From the paper:
Therefore, it is of utmost importance to control the PCR. This is possible when using a quantitative approach, and, in particular, quantitative real-time PCR (QPCR), which allows for online monitoring of the PCR and quantification of the amplified DNA thanks to the use of fluorescent probes .Comptes Rendus Palevol doi:10.1016/j.crpv.2008.02.001
Therefore, QPCR is, to my mind, the best method for amplification of ancient DNA. Up until now, however, it has rarely been used and not a single study of the genetics of ancient populations or of a domestication process has been conducted using this method. We have adapted QPCR to ancient DNA research and used it for our study of the domestication process of the aurochs in Southwest Asia with a so far unequalled success rate. We have thus been able to appreciate better:
• DNA conservation, during and after burial;
• contamination with modern DNA;
• base modifications and amplification errors.
The method has proved to be a key asset in the study of DNA preserved in fossilising bones that have been subjected to climatic and/or chemical conditions that are
unfavourable to DNA preservation. This will be discussed hereafter.
The combination of the use of freshly unearthed, unwashed fossil remains and our quantitative high-fidelity and high-sensitivity PCR approach allowed us to obtain some 60 authenticated mitochondrial sequences from between 9500- and 3000-year-old bovine remains, 30 from Southwest Asia and 30 from western Europe (mainly France) (Pruvost et al., in preparation).
The result of this large-scale analysis proves on the genetic level that it was the aurochs population from the Upper Euphrates and Tigris Basin that had been domesticated almost 10,000 years ago and then spread into Europe, since Neolithic and Bronze Age cattle in western Europe show a mitochondrial signature that is a subset of that of their ancestral populations in Southwest Asia (Pruvost et al., in preparation). They also gave rise to the extant cattle populations all over the world, although modern-day cattle in continental Europe represent only a small subset of the original populations (Pruvost et al., in preparation). In contrast, the western European aurochsen did not leave a mitochondrial signature in extant European cattle, which indicates that female western European aurochsen were not domesticated in Europe, but rather maintained their status as hunted game until at least the Bronze Age (Pruvost et al., in preparation).
Palaeogenetics of cattle domestication: Methodological challenges for the study of fossil bones preserved in the domestication centre in Southwest Asia
Recently, palaeogenetics encountered enormous success when parts of the nuclear genomes of mammoth and Neanderthal man were analysed. Their bones, however, had been preserved in environments favourable to DNA preservation, i.e., permafrost regions
and caves in temperate regions. Few studies have tackled archaeological bones from hot, arid regions, although they bear great significance for the study of evolution of humans and the precursors of modern societies. According to archaeological evidence, a key event in neolithisation, the domestication of cattle, took place around 10,000 years ago in Southwest Asia. Genetic data from prehistoric bovine bones preserved in this region might shed light on this process, but the palaeogenetic approach has been hampered by poor DNA preservation. Here, I discuss various aspects of DNA preservation in fossils and the production of reliable palaeogenetic data and present methodological improvements that have enabled us to shed light on the process of cattle domestication in Southwest Asia and its spread into western Europe.