Elsevier

Journal of Human Evolution

Volume 45, Issue 3, September 2003, Pages 203-217
Journal of Human Evolution

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

https://doi.org/10.1016/S0047-2484(03)00106-4Get rights and content

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.

Introduction

The phylogenetic relationships between modern humans (Homo sapiens) and other species of Homo are a source of much debate (e.g. Mellars, 1999). A recent approach to collecting data to investigate the relationships is to isolate genetic material from fossil specimens (e.g. Krings et al., 1997, Ovchinnikov et al., 2000, Krings et al., 2000, Schmitz et al., 2002for Neanderthals; Adcocket al., 2001for early Australians), and compare this with modern human DNA. Initial successes have led to calls for further genetic sequences, from different geographic locations and age ranges (Höss, 2000, Adcock et al., 2001); however, the quality of aDNA studies in general, has recently been brought into question (Cooper & Poinar, 2000). The isolation of DNA from fossils is a destructive process, and when dealing with valuable material such as fossil humans it is important that a precautionary approach is taken. Assessment of the likelihood of a sample containing amplifiable DNA should be a prerequisite for such work, maximising returns from researcher time, funding, and most importantly, the valuable and irreplaceable resource of the fossils themselves.

It has been observed that DNA appears to survive best in cold dry environments such as permafrost, or high altitude caves, and biochemical studies suggest it is unlikely to survive for more than 100 000 years (Wayne et al., 1999). Yet, there has been little systematic work on the long-term survival of DNA in the fossil environment, and consequently assessments of the prospects ofDNA survival remain anecdotal. The need to find further fossil human DNA sequences from wider geographical and temporal ranges is compelling. The proposed upper bound to survival of 100 000 years encompasses both the extinction of the Neanderthals, and the diversification of modern humans, but the oldest successful amplifications are from permafrost, not sites of human occupation.

While it is apparent that fossils from cold environments will have better biomolecular preservation than those from hot climates, and that younger fossils will be better preserved than older ones, the distinction between an old and cold fossil and a young hot one is more difficult to assess. Attempts have been made to relate temperature dependent rates of DNA depurination to absolute copy numbers (Pääbo and Wilson, 1991, Marota et al., 2002), but they appear to have been over simplistic and as a result inaccurate (see discussion).

The preservation of biomolecules in the fossil environment is complex, especially in bone(Collins et al., 2002). In brief, bone degradation is considered to occur mainly by two processes; one rapid, mediated by microorganisms and fungi (Hackett, 1981, Bell et al., 1996), and the other, chemical degradation, which is a relatively slow process. For skeletal material to become part of the fossil record it is likely that microbial attack will have to be excluded (Trueman & Martill, 2002). If microbial taphonomy is inhibited, then the two major chemical pathways that will lead to DNA destruction are condensation (e.g. glycation of nucleobases, Pischetsrieder et al., 1999) and hydrolysis of the purine bases (Lindahl & Nyberg, 1972). The importance of cross-linking in the survival of DNA has not been investigated in detail so far (see Poinar, 1999). Principal factors that influence the rate of hydrolytic depurination are pH, amount of chemically available water and temperature. The first two factors are less significant in bone as bone itself exerts a substantial buffering effect between pH 4–9 (Bada & Shou, 1980), and the pore size distribution of bone encourages water retention (Hedges and Millard, 1995, Turner-Walker et al., in press). Deep burial will buffer temperature fluctuation, but only around an annual mean, and thus temperature is likely to play a substantial role in defining the envelope of DNA survival (Smithet al., 2001). Here we present a more detailed account of our assessment of the thermal history of fossil hominid sites from Northern Europe, and use this to rank sites according to their thermal age. We define thermal age as the time taken to produce a given degree of DNA degradation when temperature is held at a constant 10°C. The thermal age adjusts the chronological age of different sites according to their individual thermal histories, using the known temperature dependence of DNA depurination estimated in aqueous solution. A comparison is made between the DNA depurination thermal ages of sites in NW Europe and Lake Mungo, a site in Australia where controversial claims have been made for the recovery of ancient DNA (Adcock et al., 2001, Cooper et al., 2001).

Section snippets

Methods

The thermal regime of a fossil is governed by two major factors, the mean temperature and the variation about this mean, both of which will vary over time due to climatic changes. Thus, to reconstruct the thermal history of a fossil, data must be obtained for both the modern day temperature of the site and the palaeotemperature.

For a fossil buried in open ground the thermal regime of the fossil is assumed to be the same as that of the surrounding soil. It has been demonstrated that good

Results and discussion

The results of this analysis can be seen inTable 1. The Feldhofer cave site from which DNA has been amplified is ranked as ten of thirty-nine, with a thermal age of ∼19kyr@10°C. If our estimate of the Holocene temperature is 1°C in error at this site, the thermal age is approximately 3kyr@10°C(∼16%) different. The sequence of ages given for each site reveals an important feature of the thermal history. For example, at Feldhofer, if a fossil is considered to be 50 kyr, 45% of the thermal age is

Conclusion

The application of molecular techniques to fossil materials is an expanding field, and can provide invaluable data on the relationships between modern humans and their fossil relatives. At present only a few authentic sequences of fossil hominid DNA have been reported. Without a better understanding of the survival of DNA in the fossil record, valuable fossils may be damaged and destroyed and much time wasted in the search for more aDNA sequences. The thermal history of fossils is a useful

Acknowledgements

The LDEO/IRI Data Library is acknowledged for facilitating access to climatic data. Jen Hiller is thanked for allowing us access to her temperature data from Scladina cave and Marcel Otte and Dominique Bonjean for allowing access to this site.

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    1

    Present address: Museo Nacional de Ciencias Naturales, C/Jose Gutierrez Abascal, 2, 28006, Madrid, Spain.

    2

    Present address: BioArch, The King's Manor, York, Y01 7EP.

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