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Mochales-Riaño G, Burriel-Carranza B, Barros MI, Velo-Antón G, Talavera A, Spilani L, Tejero-Cicuéndez H, Crochet PA, Piris A, García-Cardenete L, Busais S, Els J, Shobrak M, Brito JC, Šmíd J, Carranza S, Martínez-Freiría F. Hidden in the sand: Phylogenomics unravel an unexpected evolutionary history for the desert-adapted vipers of the genus Cerastes. Mol Phylogenet Evol 2024; 191:107979. [PMID: 38040070 DOI: 10.1016/j.ympev.2023.107979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
The desert vipers of the genus Cerastes are a small clade of medically important venomous snakes within the family Viperidae. According to published morphological and molecular studies, the group is comprised by four species: two morphologically similar and phylogenetically sister taxa, the African horned viper (Cerastes cerastes) and the Arabian horned viper (Cerastes gasperettii); a more distantly related species, the Saharan sand viper (Cerastes vipera), and the enigmatic Böhme's sand viper (Cerastes boehmei), only known from a single specimen in captivity allegedly captured in Central Tunisia. In this study, we sequenced one mitochondrial marker (COI) as well as genome-wide data (ddRAD sequencing) from 28 and 41 samples, respectively, covering the entire distribution range of the genus to explore the population genomics, phylogenomic relationships and introgression patterns within the genus Cerastes. Additionally, and to provide insights into the mode of diversification of the group, we carried out niche overlap analyses considering climatic and habitat variables. Both nuclear phylogenomic reconstructions and population structure analyses have unveiled an unexpected evolutionary history for the genus Cerastes, which sharply contradicts the morphological similarities and previously published mitochondrial approaches. Cerastes cerastes and C. vipera are recovered as sister taxa whilst C. gasperettii is a sister taxon to the clade formed by these two species. We found a relatively high niche overlap (OI > 0.7) in both climatic and habitat variables between C. cerastes and C. vipera, contradicting a potential scenario of sympatric speciation. These results are in line with the introgression found between the northwestern African populations of C. cerastes and C. vipera. Finally, our genomic data confirms the existence of a lineage of C. cerastes in Arabia. All these results highlight the importance of genome-wide data over few genetic markers to study the evolutionary history of species.
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Affiliation(s)
| | - Bernat Burriel-Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain; Museu de Ciències Naturals de Barcelona, P° Picasso s/n, Parc Ciutadella, 08003 Barcelona, Spain
| | - Margarida Isabel Barros
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Guillermo Velo-Antón
- Universidad de Vigo, Facultad de Biología, Edificio de Ciencias Experimentales, Bloque B, Planta 2, Laboratorio 39 (Grupo GEA), E-36310 Vigo, Spain
| | - Adrián Talavera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Loukia Spilani
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Héctor Tejero-Cicuéndez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain; Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | | | - Alberto Piris
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Luis García-Cardenete
- Agencia de Medio Ambiente y Agua de Andalucía, C/Johan G. Gutenberg, 1, 41092 Seville, Spain
| | - Salem Busais
- Department of Biology, Faculty of Education, Aden University, Yemen
| | - Johannes Els
- Breeding Centre for Endangered Arabian Wildlife, Environment and Protected Areas Authority, Sharjah, United Arab Emirates
| | - Mohammed Shobrak
- National Center for Wildlife, Prince Saud Al Faisal Wildlife Research Centre, Taif, Saudi Arabia
| | - José Carlos Brito
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Jiří Šmíd
- Department of Zoology, Faculty of Science, Charles University, Vinicná 7, Prague, Czech Republic
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Fernando Martínez-Freiría
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal.
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2
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L Rocha J, Silva P, Santos N, Nakamura M, Afonso S, Qninba A, Boratynski Z, Sudmant PH, Brito JC, Nielsen R, Godinho R. North African fox genomes show signatures of repeated introgression and adaptation to life in deserts. Nat Ecol Evol 2023; 7:1267-1286. [PMID: 37308700 PMCID: PMC10527534 DOI: 10.1038/s41559-023-02094-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 04/26/2023] [Indexed: 06/14/2023]
Abstract
Elucidating the evolutionary process of animal adaptation to deserts is key to understanding adaptive responses to climate change. Here we generated 82 individual whole genomes of four fox species (genus Vulpes) inhabiting the Sahara Desert at different evolutionary times. We show that adaptation of new colonizing species to a hot arid environment has probably been facilitated by introgression and trans-species polymorphisms shared with older desert resident species, including a putatively adaptive 25 Mb genomic region. Scans for signatures of selection implicated genes affecting temperature perception, non-renal water loss and heat production in the recent adaptation of North African red foxes (Vulpes vulpes), after divergence from Eurasian populations approximately 78 thousand years ago. In the extreme desert specialists, Rueppell's fox (V. rueppellii) and fennec (V. zerda), we identified repeated signatures of selection in genes affecting renal water homeostasis supported by gene expression and physiological differences. Our study provides insights into the mechanisms and genetic underpinnings of a natural experiment of repeated adaptation to extreme conditions.
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Affiliation(s)
- Joana L Rocha
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA, USA.
| | - Pedro Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Nuno Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Mónia Nakamura
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Abdeljebbar Qninba
- Laboratory of Geophysics and Natural Hazards, Geophysics, Natural Patrimony and Green Chemistry Research Center (GEOPAC), Institut Scientifique, Mohammed V University of Rabat, Rabat, Morocco
| | - Zbyszek Boratynski
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Peter H Sudmant
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - José C Brito
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Rasmus Nielsen
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, CA, USA.
- Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
- Department of Zoology, University of Johannesburg, Auckland Park, South Africa.
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3
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Brito JC, Sow AS, Vale CG, Pizzigalli C, Hamidou D, Gonçalves DV, Martínez-Freiría F, Santarém F, Rebelo H, Campos JC, Pleguezuelos JM, Ferreira da Silva MJ, Naia M, Tarroso P, Godinho R, Silva TL, Macedo T, Boratyński Z, Sidatt ZEA, Álvares F. Diversity, distribution and conservation of land mammals in Mauritania, North-West Africa. PLoS One 2022; 17:e0269870. [PMID: 35913972 PMCID: PMC9342785 DOI: 10.1371/journal.pone.0269870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/27/2022] [Indexed: 11/18/2022] Open
Abstract
Detailed knowledge about biodiversity distribution is critical for monitoring the biological effects of global change processes. Biodiversity knowledge gaps hamper the monitoring of conservation trends and they are especially evident in the desert biome. Mauritania constitutes a remarkable example on how remoteness and regional insecurity affect current knowledge gaps. Mammals remain one of the least studied groups in this country, without a concerted species checklist, the mapping of regions concentrating mammal diversity, or a national assessment of their conservation status. This work assessed the diversity, distribution, and conservation of land mammals in Mauritania. A total of 6,718 published and original observations were assembled in a spatial database and used to update the occurrence status, distribution area, and conservation status. The updated taxonomic list comprises 107 species, including 93 extant, 12 Regionally Extinct, and 2 Extinct in the Wild. Mapping of species distributions allowed locating concentrations of extant mammal species richness in coastal areas, along the Senegal River valley, and in mountain plateaus. Recent regional extinction of large-sized Artiodactyla and Carnivora has been very high (11% extinct species). From the extant mammals, 11% are threatened, including flagship species (e.g., Addax nasomaculatus and Panthera pardus). Species richness is poorly represented by the current protected areas. Despite the strong advances made, 23% of species categorise as Data Deficient. Persisting systematics and distribution uncertainties require further research. Field surveys in currently unexplored areas (northern and south-eastern regions) are urgently needed to increase knowledge about threatened mammals. The long-term conservation of land mammals in Mauritania is embedded in a complex web of socioeconomic and environmental factors that call for collaborative action and investment in sustainable human development. The current work sets the baseline for the future development of detailed research studies and to address the general challenges faced by mammals and biodiversity in the country.
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Affiliation(s)
- José Carlos Brito
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- * E-mail:
| | - Andack Saad Sow
- Green Sahel Expertise: Bureau d’Études Spécialise en Environnement, Nouakchott, R.I. Mauritanie
| | - Cândida Gomes Vale
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
| | - Cristian Pizzigalli
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Dieng Hamidou
- Faculté des Sciences et Techniques, Université des Sciences, de Technologie et de Médecine de Nouakchott, Nouakchott, R.I. Mauritanie
| | - Duarte Vasconcelos Gonçalves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
| | - Fernando Martínez-Freiría
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Frederico Santarém
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Hugo Rebelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - João Carlos Campos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | | | - Maria Joana Ferreira da Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Marisa Naia
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
| | - Pedro Tarroso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| | - Teresa Luísa Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
| | - Tiago Macedo
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Zbyszek Boratyński
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | | | - Francisco Álvares
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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4
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Adavoudi R, Pilot M. Consequences of Hybridization in Mammals: A Systematic Review. Genes (Basel) 2021; 13:50. [PMID: 35052393 PMCID: PMC8774782 DOI: 10.3390/genes13010050] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
Hybridization, defined as breeding between two distinct taxonomic units, can have an important effect on the evolutionary patterns in cross-breeding taxa. Although interspecific hybridization has frequently been considered as a maladaptive process, which threatens species genetic integrity and survival via genetic swamping and outbreeding depression, in some cases hybridization can introduce novel adaptive variation and increase fitness. Most studies to date focused on documenting hybridization events and analyzing their causes, while relatively little is known about the consequences of hybridization and its impact on the parental species. To address this knowledge gap, we conducted a systematic review of studies on hybridization in mammals published in 2010-2021, and identified 115 relevant studies. Of 13 categories of hybridization consequences described in these studies, the most common negative consequence (21% of studies) was genetic swamping and the most common positive consequence (8%) was the gain of novel adaptive variation. The total frequency of negative consequences (49%) was higher than positive (13%) and neutral (38%) consequences. These frequencies are biased by the detection possibilities of microsatellite loci, the most common genetic markers used in the papers assessed. As negative outcomes are typically easier to demonstrate than positive ones (e.g., extinction vs hybrid speciation), they may be over-represented in publications. Transition towards genomic studies involving both neutral and adaptive variation will provide a better insight into the real impacts of hybridization.
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Affiliation(s)
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, ul. Nadwiślańska 108, 80-680 Gdańsk, Poland;
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5
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El-Farhati H, Hizem MW, Nouira S. Original record of deposited skins of hedgehogs (Erinaceidae) at red fox den. MAMMALIA 2021. [DOI: 10.1515/mammalia-2020-0098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
From 2015 to 2018, a total of 60 dens of red fox Vulpes vulpes have been visited in three sites of southern Tunisia. In this arid habitat, we recorded deposited skins of hedgehogs in front of 34 dens, an uncommon behaviour to our knowledge. These sightings suggest that red fox can be the main predator of hedgehogs in arid zones of North Africa.
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Affiliation(s)
- Haithem El-Farhati
- Department of Biological Sciences , Research Unit (Wildlife Ecology), Tunis Faculty of Sciences, Tunis El-Manar University , 2092 Tunis , Tunisia
| | - Mohamed Wassim Hizem
- Department of Biological Sciences , Research Unit (Wildlife Ecology), Tunis Faculty of Sciences, Tunis El-Manar University , 2092 Tunis , Tunisia
| | - Saïd Nouira
- Department of Biological Sciences , Research Unit (Wildlife Ecology), Tunis Faculty of Sciences, Tunis El-Manar University , 2092 Tunis , Tunisia
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6
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Brito JC, Del Barrio G, Stellmes M, Pleguezuelos JM, Saarinen J. Drivers of change and conservation needs for vertebrates in drylands: an assessment from global scale to Sahara-Sahel wetlands. THE EUROPEAN ZOOLOGICAL JOURNAL 2021. [DOI: 10.1080/24750263.2021.1991496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- J. C. Brito
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da, Universidade do Porto, Portugal
- Departamento de Biologia da Faculdade de Ciências da, Universidade do Porto, Portugal
| | - G. Del Barrio
- Estación Experimental de Zonas Áridas (CSIC), Ctra. Sacramento sn, La Cañada, Spain
| | - M. Stellmes
- Institute of Geographical Sciences, Remote Sensing and Geoinformatics, Freie Universität Berlin, Germany
| | - J. M. Pleguezuelos
- Departamento de Zoología, Facultad de Ciencias, Universidad de Granada, Spain
| | - J. Saarinen
- Geography Research Unit, University of Oulu, Finland
- School of Tourism and Hospitality, University of Johannesburg, South Africa
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7
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Meliane MK, Saidi A, Boufaroua M, Petretto M, Riordan P, Gilbert T. Rüppell's fox (
V
ulpes rueppellii
) and its habitat in Jbil National Park, Tunisia. Afr J Ecol 2021. [DOI: 10.1111/aje.12868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Mohamed Khalil Meliane
- Marwell Wildlife Colden Common Winchester UK
- Research Laboratory of Biodiversity Management and Conservation of Biological Systems Faculty of Science of TunisUniversity of Tunis El Manar Tunis Tunisia
| | - Amira Saidi
- Marwell Wildlife Colden Common Winchester UK
- Research Laboratory of Biodiversity Management and Conservation of Biological Systems Faculty of Science of TunisUniversity of Tunis El Manar Tunis Tunisia
| | - Mohamed Boufaroua
- Direction Générale des Forêts Ministre de l'Agriculture des Ressources Hydrauliques et de la Pêche Maritime Tunis Tunisia
| | | | - Philip Riordan
- Marwell Wildlife Colden Common Winchester UK
- Biological Sciences Faculty of Environmental and Life Sciences University of Southampton Southampton UK
| | - Tania Gilbert
- Marwell Wildlife Colden Common Winchester UK
- Biological Sciences Faculty of Environmental and Life Sciences University of Southampton Southampton UK
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8
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Sarabia C, vonHoldt B, Larrasoaña JC, Uríos V, Leonard JA. Pleistocene climate fluctuations drove demographic history of African golden wolves (Canis lupaster). Mol Ecol 2020; 30:6101-6120. [PMID: 33372365 DOI: 10.1111/mec.15784] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/03/2020] [Accepted: 12/14/2020] [Indexed: 12/31/2022]
Abstract
Pleistocene climate change impacted entire ecosystems throughout the world. In the northern hemisphere, the distribution of Arctic species expanded during glacial periods, while more temperate and mesic species contracted into climatic refugia, where isolation drove genetic divergence. Cycles of local cooling and warming in the Sahara region of northern Africa caused repeated contractions and expansions of savannah-like environments which connected mesic species isolated in refugia during interglacial times, possibly driving population expansions and contractions; divergence and geneflow in the associated fauna. Here, we use whole genome sequences of African golden wolves (Canis lupaster), a generalist mesopredator with a wide distribution in northern Africa to estimate their demographic history and past episodes of geneflow. We detect a correlation between divergence times and cycles of increased aridity-associated Pleistocene glacial cycles. A complex demographic history with responses to local climate change in different lineages was found, including a relict lineage north of the High Atlas Mountains of Morocco that has been isolated for more than 18,000 years, possibly a distinct ecotype.
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Affiliation(s)
- Carlos Sarabia
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC, Seville, Spain
| | - Bridgett vonHoldt
- Faculty of Ecology and Evolutionary Biology, University of Princeton, Princeton, NJ, USA
| | | | - Vicente Uríos
- Vertebrate Zoology Research Group, University of Alicante, Alicante, Spain
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC, Seville, Spain
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9
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Dell'Arte GL, Leonardi G. Scat‐marking behaviour of red foxes (
Vulpes vulpes
) in a semi‐arid island of Tunisia. Afr J Ecol 2020. [DOI: 10.1111/aje.12763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Albrecht F, Hering J, Fuchs E, Illera JC, Ihlow F, Shannon TJ, Collinson JM, Wink M, Martens J, Päckert M. Phylogeny of the Eurasian Wren Nannus troglodytes (Aves: Passeriformes: Troglodytidae) reveals deep and complex diversification patterns of Ibero-Maghrebian and Cyrenaican populations. PLoS One 2020; 15:e0230151. [PMID: 32191719 PMCID: PMC7082076 DOI: 10.1371/journal.pone.0230151] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 02/22/2020] [Indexed: 11/19/2022] Open
Abstract
The Mediterranean Basin represents a Global Biodiversity Hotspot where many organisms show high inter- and intraspecific differentiation. Extant phylogeographic patterns of terrestrial circum-Mediterranean faunas were mainly shaped through Pleistocene range shifts and range fragmentations due to retreat into different glacial refugia. Thus, several extant Mediterranean bird species have diversified by surviving glaciations in different hospitable refugia and subsequently expanded their distribution ranges during the Holocene. Such a scenario was also suggested for the Eurasian Wren (Nannus troglodytes) despite the lack of genetic data for most Mediterranean subspecies. Our phylogenetic multi-locus analysis comprised 18 out of 28 currently accepted subspecies of N. troglodytes, including all but one subspecies which are present in the Mediterranean Basin. The resulting phylogenetic reconstruction dated the onset of the entire Holarctic radiation of three Nannus species to the early Pleistocene. In the Eurasian Wren, two North African subspecies represented separate basal lineages from the Maghreb (N. t. kabylorum) and from the Libyan Cyrenaica (N. t. juniperi), being only distantly related to other Mediterranean populations. Although N. troglodytes appeared to be paraphyletic with respect to the Nearctic Winter Wren (N. hiemalis), respective nodes did not receive strong statistical support. In contrast, paraphyly of the Ibero-Maghrebian taxon N. t. kabylorum was strongly supported. Southern Iberian populations of N. t. kabylorum did not clade with Maghrebian populations of the same subspecies but formed a sister clade to a highly diverse European clade (including nominate N. t. troglodytes and eight further taxa). In accordance with a pattern also found in other birds, Eurasian populations were split into a western clade (Europe, Caucasus) and an eastern clade (Central Asia, Sino-Himalayas, East Asia). This complex phylogeographic pattern revealed cryptic diversification in N. troglodytes, especially in the Iberio-Maghrebian region.
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Affiliation(s)
- Frederik Albrecht
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System Research, Dresden, Saxony, Germany
- * E-mail:
| | - Jens Hering
- Verein Sächsischer Ornithologen e.V., Limbach-Oberfrohna, Saxony, Germany
| | - Elmar Fuchs
- Verein Sächsischer Ornithologen e.V., Weimar, Thuringia, Germany
| | - Juan Carlos Illera
- Research Unit of Biodiversity (UO-CSIC-PA), Oviedo University, Asturias, Spain
| | - Flora Ihlow
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System Research, Dresden, Saxony, Germany
| | - Thomas J. Shannon
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - J. Martin Collinson
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Jochen Martens
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Rhineland-Palatinate, Germany
| | - Martin Päckert
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System Research, Dresden, Saxony, Germany
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11
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Moutinho AF, Serén N, Paupério J, Silva TL, Martínez-Freiría F, Sotelo G, Faria R, Mappes T, Alves PC, Brito JC, Boratyński Z. Evolutionary history of two cryptic species of northern African jerboas. BMC Evol Biol 2020; 20:26. [PMID: 32054437 PMCID: PMC7020373 DOI: 10.1186/s12862-020-1592-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/03/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Climatic variation and geologic change both play significant roles in shaping species distributions, thus affecting their evolutionary history. In Sahara-Sahel, climatic oscillations shifted the desert extent during the Pliocene-Pleistocene interval, triggering the diversification of several species. Here, we investigated how these biogeographical and ecological events have shaped patterns of genetic diversity and divergence in African Jerboas, desert specialist rodents. We focused on two sister and cryptic species, Jaculus jaculus and J. hirtipes, where we (1) evaluated their genetic differentiation, (2) reconstructed their evolutionary and demographic history; (3) tested the level of gene flow between them, and (4) assessed their ecological niche divergence. RESULTS The analyses based on 231 individuals sampled throughout North Africa, 8 sequence fragments (one mitochondrial and seven single copy nuclear DNA, including two candidate genes for fur coloration: MC1R and Agouti), 6 microsatellite markers and ecological modelling revealed: (1) two distinct genetic lineages with overlapping distributions, in agreement with their classification as different species, J. jaculus and J. hirtipes, with (2) low levels of gene flow and strong species divergence, (3) high haplotypic diversity without evident geographic structure within species, and (4) a low level of large-scale ecological divergence between the two taxa, suggesting species micro-habitat specialization. CONCLUSIONS Overall, our results suggest a speciation event that occurred during the Pliocene-Pleistocene transition. The contemporary distribution of genetic variation suggests ongoing population expansions. Despite the largely overlapping distributions at a macrogeographic scale, our genetic results suggest that the two species remain reproductively isolated, as only negligible levels of gene flow were observed. The overlapping ecological preferences at a macro-geographic scale and the ecological divergence at the micro-habitat scale suggest that local adaptation may have played a crucial role in the speciation process of these species.
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Affiliation(s)
- Ana Filipa Moutinho
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany.
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal.
- Department of Biology, Faculty of Science, University of Porto, Porto, Portugal.
| | - Nina Serén
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
- Department of Biology, Faculty of Science, University of Porto, Porto, Portugal
- Division of Ecology and Evolutionary Biology, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Joana Paupério
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
| | - Teresa Luísa Silva
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
| | - Fernando Martínez-Freiría
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
| | - Graciela Sotelo
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
| | - Rui Faria
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
| | - Tapio Mappes
- Division of Ecology and Evolutionary Biology, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Paulo Célio Alves
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
- Department of Biology, Faculty of Science, University of Porto, Porto, Portugal
| | - José Carlos Brito
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
- Department of Biology, Faculty of Science, University of Porto, Porto, Portugal
| | - Zbyszek Boratyński
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal.
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12
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Telcİoğlu M, İbİş O, Aksöyek E, Özcan S, Moradİ M, Gürkan ÖFİ, Tez C. Genetic analysis of Iranian and Turkish red foxes ( Vulpes vulpes) based on mitochondrial DNA (D-loop) sequences. ETHOL ECOL EVOL 2019. [DOI: 10.1080/03949370.2019.1639079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Murat Telcİoğlu
- Graduate School of Natural and Applied Sciences, Erciyes University, Kayseri, Turkey
| | - Osman İbİş
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey
- Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
| | - Eren Aksöyek
- Graduate School of Natural and Applied Sciences, Erciyes University, Kayseri, Turkey
| | - Servet Özcan
- Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
- Department of Biology, Faculty of Sciences, Erciyes University, Kayseri, Turkey
| | - Mohammad Moradİ
- Department of Biology, Faculty of Science, University of Zanjan, Zanjan, Iran
| | - Ömer Fİkret Gürkan
- Graduate School of Natural and Applied Sciences, Erciyes University, Kayseri, Turkey
| | - Coşkun Tez
- Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
- Department of Biology, Faculty of Sciences, Erciyes University, Kayseri, Turkey
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13
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Sacks BN, Lounsberry ZT, Statham MJ. Nuclear Genetic Analysis of the Red Fox Across its Trans-Pacific Range. J Hered 2019; 109:573-584. [PMID: 29889225 DOI: 10.1093/jhered/esy028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 06/05/2018] [Indexed: 11/14/2022] Open
Abstract
The red fox (Vulpes vulpes) occurs on multiple continents in diverse habitats, making it an informative system for evolutionary genomic research. However, its phylogeography remains unclear. Previously, mitochondrial DNA and small numbers of nuclear loci provided discordant views. Both markers indicated deep divergence (~ 0.5 million years [MY]) between Eurasian and southern North American populations but differed in the apparent continental affinity of Alaskan red foxes, implying some degree of gene exchange during secondary contact (~0.1 MY). We assayed >173000 nuclear genomic sites in 52 red foxes, along with 2 Rueppell's foxes (Vulpes rueppellii) and a gray wolf (Canis lupus) using the Illumina CanineHD BeadChip. We obtained 5107 single nucleotide polymorphisms (SNPs) in the foxes. Consistent with the Afro-Eurasian origins of red foxes, genetic diversity was higher in Eurasian than North American samples. Phylogenetic trees indicated that Alaskan and southern North American red foxes formed a monophyletic group nested within the Eurasian clade. However, admixture models suggested Alaskan red foxes contained up to 40% Eurasian ancestry. We hypothesize that North American red foxes either hybridized with Eurasian foxes in Beringia at the start of the last glaciation or merged with a Beringian population after the last glaciation. Future work is needed to test between these scenarios and assess speciation.
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Affiliation(s)
- Benjamin N Sacks
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, Davis, CA.,Department of Population Health and Reproduction, University of California, Davis, Davis, CA
| | - Zachary T Lounsberry
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, Davis, CA
| | - Mark J Statham
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, Davis, CA.,Department of Population Health and Reproduction, University of California, Davis, Davis, CA
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14
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Karssene Y, Godinho R, Chammem M, Cocchiararo B, Nouira S, Nowak C. Noninvasive DNA sampling and camera trapping suggest dramatic regional conservation status of an understudied carnivore: the Rüppell’s fox in Tunisia. J NAT HIST 2019. [DOI: 10.1080/00222933.2019.1656295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Yamna Karssene
- Département de Biologie, Faculté des Sciences de Tunis, Université de Tunis El- Manar, Tunis, Tunisia
- Laboratoire d’Elevage et de la Faune Sauvage, Institut des Régions Arides de Médenine, Médenine, Tunisia
| | - Raquel Godinho
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Department of Zoology, University of Johannesburg, Auckland Park, South Africa
| | - Mohsen Chammem
- Laboratoire d’Elevage et de la Faune Sauvage, Institut des Régions Arides de Médenine, Médenine, Tunisia
| | - Berardino Cocchiararo
- Senckenberg Research Institute and Natural History Museum Frankfurt, Conservation Genetics Group, Gelnhausen, Germany
| | - Said Nouira
- Département de Biologie, Faculté des Sciences de Tunis, Université de Tunis El- Manar, Tunis, Tunisia
| | - Carsten Nowak
- Senckenberg Research Institute and Natural History Museum Frankfurt, Conservation Genetics Group, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
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15
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Karssene Y, Nowak C, Chammem M, Cocchiararo B, Nouira S. Genetic diversity of the genus Vulpes (Red fox and Fennec fox) in Tunisia based on mitochondrial DNA and noninvasive DNA sampling. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2018.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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16
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Intraspecific genetic diversity and distribution of North African hedgehogs (Mammalia: Erinaceidae). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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17
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Castañeda I, Bellard C, Jarić I, Pisanu B, Chapuis J, Bonnaud E. Trophic patterns and home‐range size of two generalist urban carnivores: a review. J Zool (1987) 2018. [DOI: 10.1111/jzo.12623] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- I. Castañeda
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR 7204) Sorbonne Universités MNHN CNRS UPMC Paris France
- Ecologie, Systématique et Evolution (UMR CNRS 8079) Université Paris‐Sud XI Orsay Cedex France
| | - C. Bellard
- Unité Biologie des Organismes et Écosystèmes Aquatiques (BOREA UMR 7208) Sorbonne Universités Muséum National d'Histoire Naturelle Université Pierre et Marie Curie Université de Caen Normandie CNRS, IRD Université des Antilles Paris France
| | - I. Jarić
- Biology Centre of the Czech Academy of Sciences Institute of Hydrobiology České Budějovice Czech Republic
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries Berlin Germany
- Institute for Multidisciplinary Research University of Belgrade Belgrade Serbia
| | - B. Pisanu
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR 7204) Sorbonne Universités MNHN CNRS UPMC Paris France
- UMS 2006 Patrimoine Naturel AFB, MNHN CNRS Paris France
| | - J.‐L. Chapuis
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR 7204) Sorbonne Universités MNHN CNRS UPMC Paris France
| | - E. Bonnaud
- Ecologie, Systématique et Evolution (UMR CNRS 8079) Université Paris‐Sud XI Orsay Cedex France
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18
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Noninvasive genetic assessment provides evidence of extensive gene flow and possible high movement ability in the African golden wolf. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2018.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Abstract
Abstract
Conservation planning of threatened taxa relies upon accurate data on systematics, ecological traits and suitable habitats. The genus Gazella includes taxa with distinct morphologies and ecological traits, but close phylogenetic relationships. The North African Gazella cuvieri and Gazella leptoceros loderi share morphological and physiological characters but the former is darker and found in mountain areas, while the latter is lighter and associated with sand dunes. Here we aim to assess the genetic distinctiveness of these taxa, to characterize their ecological niches and to identify potential occurrence areas, by analysing 327 samples across North-West Africa. Phylogenetic analyses based on mitochondrial (CYTB) and five nuclear gene fragments (KCAS, LAC, SPTBN1, PRKCI and THYR) show that both taxa comprise a single monophyletic group. However, ecological niche-based modelling suggests that populations of these taxa occupy distinct geographic areas and specific environments. Predicted areas of sympatry were restricted, as a consequence of local sharp transitions in climatic traits. The lack of genetic differentiation between these taxa suggests they should be lumped into G. cuvieri, while ecological and morphological differences indicate they correspond to distinct ecotypes. Conservation planning of G. cuvieri should consider the preservation of both mountain and lowland ecotypes to maintain the overall adaptive potential of the species. This integrative approach provides valuable insights in identifying evolutionary units and should be extended to other gazelles.
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