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. RyderDavid 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

Research output: Contribution to journalArticlepeer-review

Abstract

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 (US)
Pages (from-to)E2566-E2574
JournalProceedings of the National Academy of Sciences of the United States of America
Volume115
Issue number11
DOIs
StatePublished - 2018

Keywords

  • Admixture
  • Elephantid evolution
  • Mammoth
  • Paleogenomics
  • Species divergence

ASJC Scopus subject areas

  • General

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