ArticleBMC genomics2020
Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Multidisciplinary Exploration of Computed-Tomographic and Ancient-DNA Data of an Iron Age Skull From Latvia With Multiple Lytic Bone Lesions: Differential Diagnosis Between Metastatic Carcinoma, Multiple Myeloma and Skeletal Tuberculosis.Ecology and evolution · 2026Article
- Evolution of Resistance to Avian Malaria Infection in an Endemic Hawaiian Honeycreeper.Ecology and evolution · 2026Article
- Biogeographic history of the Late Pleistocene and Holocene European small hamsters (subfamily Cricetinae).Scientific reports · 2026Article
- A High-Throughput Ancient DNA Extraction Method for Large-Scale Sample Screening.Molecular ecology resources · 2025Article
- Article
- Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping.Briefings in bioinformatics · 2024Article
- Unravelling reference bias in ancient DNA datasets.Bioinformatics (Oxford, England) · 2024Article
- Ancient DNA of narrow-headed vole reveal common features of the Late Pleistocene population dynamics in cold-adapted small mammals.Proceedings. Biological sciences · 2023Article
- Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections.Biodiversity data journal · 2023Article
- HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data.PLoS computational biology · 2022Article
- Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome.iScience · 2022Article
- A theoretical analysis of taxonomic binning accuracy.Molecular ecology resources · 2022Article
- Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA.Genes · 2022Article
- Revisiting proboscidean phylogeny and evolution through total evidence and palaeogenetic analyses includingiScience · 2022Article
- Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment.Current biology : CB · 2021Article
- Inferring archaic introgression from hominin genetic data.Evolutionary anthropology · 2021Review
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15 authors.
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Abstract
backgroundAfter over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.
resultsHere we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.
conclusionsWe propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.
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