A comprehensive genomic history of extinct and living elephants

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal article

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

In: Proceedings of the National Academy of Sciences of the United States of America, 26.02.2018.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal article

Harvard

Palkopoulou, E, Lipson, M, Mallick, S, Nielsen, S, Rohland, N, Baleka, S, Karpinski, E, Ivancevic, AM, To, T-H, Kortschak, RD, Raison, JM, Qu, Z, Chin, T-J, Alt, KW, Claesson, S, Dalén, L, MacPhee, RDE, Meller, H, Roca, AL, Ryder, OA, Heiman, D, Young, S, Breen, M, Williams, C, Aken, BL, Ruffier, M, Karlsson, E, Johnson, J, Di Palma, F, Alfoldi, J, Adelson, DL, Mailund, T, Munch, K, Lindblad-Toh, K, Hofreiter, M, Poinar, H & Reich, D 2018, 'A comprehensive genomic history of extinct and living elephants' Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1720554115

APA

Palkopoulou, E., Lipson, M., Mallick, S., Nielsen, S., Rohland, N., Baleka, S., ... Reich, D. (2018). A comprehensive genomic history of extinct and living elephants. Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1720554115

CBE

Palkopoulou E, Lipson M, Mallick S, Nielsen S, Rohland N, Baleka S, Karpinski E, Ivancevic AM, To T-H, Kortschak RD, Raison JM, Qu Z, Chin T-J, Alt KW, Claesson S, Dalén L, MacPhee RDE, Meller H, Roca AL, Ryder OA, Heiman D, Young S, Breen M, Williams C, Aken BL, Ruffier M, Karlsson E, Johnson J, Di Palma F, Alfoldi J, Adelson DL, Mailund T, Munch K, Lindblad-Toh K, Hofreiter M, Poinar H, Reich D. 2018. A comprehensive genomic history of extinct and living elephants. Proceedings of the National Academy of Sciences of the United States of America. Available from: 10.1073/pnas.1720554115

MLA

Palkopoulou, Eleftheria et al."A comprehensive genomic history of extinct and living elephants". Proceedings of the National Academy of Sciences of the United States of America. 2018. Available: 10.1073/pnas.1720554115

Vancouver

Palkopoulou E, Lipson M, Mallick S, Nielsen S, Rohland N, Baleka S et al. A comprehensive genomic history of extinct and living elephants. Proceedings of the National Academy of Sciences of the United States of America. 2018 Feb 26. Available from, DOI: 10.1073/pnas.1720554115

Author

Palkopoulou, Eleftheria ; Lipson, Mark ; Mallick, Swapan ; Nielsen, Svend ; Rohland, Nadin ; Baleka, Sina ; Karpinski, Emil ; Ivancevic, Atma M ; To, Thu-Hien ; Kortschak, R Daniel ; Raison, Joy M ; Qu, Zhipeng ; Chin, Tat-Jun ; Alt, Kurt W ; Claesson, Stefan ; Dalén, Love ; MacPhee, Ross D E ; Meller, Harald ; Roca, Alfred L ; Ryder, Oliver A ; Heiman, David ; Young, Sarah ; Breen, Matthew ; Williams, Christina ; Aken, Bronwen L ; Ruffier, Magali ; Karlsson, Elinor ; Johnson, Jeremy ; Di Palma, Federica ; Alfoldi, Jessica ; Adelson, David L ; Mailund, Thomas ; Munch, Kasper ; Lindblad-Toh, Kerstin ; Hofreiter, Michael ; Poinar, Hendrik ; Reich, David. / A comprehensive genomic history of extinct and living elephants. In: Proceedings of the National Academy of Sciences of the United States of America. 2018

Bibtex

@article{7997bd959f134c66957f12f001f29ab7,
title = "A comprehensive genomic history of extinct and living elephants",
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.",
keywords = "Journal Article",
author = "Eleftheria Palkopoulou and Mark Lipson and Swapan Mallick and Svend Nielsen and Nadin Rohland and Sina Baleka and Emil Karpinski and Ivancevic, {Atma M} and Thu-Hien To and Kortschak, {R Daniel} and Raison, {Joy M} and Zhipeng Qu and Tat-Jun Chin and Alt, {Kurt W} and Stefan Claesson and Love Dal{\'e}n and MacPhee, {Ross D E} and Harald Meller and Roca, {Alfred L} and Ryder, {Oliver A} and David Heiman and Sarah Young and Matthew Breen and Christina Williams and Aken, {Bronwen L} and Magali Ruffier and Elinor Karlsson and Jeremy Johnson and {Di Palma}, Federica and Jessica Alfoldi and Adelson, {David L} and Thomas Mailund and Kasper Munch and Kerstin Lindblad-Toh and Michael Hofreiter and Hendrik Poinar and David Reich",
year = "2018",
month = "2",
day = "26",
doi = "10.1073/pnas.1720554115",
language = "English",
journal = "Proceedings of the National Academy of Sciences of the United States of America",
issn = "0027-8424",
publisher = "NATL ACAD SCIENCES 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA",

}

RIS

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 - Kortschak,R Daniel

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 - Di Palma,Federica

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

PY - 2018/2/26

Y1 - 2018/2/26

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 - Journal Article

U2 - 10.1073/pnas.1720554115

DO - 10.1073/pnas.1720554115

M3 - Journal article

JO - Proceedings of the National Academy of Sciences of the United States of America

T2 - 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

SN - 0027-8424

ER -