A comprehensive genomic history of extinct and living elephants

  • Eleftheria Palkopoulou
    Department of Genetics, Harvard Medical School, Boston, MA 02115;
  • Mark Lipson
    Department of Genetics, Harvard Medical School, Boston, MA 02115;
  • Swapan Mallick
    Department of Genetics, Harvard Medical School, Boston, MA 02115;
  • Svend Nielsen
    Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus, Denmark;
  • Nadin Rohland
    Department of Genetics, Harvard Medical School, Boston, MA 02115;
  • 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
    McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, 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
    Center of Natural and Cultural Human History, Danube Private University, A-3500 Krems, Austria;
  • Stefan Claesson
    Institute of Maritime History, Tall Timbers, MD 20690;
  • Love Dalén
    Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-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
    Department of Animal Sciences, 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, MA 02142;
  • Sarah Young
    Broad Institute of MIT and Harvard, Cambridge, MA 02142;
  • 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
    European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD Cambridge, United Kingdom;
  • Magali Ruffier
    European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD Cambridge, United Kingdom;
  • Elinor Karlsson
    Broad Institute of MIT and Harvard, Cambridge, MA 02142;
  • Jeremy Johnson
    Broad Institute of MIT and Harvard, Cambridge, MA 02142;
  • Federica Di Palma
    Earlham Institute, NR4 7UZ Norwich, United Kingdom;
  • Jessica Alfoldi
    Broad Institute of MIT and Harvard, Cambridge, MA 02142;
  • David L. Adelson
    Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia;
  • Thomas Mailund
    Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus, Denmark;
  • Kasper Munch
    Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus, Denmark;
  • Kerstin Lindblad-Toh
    Broad Institute of MIT and Harvard, Cambridge, MA 02142;
  • 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
    McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada;
  • David Reich
    Department of Genetics, Harvard Medical School, Boston, MA 02115;

抄録

<jats:title>Significance</jats:title> <jats:p>Elephantids were once among the most widespread megafaunal families. However, only three species of this family exist today. To reconstruct their evolutionary history, we generated 14 genomes from living and extinct elephantids and from the American mastodon. While previous studies examined only simple bifurcating relationships, we found that gene flow between elephantid species was common in the past. Straight-tusked elephants descend from a mixture of three ancestral populations related to the ancestor of African elephants, woolly mammoths, and present-day forest elephants. We detected interbreeding between North American woolly and Columbian mammoths but found no evidence of recent gene flow between forest and savanna elephants, demonstrating that both gene flow and isolation have been central in the evolution of elephantids.</jats:p>

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