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 degradationthrough time. By analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of theextinct 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 be521 years for a 242 bp mtDNA sequence, corresponding to a per nucleotide fragmentation rate (k) of5.50 ! 10–6 per year. With an effective burial temperature of 13.18C, the rate is almost 400 timesslower than predicted from published kinetic data of in vitro DNA depurination at pH 5. Althoughbest described by an exponential model (R2 ¼ 0.39), considerable sample-to-sample variance in DNApreservation could not be accounted for by geologic age. This variation likely derives from differencesin taphonomy and bone diagenesis, which have confounded previous, less spatially constrained attempt 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.