Editorial

Keri A. Brown, University of Manchester
Email: keri.brown@manchester.ac.uk

It has been an unexpected but enjoyable task to put together my own selection of papers on ancient DNA research that have appeared in JAS over the last 22 years. The history of ancient DNA research is reflected here, from its earliest beginnings in 1985 as a scientific curiosity, from the excitement of the discovery that the polymerase chain reaction could be used to amplify degraded DNA templates in the late 1980s, the first amplifications of human DNA from archaeological bone samples in 1989, the realisation in the mid-1990s that contamination was a major issue, to the concerns with establishing standards for ancient DNA research. The latter is still a live debate, as is contamination. In 2000 a pivotal paper was published entitled ‘Ancient DNA – Do it right or not at all’ (Cooper and Poinar in Science) which set out the concerns and standards for the field. Many papers have been rejected by JAS because they have not followed these standards. JAS is not to be used as a ‘dumping ground’ for work that is substandard or trivial. I have chosen papers that I feel have made a significant contribution to ancient DNA research, either methodologically or through applications to archaeological questions. This is after all a journal of Archaeological Science, so some archaeology ought to appear somewhere!

I had not realised before my ‘task’ that Svante Paabo had published his earliest ancient DNA paper in JAS in 1985. As it is concerned with DNA extraction and gel electrophoresis, this appeared before his Nature paper on ancient human DNA from an Egyptian mummy also in 1985. This was obviously one of my choices. There is then a gap of 10 years till my next choices, which deal with the issues that still trouble ancient DNA research and will probably never go away - anti-contamination measures and authentication of ancient DNA sequences (Hanni et al and Richards et al).

In 1996 we see papers on the identification of pathogen DNA from human bone samples. At that time it was not possible to distinguish between human TB and cattle TB, so the identification was of TB complex DNA. Again much optimism in the early days of research – Baron et al suggested that any disease could be identified using ancient DNA methods. Most early work concentrated on bone samples which showed the characteristic lesions associated with TB, however it is well known that only a minority of TB victims develop these bony lesions, and TB DNA has been found in asymptomatic bones.

A thorough study of a burial group appeared in 1997 which addressed the concerns with contamination from modern DNA and authentication of the DNA sequences obtained (Colson et al). A number of different methods was brought to bear on the burials – C:N ratio measurements and bone microstructure preservation were assessed in order to understand biomolecule preservation, and to assess the likelihood of ancient DNA survival. Mitochondrial DNA typing of lab personnel and excavators was carried out in order to identify sources of contamination – standard procedures now carried out by researchers to gain credibility for their results. The ancient DNA sequences were then placed in a network to compare with present-day populations.

I do not have the space to discuss all the papers I have selected in detail. 1998 sees the first ancient plant DNA paper in JAS. Ancient plant DNA has not received the media attention that ancient human DNA has, so researchers of charred, desiccated or waterlogged seeds just kept their heads down on got on with shedding light on domestication and early agriculture and its spread in the Old and New Worlds. However seeds are designed by nature to preserve DNA and other biomolecules and ancient DNA groups are now starting to realise that perhaps bones are not where it’s at after all. Schlumbaum et al published a controversial finding which has now been supported by other research.

There have been papers which attempted to identify selective infanticide by identifying the sex of infant remains, one by Faerman et al in 1998 and one by Mays and Faerman in 2001. Although sample numbers and PCR results were low, these were brave attempts to test archaeological hypotheses with ancient DNA. 2003 sees two papers on plant DNA – one on maize tracing its routes of dispersal in South America (Freitas et al) and the other on the geographical origin of vines (Manen et al). Both types of plant material, maize corn and cobs and woody grape pips, have turned out to be excellent sources of ancient DNA (see above).

A ‘high-tech’ paper by Pruvost and Geigl in 2004 describes the use of real-time PCR (also known as quantitative PCR) with ancient DNA for the first time in JAS. The piece of equipment involved is very expensive – now that prices have come down more labs are using this method, which allows a PCR to be followed as it happens and contaminating DNA to be identified, and it can also quantitate the number of starting molecules of DNA. 2005 was a good year for ancient DNA in JAS with 9 papers published, including one on syphilis by Bouwman and Brown which showed that ancient DNA has its limits. It was the first time that it was shown that pathogen DNA does not survive due to the particular development of the disease – by the tertiary stages the syphilis pathogen is NOT present in bones, but in the nervous system and brain, even though characteristic bone lesions and resorption are the classic signs of this disease in skeletal remains.

The greatest number of papers published in one year was in 2006, with a total of 12 articles covering a wide variety of research addressing all sorts of questions with ancient DNA. I picked out 2 papers for this edition – one on DNA from wood Deguilloux et al) and the other on VNTR (microsatellite) typing of leprosy (Taylor et al). The latter moves beyond the mere identification of a pathogen to the identification of the strains involved in the past – with the publication of complete genome sequences for many major pathogens PCR primers can be designed to amplify informative DNA sequences. So far in 2007, 5 ancient DNA papers have been published – the most exciting has to be the identification of a new mitochondrial DNA haplogroup in North America, which has caused a rethink over the number of founding haplogroups involved in the colonisation of the New World.

I hope that more interesting, innovative, and controversial results will be sent to JAS. What are the prospects for the future for ancient DNA research? Again a personal perspective, but I see nanotechnology being applied to ancient DNA, leading to the development of new methodologies, I see careful choice of samples and research questions, and I hope that guidelines for the sampling of archaeological remains at the point of excavation become established and MANDATORY. It is well known that most contamination takes place during excavation by archaeologists. It is also known that freshly excavated bone samples give better success rates. It is time for the archaeological field community address this issue if they want ancient DNA to be the tool for answering questions about past societies that everybody optimistically thought it would be when this research field began 22 years ago. However we scientists must also do our bit and go to archaeological conferences and spread the news – we have the technology, you have the samples, let’s get together and revolutionise our understanding of people in the past.

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