Ecological and anthropogenic effects on the genomic diversity of lemurs in Madagascar.

Autor: Orkin JD; Département d'anthropologie, Université de Montréal, Montréal, Québec, Canada. joseph.orkin@umontreal.ca.; Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada. joseph.orkin@umontreal.ca.; IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain. joseph.orkin@umontreal.ca., Kuderna LFK; IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.; Illumina Artificial Intelligence Laboratory, Illumina Inc, Foster City, CA, USA., Hermosilla-Albala N; IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain., Fontsere C; IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.; Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark., Aylward ML; Department of Field and Conservation Science, Bristol Zoological Society, Bristol, UK., Janiak MC; School of Science, Engineering & Environment, University of Salford, Salford, UK., Andriaholinirina N; Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar., Balaresque P; Centre de Recherche sur la Biodiversité et l'Environnement, CNRS UMR5300, Université Toulouse III, Université de Toulouse, CNRS IRD, Toulouse, France., Blair ME; Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY, USA., Fausser JL; Institut de Médecine Légale, Faculté de Médecine, Université de Strasbourg, Strasbourg, France., Gut IG; Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain., Gut M; Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain., Hahn MW; Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN, USA., Harris RA; Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA., Horvath JE; Research & Collections, North Carolina Museum of Natural Sciences, Raleigh, NC, USA.; Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC, USA.; Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.; Department of Evolutionary Anthropology, Duke University, Durham, NC, USA., Keyser C; Institut de Médecine Légale, Faculté de Médecine, Université de Strasbourg, Strasbourg, France., Kitchener AC; Department of Natural Sciences, National Museums Scotland, Edinburgh, UK.; UK and School of Geosciences, University of Edinburgh, Edinburgh, UK., Le MD; Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam., Lizano E; IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.; Unidad de Paleobiología, ICP-CERCA, Unidad Asociada al CSIC por el IBE UPF-CSIC, Cerdanyola del Vallès, Spain.; Institut Català de Paleontologia Miquel Crusafont (ICP-CERCA), Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Cerdanyola del Vallès, Spain., Merker S; Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany., Nadler T; Cuc Phuong Commune, Ninh Binh Province, Vietnam., Perry GH; Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA, USA.; Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA., Rabarivola CJ; Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar.; Université de l'Itasy, Antananarivo, Madagascar., Rasmussen L; Copenhagen Zoo, Frederiksberg, Denmark., Raveendran M; Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA., Roos C; Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany., Wu DD; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China., Zaramody A; Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar., Zhang G; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.; Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China.; Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.; Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.; Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China., Zinner D; Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.; Department of Primate Cognition, Georg-August-University, Göttingen, Germany.; Leibniz-ScienceCampus Primate Cognition, Göttingen, Germany., Pozzi L; Department of Anthropology, University of Texas San Antonio, San Antonio, TX, USA., Rogers J; Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA., Farh KK; Illumina Artificial Intelligence Laboratory, Illumina Inc, Foster City, CA, USA., Marques Bonet T; IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain. tomas.marques@upf.edu.; Institut Català de Paleontologia Miquel Crusafont (ICP-CERCA), Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Cerdanyola del Vallès, Spain. tomas.marques@upf.edu.; CNAG-Centre for Genomic Analyses, Barcelona, Spain. tomas.marques@upf.edu.; Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Barcelona, Spain. tomas.marques@upf.edu.
Jazyk: angličtina
Zdroj: Nature ecology & evolution [Nat Ecol Evol] 2024 Dec 27. Date of Electronic Publication: 2024 Dec 27.
DOI: 10.1038/s41559-024-02596-1
Abstrakt: Ecological variation and anthropogenic landscape modification have had key roles in the diversification and extinction of mammals in Madagascar. Lemurs represent a radiation with more than 100 species, constituting roughly one-fifth of the primate order. Almost all species of lemurs are threatened with extinction, but little is known about their genetic diversity and demographic history. Here, we analyse high-coverage genome-wide resequencing data from 162 unique individuals comprising 50 species of Lemuriformes, including multiple individuals from most species. Genomic diversity varies widely across the infraorder and yet is broadly consistent among individuals within species. We show widespread introgression in multiple genera and generally high levels of genomic diversity likely resulting from allele sharing that occurred during periods of connectivity and fragmentation during climatic shifts. We find distinct patterns of demographic history in lemurs across the ecogeographic regions of Madagascar within the last million years. Within the past 2,000 years, lemurs underwent major declines in effective population size that corresponded to the timing of human population expansion in Madagascar. In multiple regions of the island, we identified chronological trajectories of inbreeding that are consistent across genera and species, suggesting localized effects of human activity. Our results show how the extraordinary diversity of these long-neglected, endangered primates has been influenced by ecological and anthropogenic factors.
Competing Interests: Competing interests: L.F.K.K. and K.K.-H.F. are employees of Illumina as of the submission of the paper. The other authors declare no competing interests.
(© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)
Databáze: MEDLINE
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