Dufour S, Danquah E, Nutsuakor MEK, Ngua G, Missoup AD, Tedesco PA, Dernat R, Antunes A. Bushmeat genetics: setting up a reference framework for the DNA typing of African forest bushmeat. Mol Ecol Resour 2014; 15:633-51. [DOI: 10.1111/1755-0998.12334] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 09/17/2014] [Accepted: 09/19/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Philippe Gaubert
- Institut des Sciences de l'Evolution de Montpellier - UM2-CNRS-IRD; Université Montpellier 2; Place Eugène Bataillon - CC 64 34095 Montpellier Cedex 05 France
| | - Flobert Njiokou
- Laboratoire de Parasitologie et d'Ecologie; Faculté des Sciences; Université de Yaoundé I; BP 812 Yaoundé Cameroon
| | - Ayodeji Olayemi
- Natural History Museum; Obafemi Awolowo University; Ho 220005 Ile-Ife Osun State Nigeria
| | - Paolo Pagani
- Dutch Wildlife Health Centre; Faculty of Veterinary Medicine; Yalelaan 1 3584 CL Utrecht The Netherlands
| | | | - Emmanuel Danquah
- Department of Wildlife and Range Management; Faculty of Renewable Natural Resources; Kwame Nkrumah University of Science and Technology; University Post Office; Kumasi Ghana
| | - Mac Elikem K. Nutsuakor
- Department of Wildlife and Range Management; Faculty of Renewable Natural Resources; Kwame Nkrumah University of Science and Technology; University Post Office; Kumasi Ghana
| | - Gabriel Ngua
- Amigos de la Naturaleza y del Desarrollo de Guinea Ecuatorial (ANDEGE); Barrió Ukomba, S/N Bata Equatorial Guinea
| | - Alain-Didier Missoup
- Biologie de l'Evolution - Mammalogie; Département de Biologie des Organismes Animaux; Faculté des Sciences; Université de Douala; BP 24157 Douala Cameroon
| | - Pablo A. Tedesco
- Département Milieux et Peuplements Aquatiques; Muséum National d'Histoire Naturelle; UMR Biologie des ORganismes et des Ecosystèmes Aquatiques (UMR BOREA IRD 207-CNRS 7208-UPMC-MNHN); 43 rue Cuvier FR-75231 Paris Cedex France
| | - Rémy Dernat
- Institut des Sciences de l'Evolution - CNRS UMR 5554; Plateforme Bioinformatique LabEx; Université Montpellier 2; Place Eugène Bataillon 34095 Montpellier Cedex 05 France
| | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental; Universidade do Porto; Rua dos Bragas, 177 4050-123 Porto Portugal
- Departamento de Biologia; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre 4169-007 Porto Portugal
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Amroun M, Oubellil D, Gaubert P. Écologie trophique du Chacal doré dans le Parc National du Djurdjura (Kabylie, Algérie). revec 2014. [DOI: 10.3406/revec.2014.1753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Amroun M, Bensidhoum M, Delattre P, Gaubert P. Feeding habits of the common genet (Genetta genetta) in the area of Djurdjura, north of Algeria. MAMMALIA 2014. [DOI: 10.1515/mammalia-2012-0111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Gaubert P, Bloch C, Benyacoub S, Abdelhamid A, Pagani P, Djagoun CAMS, Couloux A, Dufour S. Reviving the African wolf Canis lupus lupaster in North and West Africa: a mitochondrial lineage ranging more than 6,000 km wide. PLoS One 2012; 7:e42740. [PMID: 22900047 PMCID: PMC3416759 DOI: 10.1371/journal.pone.0042740] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 07/12/2012] [Indexed: 11/19/2022] Open
Abstract
The recent discovery of a lineage of gray wolf in North-East Africa suggests the presence of a cryptic canid on the continent, the African wolf Canis lupus lupaster. We analyzed the mtDNA diversity (cytochrome b and control region) of a series of African Canis including wolf-like animals from North and West Africa. Our objectives were to assess the actual range of C. l. lupaster, to further estimate the genetic characteristics and demographic history of its lineage, and to question its taxonomic delineation from the golden jackal C. aureus, with which it has been considered synonymous. We confirmed the existence of four distinct lineages within the gray wolf, including C. lupus/familiaris (Holarctic wolves and dogs), C. l. pallipes, C. l. chanco and C. l. lupaster. Taxonomic assignment procedures identified wolf-like individuals from Algeria, Mali and Senegal, as belonging to C. l. lupaster, expanding its known distribution c. 6,000 km to the west. We estimated that the African wolf lineage (i) had the highest level of genetic diversity within C. lupus, (ii) coalesced during the Late Pleistocene, contemporaneously with Holarctic wolves and dogs, and (iii) had an effective population size of c. 80,000 females. Our results suggest that the African wolf is a relatively ancient gray wolf lineage with a fairly large, past effective population size, as also suggested by the Pleistocene fossil record. Unique field observations in Senegal allowed us to provide a morphological and behavioral diagnosis of the African wolf that clearly distinguished it from the sympatric golden jackal. However, the detection of C. l. lupaster mtDNA haplotypes in C. aureus from Senegal brings the delineation between the African wolf and the golden jackal into question. In terms of conservation, it appears urgent to further characterize the status of the African wolf with regard to the African golden jackal.
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Affiliation(s)
- Philippe Gaubert
- UMR BOREA IRD 207, Muséum National d'Histoire Naturelle, Paris, France.
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Olayemi A, Oyeyiola A, Antunes A, Bonillo C, Cruaud C, Gaubert P. Contribution of DNA-typing to bushmeat surveys: assessment of a roadside market in south-western Nigeria. Wildl Res 2011. [DOI: 10.1071/wr11015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
Following recent socioeconomic transformations in western and central Africa, the volume of bushmeat hunting, a traditional source of proteins and revenue for rural populations, has reached unsustainable levels. The morphological identification of species sold on bushmeat market stalls may be challenging because of the presence of cryptic taxa and smoked or processed carcasses.
Aims
To assess the contribution of DNA-typing to traditional bushmeat surveys. We conducted a case study at a roadside bushmeat market in Asejire, south-western Nigeria, to characterise the mammalian diversity and sketch out the dynamics of the bushmeat trade.
Methods
We generated a 402-bp Cytochrome b fragment using a ‘universal’ mitochondrial primer pair that successfully amplified across five mammalian orders, and used assignment procedures to assess the taxonomic identification of the traded species. We combined DNA-typing with morphological-based market surveys and questionnaires to half (n = 20) of the market stakeholders.
Key results
Our combined morphological–DNA-based survey revealed a total of 17 species, representing seven mammalian orders (Rodentia, Lagomorpha, Primates, Hyracoidea, Carnivora, Pholidota and Artiodactyla). DNA-typing allowed identifying the Walter’s duiker, a cryptic, newly described species from the Dahomey Gap, and diagnosing an unidentified primate as the white-throated monkey, Cercopithecus erythrogaster, a species of high conservation concern in Nigeria. K2P pairwise genetic distances among all species exceeded the 11% threshold, indicative of species-level distinction. The most hunted species were the Walter’s duiker and, to a lesser extent, the greater cane rat, Thryonomys swinderianus. Questionnaires to traders revealed that the Asejire roadside market was a straightforward trader–hunter system centralising off-takes from distant hunting sites.
Conclusions
We showed how mitochondrial DNA-typing combined with assignment procedures improved the characterisation of the mammalian diversity sold on bushmeat markets. The hunted mammalian community consisted of versatile, small- to medium-sized secondary forest species characteristic of the Dahomey Gap assemblage; their sustainable management is in doubt because of the lack of conservation and health awareness within the traders’ community.
Implications
Given the utility of mitochondrial DNA-typing in identifying species sold in bushmeat markets, we argue in favour of multi-entry investigations to reach a comprehensive characterisation of the bushmeat trade. The building of a web-accessible mtDNA database covering the spectrum of the species hunted for bushmeat would appear to be a valuable diagnostic tool that may help Nigeria and neighbouring countries to set up a rigorous monitoring of wildlife extirpation.
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Fechner LC, Vincent-Hubert F, Gaubert P, Bouchez T, Gourlay-Francé C, Tusseau-Vuillemin MH. Combined eukaryotic and bacterial community fingerprinting of natural freshwater biofilms using automated ribosomal intergenic spacer analysis. FEMS Microbiol Ecol 2010; 74:542-53. [PMID: 20883495 DOI: 10.1111/j.1574-6941.2010.00968.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Biofilms are complex communities playing an important role in aquatic ecosystems. Automated ribosomal intergenic spacer analysis (ARISA) has been used successfully to explore biofilm bacterial diversity. However, a gap remains to be filled as regards its application to biofilm eukaryotic populations. The aim of this study is to use ARISA to detect eukaryotic population shifts in biofilm. We designed a new set of primers to focus specifically on the ITS1-5.8S-ITS2 region of diatoms and tested it on natural biofilms. Additionally, we tested universal primers, used previously to perform ARISA on fungal communities. Cloning and sequencing showed that the universal primer set amplified various eukaryotes, whereas the new set was diatom specific. The new set amplified a wider variety of diatoms. Therefore, the universal set is appropriate to study the general eukaryotic population shifts in biofilms, whereas the new set is more appropriate to study diatoms specifically. We used both primer sets, along with a bacterial set, to study the population shifts in natural river biofilms. Principal component analysis of the ARISA fingerprints revealed seasonal shifts that did not coincide for bacterial and eukaryotic communities. Therefore, the use of both eukaryotic and bacterial primers provides a useful insight to assess microbial succession in biofilms.
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Affiliation(s)
- Lise C Fechner
- Cemagref - Unité de Recherche Hydrosystèmes et Bioprocédés, Antony, France.
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Gaubert P, Mézan-Muxart V. Where have the ‘black genets’ gone? A likely restriction of melanistic cases of the common genet (Genetta genetta) to its introduced range. Mamm Biol 2010. [DOI: 10.1016/j.mambio.2009.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Gaubert P, Denys G, Oberdorff T. Genus-level supertree of Cyprinidae (Actinopterygii: Cypriniformes), partitioned qualitative clade support and test of macro-evolutionary scenarios. Biol Rev Camb Philos Soc 2009; 84:653-89. [DOI: 10.1111/j.1469-185x.2009.00091.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Affiliation(s)
- P. Gaubert
- UMR BOREA IRD 207, Muséum National d'Histoire Naturelle, Paris, France
| | - M. Zenatello
- Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell'Emilia (BO), Italy
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Gaubert P, Del Cerro I, Palomares F, Godoy JA. Development and characterization of 11 microsatellite loci in a historically introduced carnivoran, the common genet (Genetta genetta). Mol Ecol Resour 2008; 8:1375-7. [PMID: 21586050 DOI: 10.1111/j.1755-0998.2008.02277.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Microsatellite markers were developed to assess population structure and patterns of translocation in the introduced European common genet (Genetta genetta). Primer pairs were designed for 60 microsatellite sequences enriched for CA, GA, CATC and TAGA repeat motifs. Eleven loci that proved to be polymorphic were genotyped in 33 individuals from southwestern France. The number of alleles per locus and observed heterozygosities varied from three to seven and from 0.2121 to 0.7576, respectively. One locus (B103) showed significant departure from Hardy-Weinberg equilibrium, probably due to the presence of null alleles. Tests of linkage disequilibrium did not detect significant associations among loci.
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Affiliation(s)
- P Gaubert
- Departamento de Biología de la Conservación, Departamento de Ecología Integrativa, Estación Biológica de Doñana, CSIC, Pabellón del Perú, Avda María Luisa s/n, 41013 Sevilla, Spain, UR IRD 131 - UMS MNHN 403, Département Milieux et Peuplements Aquatiques, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75005 Paris, France, Genética de la Conservación Animal, IRTA, Ctra de Cabrils, s/n 08348 Cabrils, Barcelona, Spain
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Gaubert P, Begg CM. Re-assessed molecular phylogeny and evolutionary scenario within genets (Carnivora, Viverridae, Genettinae). Mol Phylogenet Evol 2007; 44:920-7. [PMID: 17275350 DOI: 10.1016/j.ympev.2006.12.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Revised: 10/24/2006] [Accepted: 12/08/2006] [Indexed: 11/17/2022]
Affiliation(s)
- Philippe Gaubert
- Estación Biológica de Doñana (CSIC), Departamento de Biología Aplicada, Sevilla, Spain.
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Bichain JM, Gaubert P, Samadi S, Boisselier-Dubayle MC. A gleam in the dark: phylogenetic species delimitation in the confusing spring-snail genus Bythinella Moquin-Tandon, 1856 (Gastropoda: Rissooidea: Amnicolidae). Mol Phylogenet Evol 2007; 45:927-41. [PMID: 17923422 DOI: 10.1016/j.ympev.2007.07.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Revised: 06/26/2007] [Accepted: 07/19/2007] [Indexed: 11/26/2022]
Abstract
We re-assess the value of morphological specific descriptors within the spring-snail genus Bythinella by sequencing mitochondrial COI and nuclear ITS1 gene fragments. Taxonomic coverage represents 16 nominal species sampled among 35 populations from France. Application of monophyly and cohesive haplotype networks as criteria to delineate species allow us to identify 10 mitochondrial species-level lineages, all but one of which are recovered by ITS1. COI species thresholds that are estimated from newly delimited species (ca. 1.5%) agree with values found among other hydrobioids. Our results strongly suggest that classical morphological descriptors may not constitute valid specific criteria within Bythinella. Our analyses support a complex scenario of invasions of subterranean habitats, as illustrated by the syntopy of several mitochondrial lineages or the conflicting evolutionary histories between COI and ITS1 in caves. In addition, morphological convergence related to subterranean ecological constraints that affect shell shape and size among the hypogean springsnails studied is suspected.
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Affiliation(s)
- Jean-Michel Bichain
- Taxonomie et Collections, Département Systématique et Evolution (USM 602), Muséum National d'Histoire Naturelle, Case postale 51, 55 rue Buffon, F-75005 Paris Cedex 05, France.
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