ArticleCell2021
Ancient and modern genomes unravel the evolutionary history of the rhinoceros family.
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42 citing papers in PubMed.
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- Whole genomes of Amazonian uakari monkeys reveal complex connectivity and fast differentiation driven by high environmental dynamism.Communications biology · 2024Article
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- Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history.PLoS computational biology · 2024Article
- Improving data archiving practices in ancient genomics.Scientific data · 2024Article
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Authors and funding
39 authors.
Shanlin LiuDepartment of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark. Electronic address: shanlin.liu@cau.edu.cn.
Michael V WestburyThe GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
Nicolas DussexCentre for Palaeogenetics, Svante Arrhenius vag 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden.
Kieren J MitchellAustralian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia.
Mikkel-Holger S SindingThe GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
Peter D HeintzmanThe Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø 9037, Norway.
David A DuchêneThe GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
Joshua D KappDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Johanna von SethCentre for Palaeogenetics, Svante Arrhenius vag 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden.
Holly HeinigerAustralian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia.
Fátima Sánchez-BarreiroThe GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
Ashot MargaryanThe GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
Remi André-OlsenScience for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17121 Solna, Sweden.
Binia De CahsanThe GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
Guanliang MengChina National Genebank, BGI Shenzhen, Shenzhen 518083, China.
Chentao YangChina National Genebank, BGI Shenzhen, Shenzhen 518083, China.
Lei ChenCenter for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China.
Tom van der ValkDepartment of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
Yoshan MoodleyDepartment of Zoology, University of Venda, Thohoyandou 0950, Republic of South Africa.
Kees RookmaakerEditor of the Rhino Resource Center, Utrecht, the Netherlands.
Michael W BrufordSchool of Biosciences, Sir Martin Evans Building, Cardiff University, Cardiff CF10 3AX, UK; Sustainable Places Research Institute, Cardiff University, Cardiff CF10 3BA, UK.
Oliver RyderSan Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, San Diego, CA 92027, USA.
Cynthia SteinerSan Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, San Diego, CA 92027, USA.
Linda G R Bruins-van SonsbeekRotterdam Zoo, Rotterdam, the Netherlands.
Sergey VartanyanN.A. Shilo North-East Interdisciplinary Scientific Research Institute, Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS), Magadan 685000, Russia.
Chunxue GuoChina National Genebank, BGI Shenzhen, Shenzhen 518083, China.
Alan CooperSouth Australian Museum, Adelaide, SA 5000, Australia.
Pavel KosintsevInstitute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia; Ural Federal University, Yekaterinburg, Russia.
Irina KirillovaInstitute of Geography, Russian Academy of Sciences, Moscow 119017, Russia.
Adrian M ListerDepartment of Earth Sciences, Natural History Museum, London, UK.
Tomas Marques-BonetInstitute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain; Centre Nacional d'Anàlisi Genòmica, Centre for Genomic Regulation (CNAG-CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain.
Shyam GopalakrishnanThe GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
Robert R DunnThe GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA.
Eline D LorenzenThe GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
Beth ShapiroDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 96050, USA.
Guojie ZhangChina National Genebank, BGI Shenzhen, Shenzhen 518083, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
Pierre-Olivier AntoineInstitut des Sciences de l'Évolution, Université Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France.
Love DalénCentre for Palaeogenetics, Svante Arrhenius vag 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden. Electronic address: love.dalen@nrm.se.
M Thomas P GilbertThe GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; Norwegian University of Science and Technology (NTNU) University Museum, Trondheim 7012, Norway. Electronic address: tgilbert@sund.ku.dk.
Funding
European Research Council 681396
Abstract
Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.
Indexed as
Evolution, MolecularGenomeAnimalsDemographyGene FlowGenetic VariationGeographyHeterozygoteHomozygoteHost SpecificityMarkov ChainsMutationPerissodactylaPhylogenySpecies SpecificityTime FactorsRhinoceros, Perissodactyl, Conservation genomics, Phylogenomics, Genomic diversity.
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