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Separating endogenous ancient DNA from modern-day contamination: application to a Siberian Neandertal
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103 Germany .
Palaeolithic Department, Institute of Archaeology & Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia.
Palaeolithic Department, Institute of Archaeology & Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia.
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2014 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 111, no 6, 2229-2234 p.Article in journal (Refereed) Published
Abstract [en]

One of the main impediments for obtaining DNA sequences from ancient humanskeletons is the presence of contaminating modern human DNA molecules in many fossil samples and laboratory reagents. However, DNA fragments isolated from ancient specimens show a characteristic DNA damage pattern, caused by miscoding lesions, that differs from present-day DNA sequences. Here, we develop a framework for evaluating the likelihood of a sequence originating from a model with post-mortem degradation (PMD)—summarized in a PMD score—which allows the identification of DNA fragments that are unlikely to originate from present-day sources. We apply this approach to a contaminated Neandertal specimen from the Okladnikov cave in Siberia in order to isolate its endogenous DNA from modern human contaminants, and show that the reconstructed mitochondrial genome sequence is more closely related to the variation of Western Neandertals than what was discernible from previous analyses. Our method opens up the potential for genomic analysis of contaminated fossil material.

Place, publisher, year, edition, pages
2014. Vol. 111, no 6, 2229-2234 p.
National Category
Biological Sciences
Research subject
Evolutionary Genetics
Identifiers
URN: urn:nbn:se:uu:diva-206755DOI: 10.1073/pnas.1318934111ISI: 000330999600045OAI: oai:DiVA.org:uu-206755DiVA: diva2:645387
Available from: 2013-09-04 Created: 2013-09-04 Last updated: 2017-12-06Bibliographically approved
In thesis
1. Reconstructing the Human Past using Ancient and Modern Genomes
Open this publication in new window or tab >>Reconstructing the Human Past using Ancient and Modern Genomes
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The study of DNA variation is one of the most promising avenues for learning about the evolutionary and historical past of humans and other species. However, the difficulty associated with obtaining DNA directly from ancient remains have for long kept genomic studies of population history trapped in time; confined to interpreting patterns of modern-day variation without direct historical observations. In this thesis, I outline new approaches for the retrieval, analysis and interpretation of large-scale genomic data from ancient populations, including solutions to overcome problems associated with limited genome coverage, modern-day contamination, temporal differences between samples, and post-mortem DNA damage. I integrate large-scale genomic data sets from ancient remains with modern-day variation to trace the human past; from traits targeted by natural selection in the early ancestors of anatomically modern humans, to their descendants' interbreeding with archaic populations in Eurasia and the spread of agriculture in Europe and Africa. By first reconstructing the earliest population diversification events of early modern humans using a novel large-scale genomic data set from Khoe-San populations in southern Africa, I devise a new approach to search for genomic patterns of selective sweeps in ancestral populations and report evidence for skeletal development as a major target of selection during the emergence of early modern humans. Comparing publicly available genomes from archaic humans, I further find that the distribution of archaic human ancestry in Eurasia is more complex than previously thought. In the first direct genomic study of population structure in prehistoric populations, I demonstrate that individuals associated with farming- and hunter-gatherer complexes in Neolithic Scandinavia were strongly genetically differentiated, and direct comparisons with modern-day populations as well as other prehistoric individuals from Southern Europe suggest that this structure originated from Northward expansion of Neolithic farming populations. Finally, I develop a bioinformatic approach for removing modern-day contamination from large-scale ancient DNA sequencing data, and use this method to reconstruct the complete mitochondrial genome sequence of a Siberian Neandertal that is affected by substantial modern-day contamination.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2013. 68 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1069
Keyword
population genetics, paleogenomics, human evolution
National Category
Evolutionary Biology Genetics
Research subject
Evolutionary Genetics
Identifiers
urn:nbn:se:uu:diva-206787 (URN)978-91-554-8744-7 (ISBN)
Public defence
2013-10-18, Zootissalen, Evolutionary Biology Centre, Norbyvägen 18C, Uppsala, 10:00 (English)
Opponent
Supervisors
Available from: 2013-09-27 Created: 2013-09-04 Last updated: 2014-01-23

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Jakobsson, Mattias

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