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

Morten Erik Allentoft; Matthew Collins; David Harker; James Haile; Charlotte L. Oskam; Marie L. Hale; Paula Campos; Jose Alfredo Samaniego Castruita; Tom Gilbert; Eske Willerslev; Guojie Zhang; R. Paul Scofield; Richard N. Holdaway; Michael Bunce

doi:10.1098/rspb.2012.1745

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

Morten Erik Allentoft, Matthew Collins, David Harker, James Haile, Charlotte L. Oskam, Marie L. Hale, Paula Campos, Jose Alfredo Samaniego Castruita, Tom Gilbert, Eske Willerslev, Guojie Zhang, R. Paul Scofield, Richard N. Holdaway, Michael Bunce

273 Citations (Scopus)

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 × 10^-6 per year. With an effective burial temperature of 13.1°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 (R² = 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.

Original language	English
Journal	Proceedings of the Royal Society B: Biological Sciences
Volume	279
Issue number	1748
Pages (from-to)	4724-4733
Number of pages	10
DOIs	https://doi.org/10.1098/rspb.2012.1745
Publication status	Published - 2012

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Allentoft, M. E., Collins, M., Harker, D., Haile, J., Oskam, C. L., Hale, M. L., Campos, P., Samaniego Castruita, J. A., Gilbert, T., Willerslev, E., Zhang, G., Scofield, R. P., Holdaway, R. N., & 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

Allentoft, ME, Collins, M, Harker, D, Haile, J, Oskam, CL, Hale, ML, Campos, P, Samaniego Castruita, JA, Gilbert, T , 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

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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 × 10-6 per year. With an effective burial temperature of 13.1°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 (R2 = 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.",

author = "Allentoft, {Morten Erik} and Matthew Collins and David Harker and James Haile and Oskam, {Charlotte L.} and Hale, {Marie L.} and Paula Campos and {Samaniego Castruita}, {Jose Alfredo} and Tom Gilbert and Eske Willerslev and Guojie Zhang and Scofield, {R. Paul} and Holdaway, {Richard N.} and Michael Bunce",

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T2 - measuring decay kinetics in 158 dated fossils

AU - Allentoft, Morten Erik

AU - Collins, Matthew

AU - Harker, David

AU - Haile, James

AU - Oskam, Charlotte L.

AU - Hale, Marie L.

AU - Campos, Paula

AU - Samaniego Castruita, Jose Alfredo

AU - Gilbert, Tom

AU - Willerslev, Eske

AU - Zhang, Guojie

AU - Scofield, R. Paul

AU - Holdaway, Richard N.

AU - Bunce, Michael

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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 × 10-6 per year. With an effective burial temperature of 13.1°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 (R2 = 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 × 10-6 per year. With an effective burial temperature of 13.1°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 (R2 = 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.

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DO - 10.1098/rspb.2012.1745

M3 - Journal article

SN - 1471-2954

VL - 279

SP - 4724

EP - 4733

JO - Proceedings of the Royal Society B: Biological Sciences

JF - Proceedings of the Royal Society B: Biological Sciences

IS - 1748

ER -

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

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