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 (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.

Figure 1.

DNA fragmentation theory. (a) The exponential relationship caused by random fragmentation of DNA. Post-mortem, the template fragment length (L) distribution follows an exponential decline determined by the proportion of damaged sites (λ). This relationship has been described from both modern and ancient samples [–25]. Here, a fragment size distribution representing λ = 0.02 (2% of the bonds in the DNA backbone are broken). (b) A hypothetical signal of temporal DNA decay, which has, prior to this study, been extremely difficult to demonstrate. The model assumes that the observed damage fraction (λ) can be converted to a rate of decay (k) when the age (T) of a sample is known. It implies that the number of DNA copies of a given length (L) will decline exponentially with time—hence the notion that DNA has a half-life. Here, the theoretical decay kinetics of a 50 bp DNA fragment, assuming a k of 2% per site per year. k is converted to a 50 bp decay rate (k₅₀), according to a Poisson distribution as: k₅₀ = 1 – (e^−0.02*50).

Figure 2.

Study site. The three fossil deposits, PV (42°58′22.0″ S, 172°35′49.0″ E), BHV (42°58′19.36″ S, 172°39′56.15″ E) and Rosslea (42°57′53.83″ S, 172°39′22.39″ E), from which 158 radiocarbon-dated moa fossils were characterized for DNA decay kinetics. The sites in North Canterbury, South Island, New Zealand are located within a 5 km radius in the eastern rain shadows of the Southern Alps. Most of the area is more than 200 m a.s.l. and consists of flat alluvial plains and rolling downlands. Information on calibrated radiocarbon ages and DNA preservation (C_T values) are shown for each site. m, mean age.

Figure 3.

Correlations between age and DNA preservation. Relative mtDNA copy numbers (determined by qPCR) in moa bone plotted against age for all 158 fossils (a), and for each of the three deposits respectively (b). The exponential correlations are significant (p < 0.005) except for the BHV data (p = 0.1) when tested alone. Although a faster average decay is observed at Rosslea, the decay rates (slopes) did not differ significantly from each other.

Figure 4.

Observed and predicted rates of DNA decay. The predicted survival of DNA in bone through time, measured as intact phosphodiester bonds in the DNA backbone (a), and survival of a 242 bp fragment (b). The depicted survival rates are based on: (i) the average mtDNA decay rate measured directly from qPCR of 158 moa bones; (ii) the rate of depurination measured from DNA in solution at pH 5 in Lindahl & Nyberg [22] but adjusted to 13.1°C to allow comparison with the moa data; (iii) the same rate adjusted further to pH 7.5, as expected inside a bone; (iv) mtDNA and nuDNA decay rates calculated based on Illumina HiSeq data from two moa samples (HiSeq 1 from sample S40114, HiSeq 2 from sample S39946-3). The estimated decay rate (k, per site per year) is listed for each of the seven datasets.