TY - JOUR
T1 - A comprehensive genomic history of extinct and living elephants
AU - Palkopoulou, Eleftheria
AU - Lipson, Mark
AU - Mallick, Swapan
AU - Nielsen, Svend
AU - Rohland, Nadin
AU - Baleka, Sina
AU - Karpinski, Emil
AU - Ivancevic, Atma M.
AU - To, Thu Hien
AU - Daniel Kortschak, R.
AU - Raison, Joy M.
AU - Qu, Zhipeng
AU - Chin, Tat Jun
AU - Alt, Kurt W.
AU - Claesson, Stefan
AU - Dalén, Love
AU - MacPhee, Ross D.E.
AU - Meller, Harald
AU - Roca, Alfred L.
AU - Ryder, Oliver A.
AU - Heiman, David
AU - Young, Sarah
AU - Breen, Matthew
AU - Williams, Christina
AU - Aken, Bronwen L.
AU - Ruffier, Magali
AU - Karlsson, Elinor
AU - Johnson, Jeremy
AU - Palma, Federica Di
AU - Alfoldi, Jessica
AU - Adelson, David L.
AU - Mailund, Thomas
AU - Munch, Kasper
AU - Lindblad-Toh, Kerstin
AU - Hofreiter, Michael
AU - Poinar, Hendrik
AU - Reich, David
N1 - Funding Information:
ACKNOWLEDGMENTS. We thank Bruce Upchurch and Teri Hermann (Woodland Park Zoological Gardens), Melissa Dickson (Dickerson Park Zoo), David Shepherdson (Oregon Zoo), and Nicholas J. Georgiadis (University of Washington) for providing elephant samples; Bernard Buigues (International Mammoth Committee), Pamela Groves (Institute of Arctic Biology), Daniel Fisher (University of Michigan), Mark Clementz (University of Wyoming), and Paul Matheus and Dale Guthrie (University of Alaska, Fairbanks) for providing ancient proboscidean samples; Jacob Enk (McMaster University and MYcroarray) for assisting in laboratory analyses; Pontus Skoglund (Harvard Medical School) for providing software for population genetic analyses; Yasuko Ishida (University of Illinois) for quantifying and sending elephant samples to the Broad Institute; and Karol Schauer for the proboscidean drawings in Figs. 1 and 3. Deep sequencing of the straight-tusked elephant sample (P. antiquus_N) was funded by National Human Genome Research Institute Grant U54 HG003067-08. A.L.R. was supported by the US Fish and Wildlife Service African Elephant Conservation Fund. B.L.A. and M.R. were funded by Wellcome Trust Grants WT098051 and WT108749/Z/15/Z and by the European Molecular Biology Laboratory. M.H. was supported by European Research Council Consolidator Grant 310763 GeneFlow. H.P. was funded through a Natural Sciences and Engineering Research Council of Canada Discovery Grant RFMAC-10539150 and the Canada Research Chairs program. D.R. was funded by NSF (HOMINID) Grant BCS-1032255 and NIH (National Institute of General Medical Sciences) Grant GM100233 and is an Investigator of the Howard Hughes Medical Institute.
Funding Information:
We thank Bruce Upchurch and Teri Hermann (Woodland Park Zoological Gardens), Melissa Dickson (Dickerson Park Zoo), David Shepherdson (Oregon Zoo), and Nicholas J. Georgiadis (University of Washington) for providing elephant samples; Bernard Buigues (International Mammoth Committee), Pamela Groves (Institute of Arctic Biology), Daniel Fisher (University of Michigan), Mark Clementz (University of Wyoming), and Paul Matheus and Dale Guthrie (University of Alaska, Fairbanks) for providing ancient proboscidean samples; Jacob Enk (McMaster University and MYcroarray) for assisting in laboratory analyses; Pontus Skoglund (Harvard Medical School) for providing software for population genetic analyses; Yasuko Ishida (University of Illinois) for quantifying and sending elephant samples to the Broad Institute; and Karol Schauer for the proboscidean drawings in Figs. 1 and 3. Deep sequencing of the straight-tusked elephant sample (P. antiquus_N) was funded by National Human Genome Research Institute Grant U54 HG003067-08. A.L.R. was supported by the US Fish and Wildlife Service African Elephant Conservation Fund. B.L.A. and M.R. were funded by Wellcome Trust Grants WT098051 and WT108749/Z/15/Z and by the European Molecular Biology Laboratory. M.H. was supported by European Research Council Consolidator Grant 310763 GeneFlow. H.P. was funded through a Natural Sciences and Engineering Research Council of Canada Discovery Grant RFMAC-10539150 and the Canada Research Chairs program. D.R. was funded by NSF (HOMINID) Grant BCS-1032255 and NIH (National Institute of General Medical Sciences) Grant GM100233 and is an Investigator of the Howard Hughes Medical Institute.
Publisher Copyright:
© 2018 National Academy of Sciences. All Rights Reserved.
PY - 2018
Y1 - 2018
N2 - 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.
AB - 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.
KW - Admixture
KW - Elephantid evolution
KW - Mammoth
KW - Paleogenomics
KW - Species divergence
UR - http://www.scopus.com/inward/record.url?scp=85043762317&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85043762317&partnerID=8YFLogxK
U2 - 10.1073/pnas.1720554115
DO - 10.1073/pnas.1720554115
M3 - Article
C2 - 29483247
AN - SCOPUS:85043762317
SN - 0027-8424
VL - 115
SP - E2566-E2574
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 11
ER -