ArticlePLoS genetics2016
Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans.
Article in PLoS genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 27 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
27 citing papers in PubMed.
- CHARON: estimating the drift time and the number of individuals in environmental DNA with diploid individuals.G3 (Bethesda, Md.) · 2026Article
- Evidence of long-term purging of mutation burden in killer whale Orcinus orca genomes.Heredity · 2025Article
- Optimized in-solution enrichment of over a million ancient human SNPs.Genome biology · 2025Article
- Accounting for population structure and data quality in demographic inference with linkage disequilibrium methods.Nature communications · 2025Article
- hapCon: estimating contamination of ancient genomes by copying from reference haplotypes.Bioinformatics (Oxford, England) · 2022Article
- Inline index helped in cleaning up data contamination generated during library preparation and the subsequent steps.Molecular biology reports · 2022Article
- A Minimally Morphologically Destructive Approach for DNA Retrieval and Whole-Genome Shotgun Sequencing of Pinned Historic Dipteran Vector Species.Genome biology and evolution · 2021Article
- Whole-Genome Sequencing of a 900-Year-Old Human Skeleton Supports Two Past Migration Events from the Russian Far East to Northern Japan.Genome biology and evolution · 2021Article
- Article
- AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination.Genome biology · 2020Article
- ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium.Genome biology · 2020Article
- Inference of natural selection from ancient DNA.Evolution letters · 2020Article
- A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data.Bioinformatics (Oxford, England) · 2020Article
- The presence and impact of reference bias on population genomic studies of prehistoric human populations.PLoS genetics · 2019Article
- Inference and visualization of DNA damage patterns using a grade of membership model.Bioinformatics (Oxford, England) · 2019Article
- An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies.GigaScience · 2019Article
- snpAD: an ancient DNA genotype caller.Bioinformatics (Oxford, England) · 2018Article
- Origins and genetic legacies of the Caribbean Taino.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans.Nature · 2018Article
- Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
Abstract
When sequencing an ancient DNA sample from a hominin fossil, DNA from present-day humans involved in excavation and extraction will be sequenced along with the endogenous material. This type of contamination is problematic for downstream analyses as it will introduce a bias towards the population of the contaminating individual(s). Quantifying the extent of contamination is a crucial step as it allows researchers to account for possible biases that may arise in downstream genetic analyses. Here, we present an MCMC algorithm to co-estimate the contamination rate, sequencing error rate and demographic parameters-including drift times and admixture rates-for an ancient nuclear genome obtained from human remains, when the putative contaminating DNA comes from present-day humans. We assume we have a large panel representing the putative contaminant population (e.g. European, East Asian or African). The method is implemented in a C++ program called 'Demographic Inference with Contamination and Error' (DICE). We applied it to simulations and genome data from ancient Neanderthals and modern humans. With reasonable levels of genome sequence coverage (>3X), we find we can recover accurate estimates of all these parameters, even when the contamination rate is as high as 50%.
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