AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination

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Abstract

Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. We present AuthentiCT, a command-line tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded DNA libraries. The prediction is based solely on the patterns of post-mortem damage observed on ancient DNA sequences. The method has the power to quantify contamination from as few as 10,000 mapped sequences, making it particularly useful for analysing specimens that are poorly preserved or for which little data is available.

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Most cited references 52

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The complete genome sequence of a Neandertal from the Altai Mountains

Kay Prüfer, Fernando Racimo, Nick Patterson … (2014)

We present a high-quality genome sequence of a Neandertal woman from Siberia. We show that her parents were related at the level of half siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neandertal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neandertals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high quality Neandertal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neandertals and Denisovans.

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A high-coverage genome sequence from an archaic Denisovan individual.

Matthias Meyer, Martin Kircher, Marie-Theres Gansauge … (2012)

We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.

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Massive migration from the steppe was a source for Indo-European languages in Europe

Wolfgang Haak, Iosif Lazaridis, Nick Patterson … (2015)

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of Western and Far Eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ∼8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ∼24,000-year-old Siberian. By ∼6,000-5,000 years ago, farmers throughout much of Europe had more hunter-gatherer ancestry than their predecessors, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ∼4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ∼75% of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ∼3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for a steppe origin of at least some of the Indo-European languages of Europe.

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Author and article information

Contributors

Stéphane Peyrégne:

ORCID: http://orcid.org/0000-0002-9823-9102

stephane.peyregne@gmail.com

Journal

Journal ID (nlm-ta): Genome Biol

Journal ID (iso-abbrev): Genome Biol

Title: Genome Biology

Publisher: BioMed Central (London )

ISSN (Print): 1474-7596

ISSN (Electronic): 1474-760X

Publication date (Electronic): 15 September 2020

Publication date PMC-release: 15 September 2020

Publication date Collection: 2020

Volume: 21

Electronic Location Identifier: 246

Affiliations

GRID grid.419518.0, ISNI 0000 0001 2159 1813, Department of Evolutionary Genetics, , Max Planck Institute for Evolutionary Anthropology, ; 04103 Leipzig, Germany

Author information

Stéphane Peyrégne http://orcid.org/0000-0002-9823-9102

Article

Publisher ID: 2123

DOI: 10.1186/s13059-020-02123-y

PMC ID: 7490890

PubMed ID: 32933569

SO-VID: dcc22e85-53e0-4758-b501-1049ee0fa563

License:

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

History

Date received : 12 March 2020

Date accepted : 27 July 2020

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100004189, Max-Planck-Gesellschaft;

Funded by: European Research Council

Award ID: 694707

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: contamination,ancient dna,deamination,damage patterns

Data availability:

ScienceOpen disciplines: Genetics

Keywords: contamination, ancient dna, deamination, damage patterns

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AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination

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Genome Integrity

Most cited references 52

The complete genome sequence of a Neandertal from the Altai Mountains

A high-coverage genome sequence from an archaic Denisovan individual.

Massive migration from the steppe was a source for Indo-European languages in Europe

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