A comprehensive genomic history of extinct and living elephants

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    Eleftheria Palkopoulou, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA, Mark Lipson, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA, Swapan Mallick, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA,
  • Svend Nielsen
  • Nadin Rohland, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA, Sina Baleka, Unit of General Zoology-Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Mathematics and Life Sciences, University of Potsdam, 14476 Potsdam, Germany., Emil Karpinski, The Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada., Atma M Ivancevic, Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia., Thu-Hien To, Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia., R Daniel Kortschak, Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia., Joy M Raison, Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia., Zhipeng Qu, Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia., Tat-Jun Chin, School of Computer Science, The University of Adelaide, 5005 SA, Australia., Kurt W Alt, Integrative Prehistory and Archaeological Science, University of Basel, CH-4055 Basel, Switzerland., Stefan Claesson, Institute of Maritime History, Tall Timbers, MD 20690., Love Dalén, Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, 10405, Stockholm, Sweden., Ross D E MacPhee, Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, New York, NY 10024., Harald Meller, State Office for Heritage Management and Archaeology, 06114 Halle (Saale), Germany., Alfred L Roca, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801., Oliver A Ryder, Institute for Conservation Research, San Diego Zoo, Escondido, CA 92027., David Heiman, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA, Sarah Young, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA, Matthew Breen, Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607., Christina Williams, Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607., Bronwen L Aken, Wellcome Sanger Institute, Hinxton, CB10 1SD Cambridge, United Kingdom., Magali Ruffier, Wellcome Sanger Institute, Hinxton, CB10 1SD Cambridge, United Kingdom., Elinor Karlsson, Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655., Jeremy Johnson, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA, Federica Di Palma, Earlham Institute, NR4 7UZ Norwich, United Kingdom., Jessica Alfoldi, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA, David L Adelson, Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia.,
  • Thomas Mailund
  • Kasper Munch
  • Kerstin Lindblad-Toh, Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden., Michael Hofreiter, Unit of General Zoology-Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Mathematics and Life Sciences, University of Potsdam, 14476 Potsdam, Germany., Hendrik Poinar, The Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada., David Reich, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115.

Elephantids are the world's most iconic megafaunal family, yet there is no comprehensive genomic assessment of their relationships. We report a total of 14 genomes, including 2 from the American mastodon, which is an extinct elephantid relative, and 12 spanning all three extant and three extinct elephantid species including an ∼120,000-y-old straight-tusked elephant, a Columbian mammoth, and woolly mammoths. Earlier genetic studies modeled elephantid evolution via simple bifurcating trees, but here we show that interspecies hybridization has been a recurrent feature of elephantid evolution. We found that the genetic makeup of the straight-tusked elephant, previously placed as a sister group to African forest elephants based on lower coverage data, in fact comprises three major components. Most of the straight-tusked elephant's ancestry derives from a lineage related to the ancestor of African elephants while its remaining ancestry consists of a large contribution from a lineage related to forest elephants and another related to mammoths. Columbian and woolly mammoths also showed evidence of interbreeding, likely following a latitudinal cline across North America. While hybridization events have shaped elephantid history in profound ways, isolation also appears to have played an important role. Our data reveal nearly complete isolation between the ancestors of the African forest and savanna elephants for ∼500,000 y, providing compelling justification for the conservation of forest and savanna elephants as separate species.

Original languageEnglish
JournalProceedings of the National Academy of Sciences of the United States of America
ISSN0027-8424
DOIs
StateE-pub ahead of print - 26 Feb 2018

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  • Journal Article

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ID: 121922709