The thermal history of human fossils and the likelihood of successful DNA amplification

Abstract

Recent success in the amplification of ancient DNA (aDNA) from fossil humans has led to calls for further tests to be carried out on similar material. However, there has been little systematic research on the survival of DNA in the fossil record, even though the environment of the fossil is known to be of paramount importance for the survival of biomolecules over archaeological and geological timescales. A better understanding of aDNA survival would enable research to focus on material with greater chances of successful amplification, thus preventing the unnecessary loss of material and valuable researcher time. We argue that the thermal history of a fossil is a key parameter for the survival of biomolecules. The thermal history of a number of northwest European Neanderthal cave sites is reconstructed here and they are ranked in terms of the relative likelihood of aDNA survival at the sites, under the assumption that DNA depurination is the principal mechanism of degradation. The claims of aDNA amplification from material found at Lake Mungo, Australia, are also considered in the light of the thermal history of this site.

Revising the recent evolutionary history of equids using ancient DNA

“…Thirteen fossils did not yield any aDNA information despite extensive extraction and PCR attempts (Table S1B), and by default, also acted as cross-contamination controls in different extraction experiments. The poor DNA yields from these fossils are in agreement with their preservation state [high thermal age (26); see SI Text]. Thirteen of the samples were successfully amplified and sequenced in two independent laboratories [Lyon and Australian Centre for Ancient DNA (ACAD)], using different extraction methods, PCR conditions, and sequencing strategies (cloning/sequencing of different amplicons in Lyon versus direct sequencing at ACAD).…”

The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)

“…By comparison, in one woolly mammoth mitochondrial genome (Miller et al 2008), the rate was 0.14%. This is most likely explained by either the probable higher thermal age (Smith et al 2003;Gilbert et al 2007a) of the thylacine samples in comparison to the mammoth sample, the effect of the preservation/storage process (tanning process or longterm storage in dilute ethanol), or a combination thereof (see Supplemental Material). On the other hand, the damage rate is less than that for a mammoth bone sample (Gilbert et al 2007b), confirming the utility of hair shafts as an excellent reservoir for ancient DNA.…”

“…While a draft version of the woolly mammoth (Mammuthus primigenis) nuclear genome has recently been produced (Miller et al 2008), much of the success of that project has been attributed to the fact that mammoth specimens, in general, have a cold storage history. In contrast, the thermal age (Smith et al 2003;Gilbert et al 2007a) of all thylacine specimens is high, as no efforts were made a century ago to preserve tissues other than tanned or ethanol stored. However, the observed average read length for sample 1 of 87.5 bp, with a substantial number of reads at the maximum read length of the current Roche FLX instruments (;250 bp), suggests that up to 50 Mb of sequence could be generated in a single run.…”

Back to the roots and routes of dromedary domestication

“…In the absence of a living wild population, the authors tested these scenarios by generating ancient DNA sequence data from archaeological remains, succeeding, in a technical tour-de-force, to sequence 531 bp of mtDNA in 15 ancient remains, despite the extremely fast rates of DNA decay in warm environments (15). The oldest remain was ∼7,000 y old and was excavated in the United Arab Emirates (UAE), a country where summer temperatures can reach 45°C.…”