A comprehensive genomic history of extinct and living elephants.
Eleftheria Palkopoulou, Mark Lipson, Swapan Mallick, Svend Nielsen, Nadin Rohland, Sina Baleka, Emil Karpinski, Atma M Ivancevic, Thu-Hien To, R Daniel Kortschak, Joy M Raison, Zhipeng Qu, Tat-Jun Chin, Kurt W Alt, Stefan Claesson, Love Dalén, Ross D E MacPhee, Harald Meller, Alfred L Roca, Oliver A Ryder, David Heiman, Sarah Young, Matthew Breen, Christina Williams, Bronwen L Aken, Magali Ruffier, Elinor Karlsson, Jeremy Johnson, Federica Di Palma, Jessica Alfoldi, David L Adelson, Thomas Mailund, Kasper Munch, Kerstin Lindblad-Toh, Michael Hofreiter, Hendrik Poinar, David Reich
Author Information
Eleftheria Palkopoulou: Department of Genetics, Harvard Medical School, Boston, MA 02115; elle.palkopoulou@gmail.com reich@genetics.med.harvard.edu.
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. ORCID
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. ORCID
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; elle.palkopoulou@gmail.com reich@genetics.med.harvard.edu.
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.
