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van Elst T, Sgarlata GM, Schüßler D, Tiley GP, Poelstra JW, Scheumann M, Blanco MB, Aleixo-Pais IG, Rina Evasoa M, Ganzhorn JU, Goodman SM, Hasiniaina AF, Hending D, Hohenlohe PA, Ibouroi MT, Iribar A, Jan F, Kappeler PM, Le Pors B, Manzi S, Olivieri G, Rakotonanahary AN, Rakotondranary SJ, Rakotondravony R, Ralison JM, Ranaivoarisoa JF, Randrianambinina B, Rasoloarison RM, Rasoloharijaona S, Rasolondraibe E, Teixeira H, Zaonarivelo JR, Louis EE, Yoder AD, Chikhi L, Radespiel U, Salmona J. Integrative taxonomy clarifies the evolution of a cryptic primate clade. Nat Ecol Evol 2024:10.1038/s41559-024-02547-w. [PMID: 39333396 DOI: 10.1038/s41559-024-02547-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 08/23/2024] [Indexed: 09/29/2024]
Abstract
Global biodiversity is under accelerating threats, and species are succumbing to extinction before being described. Madagascar's biota represents an extreme example of this scenario, with the added complication that much of its endemic biodiversity is cryptic. Here we illustrate best practices for clarifying cryptic diversification processes by presenting an integrative framework that leverages multiple lines of evidence and taxon-informed cut-offs for species delimitation, while placing special emphasis on identifying patterns of isolation by distance. We systematically apply this framework to an entire taxonomically controversial primate clade, the mouse lemurs (genus Microcebus, family Cheirogaleidae). We demonstrate that species diversity has been overestimated primarily due to the interpretation of geographic variation as speciation, potentially biasing inference of the underlying processes of evolutionary diversification. Following a revised classification, we find that crypsis within the genus is best explained by a model of morphological stasis imposed by stabilizing selection and a neutral process of niche diversification. Finally, by clarifying species limits and defining evolutionarily significant units, we provide new conservation priorities, bridging fundamental and applied objectives in a generalizable framework.
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Affiliation(s)
- Tobias van Elst
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Germany.
| | - Gabriele M Sgarlata
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
- Department of Evolution and Ecology, University of California, Davis, CA, USA.
| | - Dominik Schüßler
- Institute of Biology and Chemistry, University of Hildesheim, Hildesheim, Germany.
| | - George P Tiley
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Biology, Duke University, Durham, NC, USA
| | - Jelmer W Poelstra
- Department of Biology, Duke University, Durham, NC, USA
- Molecular and Cellular Imaging Center, The Ohio State University, Columbus, OH, USA
| | - Marina Scheumann
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Germany
| | | | - Isa G Aleixo-Pais
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, Bragança, Portugal
| | - Mamy Rina Evasoa
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Germany
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga, Madagascar
| | - Jörg U Ganzhorn
- Department of Biology, Universität Hamburg, Hamburg, Germany
| | - Steven M Goodman
- Field Museum of Natural History, Chicago, IL, USA
- Association Vahatra, Antananarivo, Madagascar
| | - Alida F Hasiniaina
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Germany
- School for International Training, Antananarivo, Madagascar
| | - Daniel Hending
- John Krebs Field Station, Department of Biology, University of Oxford, Wytham, UK
| | - Paul A Hohenlohe
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Mohamed T Ibouroi
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Université de La Réunion, Saint-Denis de La Réunion, France
| | - Amaia Iribar
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR5300 Université Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 Paul Sabatier (UT3), Toulouse, France
| | - Fabien Jan
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Peter M Kappeler
- Department Sociobiology/Anthropology, Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University Göttingen, Göttingen, Germany
- Behavioral Ecology and Sociobiology Unit, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | | | - Sophie Manzi
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR5300 Université Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 Paul Sabatier (UT3), Toulouse, France
| | - Gillian Olivieri
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Germany
- University of Warwick, Coventry, UK
| | - Ando N Rakotonanahary
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga, Madagascar
| | - S Jacques Rakotondranary
- Mention Anthropobiologie et Développement Durable, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Romule Rakotondravony
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga, Madagascar
- Ecole Doctorale Ecosystèmes Naturels (EDEN), Université de Mahajanga, Mahajanga, Madagascar
| | - José M Ralison
- Département de Biologie Animale, Université d'Antananarivo, Antananarivo, Madagascar
| | - J Freddy Ranaivoarisoa
- Mention Anthropobiologie et Développement Durable, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Blanchard Randrianambinina
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga, Madagascar
- Ecole Doctorale Ecosystèmes Naturels (EDEN), Université de Mahajanga, Mahajanga, Madagascar
| | - Rodin M Rasoloarison
- Department Sociobiology/Anthropology, Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University Göttingen, Göttingen, Germany
| | | | | | - Helena Teixeira
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Germany
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), Saint-Denis de La Réunion, France
| | - John R Zaonarivelo
- Département des Sciences de la Nature et de l'Environnement, Université d'Antsiranana, Antsiranana, Madagascar
| | - Edward E Louis
- Madagascar Biodiversity Partnership, Antananarivo, Madagascar
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR5300 Université Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 Paul Sabatier (UT3), Toulouse, France
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Jordi Salmona
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR5300 Université Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 Paul Sabatier (UT3), Toulouse, France.
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Paietta EN, Kraberger S, Lund MC, Vargas KL, Custer JM, Ehmke E, Yoder AD, Varsani A. Diverse Circular DNA Viral Communities in Blood, Oral, and Fecal Samples of Captive Lemurs. Viruses 2024; 16:1099. [PMID: 39066262 PMCID: PMC11281440 DOI: 10.3390/v16071099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
Few studies have addressed viral diversity in lemurs despite their unique evolutionary history on the island of Madagascar and high risk of extinction. Further, while a large number of studies on animal viromes focus on fecal samples, understanding viral diversity across multiple sample types and seasons can reveal complex viral community structures within and across species. Groups of captive lemurs at the Duke Lemur Center (Durham, NC, USA), a conservation and research center, provide an opportunity to build foundational knowledge on lemur-associated viromes. We sampled individuals from seven lemur species, i.e., collared lemur (Eulemur collaris), crowned lemur (Eulemur coronatus), blue-eyed black lemur (Eulemur flavifrons), ring-tailed lemur (Lemur catta), Coquerel's sifaka (Propithecus coquereli), black-and-white ruffed lemur (Varecia variegata variegata), and red ruffed lemur (Varecia rubra), across two lemur families (Lemuridae, Indriidae). Fecal, blood, and saliva samples were collected from Coquerel's sifaka and black-and-white ruffed lemur individuals across two sampling seasons to diversify virome biogeography and temporal sampling. Using viral metagenomic workflows, the complete genomes of anelloviruses (n = 4), cressdnaviruses (n = 47), caudoviruses (n = 15), inoviruses (n = 34), and microviruses (n = 537) were determined from lemur blood, feces, and saliva. Many virus genomes, especially bacteriophages, identified in this study were present across multiple lemur species. Overall, the work presented here uses a viral metagenomics approach to investigate viral communities inhabiting the blood, oral cavity, and feces of healthy captive lemurs.
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Affiliation(s)
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Michael C. Lund
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Karla L. Vargas
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Joy M. Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Erin Ehmke
- Duke Lemur Center, Duke University, Durham, NC 27708, USA
| | - Anne D. Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
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