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Analysis of High-Throughput Ancient DNA Sequencing Data

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Ancient DNA

Part of the book series: Methods in Molecular Biology ((MIMB,volume 840))

Abstract

Advances in sequencing technologies have dramatically changed the field of ancient DNA (aDNA). It is now possible to generate an enormous quantity of aDNA sequence data both rapidly and inexpensively. As aDNA sequences are generally short in length, damaged, and at low copy number relative to coextracted environmental DNA, high-throughput approaches offer a tremendous advantage over traditional sequencing approaches in that they enable a complete characterization of an aDNA extract. However, the particular qualities of aDNA also present specific limitations that require careful consideration in data analysis. For example, results of high-throughout analyses of aDNA libraries may include chimeric sequences, sequencing error and artifacts, damage, and alignment ambiguities due to the short read lengths. Here, I describe typical primary data analysis workflows for high-throughput aDNA sequencing experiments, including (1) separation of individual samples in multiplex experiments; (2) removal of protocol-specific library artifacts; (3) trimming adapter sequences and merging paired-end sequencing data; (4) base quality score filtering or quality score propagation during data analysis; (5) identification of endogenous molecules from an environmental background; (6) quantification of contamination from other DNA sources; and (7) removal of clonal amplification products or the compilation of a consensus from clonal amplification products, and their exploitation for estimation of library complexity.

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Acknowledgments

I thank all current and previous members of the Department of Evolutionary Genetics at the Max Planck Institute for Evolu­tionary Anthropology, and particularly members of the aDNA and sequencing group, for interesting discussions and useful insights as well as for providing their sequencing data for analysis (especially Knut Finstermeier for providing the example data set). I also thank Knut Finstermeier and Beth Shapiro for critical reading and revisions. This work was supported by a grant from the Max Planck Society.

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Authors and Affiliations

  1. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany

    Martin Kircher

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  1. Martin Kircher
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Correspondence to Martin Kircher .

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Editors and Affiliations

  1. Dept. of Ecology and Evolutionary Biolog, University of California Santa Cruz, A414 Earth & Marine Sciences, Santa Cruz, 16802, California, USA

    Beth Shapiro

  2. , Department of Biology (Area 2), University of York, Heslington, York, YO 105DD, United Kingdom

    Michael Hofreiter

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Kircher, M. (2012). Analysis of High-Throughput Ancient DNA Sequencing Data. In: Shapiro, B., Hofreiter, M. (eds) Ancient DNA. Methods in Molecular Biology, vol 840. Humana Press. https://doi.org/10.1007/978-1-61779-516-9_23

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  • DOI: https://doi.org/10.1007/978-1-61779-516-9_23

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-515-2

  • Online ISBN: 978-1-61779-516-9

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