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More on contamination: The use of asymmetric molecular behavior to identify authentic ancient human DNA
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. (Ancient DNA)
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. (Ancient DNA)
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2007 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 24, no 4, 998-1004 p.Article in journal (Refereed) Published
Abstract [en]

Authentication of ancient human DNA results is an exceedingly difficult challenge due to the presence of modern contaminant DNA sequences. Nevertheless, the field of ancient human genetics generates huge scientific and public interest, and thus researchers are rarely discouraged by problems concerning the authenticity of such data. Although several methods have been developed to the purpose of authenticating ancient DNA (aDNA) results, while they are useful in faunal research, most of the methods have proven complicated to apply to ancient human DNA. Here, we investigate in detail the reliability of one of the proposed criteria, that of appropriate molecular behavior. Using real-time polymerase chain reaction (PCR) and pyrosequencing, we have quantified the relative levels of authentic aDNA and contaminant human DNA sequences recovered from archaeological dog and cattle remains. In doing so, we also produce data that describes the efficiency of bleach incubation of bone powder and its relative detrimental effects on contaminant and authentic ancient DNA. We note that bleach treatment is significantly more detrimental to contaminant than to authentic aDNA in the bleached bone powder. Furthermore, we find that there is a substantial increase in the relative proportions of authentic DNA to contaminant DNA as the PCR target fragment size is decreased. We therefore conclude that the degradation pattern in aDNA provides a quantifiable difference between authentic aDNA and modern contamination. This asymmetrical behavior of authentic and contaminant DNA can be used to identify authentic haplotypes in human aDNA studies.

Place, publisher, year, edition, pages
2007. Vol. 24, no 4, 998-1004 p.
Keyword [en]
contamination, ancient DNA, authentication
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-96065DOI: 10.1093/molbev/msm015ISI: 000245353200013PubMedID: 17255122OAI: oai:DiVA.org:uu-96065DiVA: diva2:170522
Available from: 2007-08-31 Created: 2007-08-31 Last updated: 2011-02-08Bibliographically approved
In thesis
1. Ancient DNA as a Means to Investigate the European Neolithic
Open this publication in new window or tab >>Ancient DNA as a Means to Investigate the European Neolithic
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The transition from a hunter-gatherer lifestyle to a farming lifestyle, i.e. the Neolithisation, is arguably the most important event in human prehistory. While the geography and dating of the Neolithisation is well known, the process is still under debate, especially if it occurred through diffusion of ideas or with migrating farmers. The process accelerated when alternative use of domesticated animals increased. Especially the use of dairy products, and the consumption of unprocessed milk, appears to be of importance. As milk consumption (lactose digestion) is dependent upon genetic components, it is debated whether the genetic disposition allowed for dairy production to evolve, or if the usages of dairy products added selection pressure that eventually lead to present day allele frequencies. Molecular genetics have the potential to solve this and similar questions, but only if the contamination problem, where authentic DNA can be distinguished from modern contaminating DNA, can be resolved.

Here I investigate the nature and extent of contamination with modern human DNA in museum specimens and explore several approaches to minimise this contamination and to authenticate DNA results from ancient humans. I use real-time quantification, pyrosequencing and FLX-generated clonal sequencing assays to generate data on ancient humans and ancient dogs. I further use the techniques to study the development of lactase persistence and the nature of animal domestication.

The results presented show that sample-based contamination is extensive, but can be minimised if treated with bleach. I retrieved authentic HVSI sequences from 30 Neolithic hunter-gatherers and farmers from Sweden, of which eighteen also yielded nuclear data indicating that the farmers had a higher frequency of the allele linked to lactase persistence compared to the hunter-gatherers. I conclude that genetic data from ancient humans as well as from ancient animals can be retrieved and used, but only under high stringency.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2007. 70 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 323
Molecular genetics, aDNA, contamination, authentication, mtDNA, Neolithisation, Genetik
urn:nbn:se:uu:diva-8162 (URN)978-91-554-6940-5 (ISBN)
Public defence
2007-09-21, Lindhalsalen, Norbyvägen 14, Uppsala, 13:00 (English)
Available from: 2007-08-31 Created: 2007-08-31 Last updated: 2009-03-31Bibliographically approved

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