October 10, 2012

DNA half-life + Old Hobbits

New Scientist reports on a new paper that attempts to quantify the "half-life" of DNA. This bit caught my eye:

Unfortunately, Bunce thinks the new calculations will be difficult to apply to specific sites. "A host of other factors come into play," he says, including the season the organism died. In fact, although the moa bones in the analysis had been buried in a similar environment, the age of the specimens could account for only about 40 per cent of the variation in DNA preservation – in other words, the half-life signal is noisy. 
Alan Cooper, director of the Australian Centre for Ancient DNA at the University of Adelaide, South Australia, agrees. "The rotting process after death is very seasonal and context dependent, and has a major impact on DNA survival." 
Cooper has attempted to extract DNA from Homo floresiensis remains, but is beginning to think that none will ever be found. He says that recent unpublished dating estimates indicate that "the hobbit material may be considerably older than currently suggested".
The paper probably has implications for many areas of biology, but the recent sequencing of the Denisova hominin at high coverage, leaves me hopeful that we will have some type of ancient DNA evidence for at least the last 100 thousand years, quite a lot of it for the time since the inception of the Upper Paleolithic, and nearly everything for the time since the beginning of the Neolithic.

Proc. R. Soc. B doi: 10.1098/rspb.2012.1745

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

Morten E. Allentoft et al.

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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