Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes

M Thomas P Gilbert; Daniela I Drautz; Arthur M Lesk; Simon Y W Ho; Ji Qi; Aakrosh Ratan; Chih-Hao Hsu; Andrei Sher; Love Dalén; Anders Götherström; Lynn P Tomsho; Snjezana Rendulic; Michael Packard; Paula F Campos; Tatyana V Kuznetsova; Fyodor Shidlovskiy; Alexei Tikhonov; Eske Willerslev; Paola Iacumin; Bernard Buigues; Per G P Ericson; Mietje Germonpré; Pavel Kosintsev; Vladimir Nikolaev; Malgosia Nowak-Kemp; James R Knight; Gerard P Irzyk; Clotilde S Perbost; Karin M Fredrikson; Timothy T Harkins; Sharon Sheridan; Webb Miller; Stephan C Schuster

doi:10.1073/pnas.0802315105

Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes

M Thomas P Gilbert, Daniela I Drautz, Arthur M Lesk, Simon Y W Ho, Ji Qi, Aakrosh Ratan, Chih-Hao Hsu, Andrei Sher, Love Dalén, Anders Götherström, Lynn P Tomsho, Snjezana Rendulic, Michael Packard, Paula F Campos, Tatyana V Kuznetsova, Fyodor Shidlovskiy, Alexei Tikhonov, Eske Willerslev, Paola Iacumin, Bernard BuiguesPer G P Ericson, Mietje Germonpré, Pavel Kosintsev, Vladimir Nikolaev, Malgosia Nowak-Kemp, James R Knight, Gerard P Irzyk, Clotilde S Perbost, Karin M Fredrikson, Timothy T Harkins, Sharon Sheridan, Webb Miller, Stephan C Schuster

Microbiology

123 Citations (Scopus)

Abstract

We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades, approximately 1-2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the (14)C ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep.

Original language	English
Journal	Proceedings of the National Academy of Science of the United States of America
Volume	105
Issue number	24
Pages (from-to)	8327-32
Number of pages	5
ISSN	0027-8424
DOIs	https://doi.org/10.1073/pnas.0802315105
Publication status	Published - 2008

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Gilbert, M. T. P., Drautz, D. I., Lesk, A. M., Ho, S. Y. W., Qi, J., Ratan, A., Hsu, C-H., Sher, A., Dalén, L., Götherström, A., Tomsho, L. P., Rendulic, S., Packard, M., Campos, P. F., Kuznetsova, T. V., Shidlovskiy, F., Tikhonov, A., Willerslev, E., Iacumin, P., ... Schuster, S. C. (2008). Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proceedings of the National Academy of Science of the United States of America, 105(24), 8327-32. https://doi.org/10.1073/pnas.0802315105

Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. / Gilbert, M Thomas P; Drautz, Daniela I; Lesk, Arthur M et al.

In: Proceedings of the National Academy of Science of the United States of America, Vol. 105, No. 24, 2008, p. 8327-32.

Research output: Contribution to journal › Journal article › Research › peer-review

Gilbert, MTP, Drautz, DI, Lesk, AM, Ho, SYW, Qi, J, Ratan, A, Hsu, C-H, Sher, A, Dalén, L, Götherström, A, Tomsho, LP, Rendulic, S, Packard, M, Campos, PF, Kuznetsova, TV, Shidlovskiy, F, Tikhonov, A, Willerslev, E, Iacumin, P, Buigues, B, Ericson, PGP, Germonpré, M, Kosintsev, P, Nikolaev, V, Nowak-Kemp, M, Knight, JR, Irzyk, GP, Perbost, CS, Fredrikson, KM, Harkins, TT, Sheridan, S, Miller, W & Schuster, SC 2008, 'Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes', Proceedings of the National Academy of Science of the United States of America, vol. 105, no. 24, pp. 8327-32. https://doi.org/10.1073/pnas.0802315105

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title = "Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes",

abstract = "We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades, approximately 1-2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the (14)C ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep.",

author = "Gilbert, {M Thomas P} and Drautz, {Daniela I} and Lesk, {Arthur M} and Ho, {Simon Y W} and Ji Qi and Aakrosh Ratan and Chih-Hao Hsu and Andrei Sher and Love Dal{\'e}n and Anders G{\"o}therstr{\"o}m and Tomsho, {Lynn P} and Snjezana Rendulic and Michael Packard and Campos, {Paula F} and Kuznetsova, {Tatyana V} and Fyodor Shidlovskiy and Alexei Tikhonov and Eske Willerslev and Paola Iacumin and Bernard Buigues and Ericson, {Per G P} and Mietje Germonpr{\'e} and Pavel Kosintsev and Vladimir Nikolaev and Malgosia Nowak-Kemp and Knight, {James R} and Irzyk, {Gerard P} and Perbost, {Clotilde S} and Fredrikson, {Karin M} and Harkins, {Timothy T} and Sharon Sheridan and Webb Miller and Schuster, {Stephan C}",

note = "Keywords: Animals; Base Sequence; DNA, Mitochondrial; Elephants; Genetic Variation; Genome, Mitochondrial; Hair; Molecular Sequence Data; Paleontology; Phylogeny; Sequence Analysis, DNA",

year = "2008",

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language = "English",

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pages = "8327--32",

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T1 - Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes

AU - Gilbert, M Thomas P

AU - Drautz, Daniela I

AU - Lesk, Arthur M

AU - Ho, Simon Y W

AU - Qi, Ji

AU - Ratan, Aakrosh

AU - Hsu, Chih-Hao

AU - Sher, Andrei

AU - Dalén, Love

AU - Götherström, Anders

AU - Tomsho, Lynn P

AU - Rendulic, Snjezana

AU - Packard, Michael

AU - Campos, Paula F

AU - Kuznetsova, Tatyana V

AU - Shidlovskiy, Fyodor

AU - Tikhonov, Alexei

AU - Willerslev, Eske

AU - Iacumin, Paola

AU - Buigues, Bernard

AU - Ericson, Per G P

AU - Germonpré, Mietje

AU - Kosintsev, Pavel

AU - Nikolaev, Vladimir

AU - Nowak-Kemp, Malgosia

AU - Knight, James R

AU - Irzyk, Gerard P

AU - Perbost, Clotilde S

AU - Fredrikson, Karin M

AU - Harkins, Timothy T

AU - Sheridan, Sharon

AU - Miller, Webb

AU - Schuster, Stephan C

N1 - Keywords: Animals; Base Sequence; DNA, Mitochondrial; Elephants; Genetic Variation; Genome, Mitochondrial; Hair; Molecular Sequence Data; Paleontology; Phylogeny; Sequence Analysis, DNA

PY - 2008

Y1 - 2008

N2 - We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades, approximately 1-2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the (14)C ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep.

AB - We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades, approximately 1-2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the (14)C ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep.

U2 - 10.1073/pnas.0802315105

DO - 10.1073/pnas.0802315105

M3 - Journal article

C2 - 18541911

SN - 0027-8424

VL - 105

SP - 8327

EP - 8332

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 - 24

ER -

Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes

Abstract

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