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The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils

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The half-life of DNA in bone : measuring decay kinetics in 158 dated fossils. / Allentoft, Morten E.; Collins, Matthew; Harker, David; Haile, James; Oskam, Charlotte L.; Hale, Marie L.; Campos, Paula F.; Samaniego, Jose A.; Gilbert, M. Thomas P.; Willerslev, Eske; Zhang, Guojie; Scofield, R. Paul; Holdaway, Richard N.; Bunce, Michael.

In: PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol. 279, No. 1748, 07.12.2012, p. 4724-4733.

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Harvard

Allentoft, ME, Collins, M, Harker, D, Haile, J, Oskam, CL, Hale, ML, Campos, PF, Samaniego, JA, Gilbert, MTP, Willerslev, E, Zhang, G, Scofield, RP, Holdaway, RN & Bunce, M 2012, 'The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils', PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 279, no. 1748, pp. 4724-4733. https://doi.org/10.1098/rspb.2012.1745

APA

Allentoft, M. E., Collins, M., Harker, D., Haile, J., Oskam, C. L., Hale, M. L., ... Bunce, M. (2012). The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 279(1748), 4724-4733. https://doi.org/10.1098/rspb.2012.1745

Vancouver

Allentoft ME, Collins M, Harker D, Haile J, Oskam CL, Hale ML et al. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES. 2012 Dec 7;279(1748):4724-4733. https://doi.org/10.1098/rspb.2012.1745

Author

Allentoft, Morten E. ; Collins, Matthew ; Harker, David ; Haile, James ; Oskam, Charlotte L. ; Hale, Marie L. ; Campos, Paula F. ; Samaniego, Jose A. ; Gilbert, M. Thomas P. ; Willerslev, Eske ; Zhang, Guojie ; Scofield, R. Paul ; Holdaway, Richard N. ; Bunce, Michael. / The half-life of DNA in bone : measuring decay kinetics in 158 dated fossils. In: PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES. 2012 ; Vol. 279, No. 1748. pp. 4724-4733.

Bibtex - Download

@article{be10bca55ede4190847772e618a7e070,
title = "The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils",
abstract = "Claims of extreme survival of DNA have emphasized the need for reliable models of DNA degradation through time. By analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of the extinct New Zealand moa, we confirm empirically a long-hypothesized exponential decay relationship. The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence, corresponding to a per nucleotide fragmentation rate (k) of 5.50 x 10(-6) per year. With an effective burial temperature of 13.18 degrees C, the rate is almost 400 times slower than predicted from published kinetic data of in vitro DNA depurination at pH 5. Although best described by an exponential model (R-2 = 0.39), considerable sample-to-sample variance in DNA preservation could not be accounted for by geologic age. This variation likely derives from differences in taphonomy and bone diagenesis, which have confounded previous, less spatially constrained attempts to study DNA decay kinetics. Lastly, by calculating DNA fragmentation rates on Illumina HiSeq data, we show that nuclear DNA has degraded at least twice as fast as mtDNA. These results provide a baseline for predicting long-term DNA survival in bone.",
keywords = "aDNA, MISCODING LESIONS, decay kinetics, DNA half-life, SEQUENCE, PRESERVATION, LONG-TERM SURVIVAL, MAMMOTH DNA, ANCIENT DNA, AMPLIFICATION, DNA degradation, DEOXYRIBONUCLEIC ACID, ARCHAEOLOGICAL SITES, NEW-ZEALAND",
author = "Allentoft, {Morten E.} and Matthew Collins and David Harker and James Haile and Oskam, {Charlotte L.} and Hale, {Marie L.} and Campos, {Paula F.} and Samaniego, {Jose A.} and Gilbert, {M. Thomas P.} and Eske Willerslev and Guojie Zhang and Scofield, {R. Paul} and Holdaway, {Richard N.} and Michael Bunce",
year = "2012",
month = "12",
day = "7",
doi = "10.1098/rspb.2012.1745",
language = "English",
volume = "279",
pages = "4724--4733",
journal = "PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES",
issn = "0962-8452",
publisher = "The Royal Society",
number = "1748",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - The half-life of DNA in bone

T2 - PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

AU - Allentoft, Morten E.

AU - Collins, Matthew

AU - Harker, David

AU - Haile, James

AU - Oskam, Charlotte L.

AU - Hale, Marie L.

AU - Campos, Paula F.

AU - Samaniego, Jose A.

AU - Gilbert, M. Thomas P.

AU - Willerslev, Eske

AU - Zhang, Guojie

AU - Scofield, R. Paul

AU - Holdaway, Richard N.

AU - Bunce, Michael

PY - 2012/12/7

Y1 - 2012/12/7

N2 - Claims of extreme survival of DNA have emphasized the need for reliable models of DNA degradation through time. By analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of the extinct New Zealand moa, we confirm empirically a long-hypothesized exponential decay relationship. The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence, corresponding to a per nucleotide fragmentation rate (k) of 5.50 x 10(-6) per year. With an effective burial temperature of 13.18 degrees C, the rate is almost 400 times slower than predicted from published kinetic data of in vitro DNA depurination at pH 5. Although best described by an exponential model (R-2 = 0.39), considerable sample-to-sample variance in DNA preservation could not be accounted for by geologic age. This variation likely derives from differences in taphonomy and bone diagenesis, which have confounded previous, less spatially constrained attempts to study DNA decay kinetics. Lastly, by calculating DNA fragmentation rates on Illumina HiSeq data, we show that nuclear DNA has degraded at least twice as fast as mtDNA. These results provide a baseline for predicting long-term DNA survival in bone.

AB - Claims of extreme survival of DNA have emphasized the need for reliable models of DNA degradation through time. By analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of the extinct New Zealand moa, we confirm empirically a long-hypothesized exponential decay relationship. The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence, corresponding to a per nucleotide fragmentation rate (k) of 5.50 x 10(-6) per year. With an effective burial temperature of 13.18 degrees C, the rate is almost 400 times slower than predicted from published kinetic data of in vitro DNA depurination at pH 5. Although best described by an exponential model (R-2 = 0.39), considerable sample-to-sample variance in DNA preservation could not be accounted for by geologic age. This variation likely derives from differences in taphonomy and bone diagenesis, which have confounded previous, less spatially constrained attempts to study DNA decay kinetics. Lastly, by calculating DNA fragmentation rates on Illumina HiSeq data, we show that nuclear DNA has degraded at least twice as fast as mtDNA. These results provide a baseline for predicting long-term DNA survival in bone.

KW - aDNA

KW - MISCODING LESIONS

KW - decay kinetics

KW - DNA half-life

KW - SEQUENCE

KW - PRESERVATION

KW - LONG-TERM SURVIVAL

KW - MAMMOTH DNA

KW - ANCIENT DNA

KW - AMPLIFICATION

KW - DNA degradation

KW - DEOXYRIBONUCLEIC ACID

KW - ARCHAEOLOGICAL SITES

KW - NEW-ZEALAND

UR - http://www.scopus.com/inward/record.url?scp=84868087346&partnerID=8YFLogxK

U2 - 10.1098/rspb.2012.1745

DO - 10.1098/rspb.2012.1745

M3 - Article

VL - 279

SP - 4724

EP - 4733

JO - PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

JF - PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

SN - 0962-8452

IS - 1748

ER -