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

Morten E. Allentoft*, Matthew Collins, David Harker, James Haile, Charlotte L. Oskam, Marie L. Hale, Paula F. Campos, Jose A. Samaniego, M. Thomas P. Gilbert, Eske Willerslev, Guojie Zhang, R. Paul Scofield, Richard N. Holdaway, Michael Bunce

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Pages (from-to)4724-4733
Number of pages10
JournalPROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
Volume279
Issue number1748
Early online date10 Oct 2012
DOIs
Publication statusPublished - 7 Dec 2012

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

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