A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing

Richard E. Green; Anna Sapfo Malaspinas; Johannes Krause; Adrian W. Briggs; Philip L.F. Johnson; Caroline Uhler; Matthias Meyer; Jeffrey M. Good; Tomislav Maricic; Udo Stenzel; Kay Prüfer; Michael Siebauer; Hernán A. Burbano; Michael Ronan; Jonathan M. Rothberg; Michael Egholm; Pavao Rudan; Dejana Brajković; Željko Kućan; Ivan Gušić; Mårten Wikström; Liisa Laakkonen; Janet Kelso; Montgomery Slatkin; Svante Pääbo

doi:10.1016/j.cell.2008.06.021

A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing

Richard E. Green
, Anna Sapfo Malaspinas
, Johannes Krause
, Adrian W. Briggs
, Philip L.F. Johnson
, Caroline Uhler
, Matthias Meyer
, Jeffrey M. Good
, Tomislav Maricic
, Udo Stenzel
, Kay Prüfer
, Michael Siebauer
, Hernán A. Burbano
, Michael Ronan
, Jonathan M. Rothberg
, Michael Egholm
, Pavao Rudan
, Dejana Brajković
, Željko Kućan
, Ivan Gušić

Mårten Wikström, Liisa Laakkonen, Janet Kelso, Montgomery Slatkin, Svante Pääbo

Division of Biological and Biomedical Sciences

Research output: Contribution to journal › Article › peer-review

457 Scopus citations

Abstract

A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from ∼0.3 g of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages of 660,000 ± 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared with other primate lineages, suggesting that the effective population size of Neandertals was small.

Original language	English
Pages (from-to)	416-426
Number of pages	11
Journal	Cell
Volume	134
Issue number	3
DOIs	https://doi.org/10.1016/j.cell.2008.06.021
State	Published - Aug 8 2008

Funding

We thank the Croatian Academy of Sciences and Arts, the Berlin-Brandenburg Academy of Sciences, and the Presidential Innovation Fund of the Max Plank Society for making this work possible. We are indebted to Mark Stoneking, Weiwei Zhai, John Huelsenbeck, Jérôme Fuchs, Mario Mörl, Nick Patterson, David Reich, and Timothy White for helpful discussions. We also thank Bruce Rannala and Ziheng Yang for help with mcmctree , James Hudson Bullard for help with figures, and Christine Green for editing. A.-S.M., P.L.F.J., and M.S. are supported by NIH grant R01-GM40282. P.L.F.J. is also supported by a Chang-Lin Tien scholarship. M.E. is an employee of 454 Life Sciences, a Roche company.

Funders	Funder number
Berlin-Brandenburg Academy of Sciences and Humanities
Croatian Academy of Sciences and Arts
R01GM040282

Keywords

CHEMBIO
DNA
ECO_EVOL

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10.1016/j.cell.2008.06.021

Cite this

Green, R. E., Malaspinas, A. S., Krause, J., Briggs, A. W., Johnson, P. L. F., Uhler, C., Meyer, M., Good, J. M., Maricic, T., Stenzel, U., Prüfer, K., Siebauer, M., Burbano, H. A., Ronan, M., Rothberg, J. M., Egholm, M., Rudan, P., Brajković, D., Kućan, Ž., ... Pääbo, S. (2008). A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing. Cell, 134(3), 416-426. https://doi.org/10.1016/j.cell.2008.06.021

@article{72f435aaed3142f3816f5ad9370a9b70,

title = "A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing",

abstract = "A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from ∼0.3 g of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages of 660,000 ± 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared with other primate lineages, suggesting that the effective population size of Neandertals was small.",

keywords = "CHEMBIO, DNA, ECO\_EVOL",

author = "Green, \{Richard E.\} and Malaspinas, \{Anna Sapfo\} and Johannes Krause and Briggs, \{Adrian W.\} and Johnson, \{Philip L.F.\} and Caroline Uhler and Matthias Meyer and Good, \{Jeffrey M.\} and Tomislav Maricic and Udo Stenzel and Kay Pr{\"u}fer and Michael Siebauer and Burbano, \{Hern{\'a}n A.\} and Michael Ronan and Rothberg, \{Jonathan M.\} and Michael Egholm and Pavao Rudan and Dejana Brajkovi{\'c} and {\v Z}eljko Ku{\'c}an and Ivan Gu{\v s}i{\'c} and M{\aa}rten Wikstr{\"o}m and Liisa Laakkonen and Janet Kelso and Montgomery Slatkin and Svante P{\"a}{\"a}bo",

note = "Funding Information: We thank the Croatian Academy of Sciences and Arts, the Berlin-Brandenburg Academy of Sciences, and the Presidential Innovation Fund of the Max Plank Society for making this work possible. We are indebted to Mark Stoneking, Weiwei Zhai, John Huelsenbeck, J{\'e}r{\^o}me Fuchs, Mario M{\"o}rl, Nick Patterson, David Reich, and Timothy White for helpful discussions. We also thank Bruce Rannala and Ziheng Yang for help with mcmctree , James Hudson Bullard for help with figures, and Christine Green for editing. A.-S.M., P.L.F.J., and M.S. are supported by NIH grant R01-GM40282. P.L.F.J. is also supported by a Chang-Lin Tien scholarship. M.E. is an employee of 454 Life Sciences, a Roche company. ",

year = "2008",

month = aug,

day = "8",

doi = "10.1016/j.cell.2008.06.021",

language = "English",

volume = "134",

pages = "416--426",

journal = "Cell",

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Green, RE, Malaspinas, AS, Krause, J, Briggs, AW, Johnson, PLF, Uhler, C, Meyer, M, Good, JM, Maricic, T, Stenzel, U, Prüfer, K, Siebauer, M, Burbano, HA, Ronan, M, Rothberg, JM, Egholm, M, Rudan, P, Brajković, D, Kućan, Ž, Gušić, I, Wikström, M, Laakkonen, L, Kelso, J, Slatkin, M & Pääbo, S 2008, 'A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing', Cell, vol. 134, no. 3, pp. 416-426. https://doi.org/10.1016/j.cell.2008.06.021

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T1 - A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing

AU - Green, Richard E.

AU - Malaspinas, Anna Sapfo

AU - Krause, Johannes

AU - Briggs, Adrian W.

AU - Johnson, Philip L.F.

AU - Uhler, Caroline

AU - Meyer, Matthias

AU - Good, Jeffrey M.

AU - Maricic, Tomislav

AU - Stenzel, Udo

AU - Prüfer, Kay

AU - Siebauer, Michael

AU - Burbano, Hernán A.

AU - Ronan, Michael

AU - Rothberg, Jonathan M.

AU - Egholm, Michael

AU - Rudan, Pavao

AU - Brajković, Dejana

AU - Kućan, Željko

AU - Gušić, Ivan

AU - Wikström, Mårten

AU - Laakkonen, Liisa

AU - Kelso, Janet

AU - Slatkin, Montgomery

AU - Pääbo, Svante

N1 - Funding Information: We thank the Croatian Academy of Sciences and Arts, the Berlin-Brandenburg Academy of Sciences, and the Presidential Innovation Fund of the Max Plank Society for making this work possible. We are indebted to Mark Stoneking, Weiwei Zhai, John Huelsenbeck, Jérôme Fuchs, Mario Mörl, Nick Patterson, David Reich, and Timothy White for helpful discussions. We also thank Bruce Rannala and Ziheng Yang for help with mcmctree , James Hudson Bullard for help with figures, and Christine Green for editing. A.-S.M., P.L.F.J., and M.S. are supported by NIH grant R01-GM40282. P.L.F.J. is also supported by a Chang-Lin Tien scholarship. M.E. is an employee of 454 Life Sciences, a Roche company.

PY - 2008/8/8

Y1 - 2008/8/8

N2 - A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from ∼0.3 g of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages of 660,000 ± 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared with other primate lineages, suggesting that the effective population size of Neandertals was small.

AB - A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from ∼0.3 g of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages of 660,000 ± 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared with other primate lineages, suggesting that the effective population size of Neandertals was small.

KW - CHEMBIO

KW - DNA

KW - ECO_EVOL

UR - https://www.scopus.com/pages/publications/48649096196

U2 - 10.1016/j.cell.2008.06.021

DO - 10.1016/j.cell.2008.06.021

M3 - Article

C2 - 18692465

AN - SCOPUS:48649096196

SN - 0092-8674

VL - 134

SP - 416

EP - 426

JO - Cell

JF - Cell

IS - 3

ER -

A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing

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Keywords

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