ArticlePloS one2011
Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed, 48 citations in OpenAlex.
- Development and Validation of PCR-Based Ancient DNA Analysis for Italian and Western Balkan Archaeological Collections.Balkan journal of medical genetics : BJMG · 2026Article
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- Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA.Genes · 2022Article
- Genetic data from the extinct giant rat from Tenerife (Canary Islands) points to a recent divergence from mainland relatives.Biology letters · 2021Article
- Genomic approaches to trace the history of human brain evolution with an emerging opportunity for transposon profiling of ancient humans.Mobile DNA · 2021Review
- Successful extraction of insect DNA from recent copal inclusions: limits and perspectives.Scientific reports · 2021Article
- Current Advances in DNA Methylation Analysis Methods.BioMed research international · 2021Review
- A systematic investigation of human DNA preservation in medieval skeletons.Scientific reports · 2020Article
- Review
- Malaria was a weak selective force in ancient Europeans.Scientific reports · 2017Article
- Human evolution: a tale from ancient genomes.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Review
- A Common Genetic Origin for Early Farmers from Mediterranean Cardial and Central European LBK Cultures.Molecular biology and evolution · 2015Article
- Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA.Genome biology · 2015Article
- Reconstructing ancient genomes and epigenomes.Nature reviews. Genetics · 2015Review
- Article
- Genome flux and stasis in a five millennium transect of European prehistory.Nature communications · 2014Article
- Aspects of ancient mitochondrial DNA analysis in different populations for understanding human evolution.Balkan journal of medical genetics : BJMG · 2014Review
- Analysis of the Mitochondrial Genome of a Novosvobodnaya Culture Representative using Next-Generation Sequencing and Its Relation to the Funnel Beaker Culture.Acta naturae · 2014Article
- Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome.Genome research · 2014Article
- Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
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7 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundDespite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks. METHODOLOGY/PRINCIPALS
findingsTo investigate whether this pattern is present in ancient remains from a temperate environment, we have 454-FLX pyrosequenced different samples dated between 5,500 and 49,000 years ago: a bone from an extinct goat (Myotragus balearicus) that was treated with a depurinating agent (bleach), an Iberian lynx bone not subjected to any treatment, a human Neolithic sample from Barcelona (Spain), and a Neandertal sample from the El Sidrón site (Asturias, Spain). The efficiency of retrieval of endogenous sequences is below 1% in all cases. We have used the non-human samples to identify human sequences (0.35 and 1.4%, respectively), that we positively know are contaminants.
conclusionsWe observed that bleach treatment appears to create a depurination-associated fragmentation pattern in resulting contaminant sequences that is indistinguishable from previously described endogenous sequences. Furthermore, the nucleotide composition pattern observed in 5' and 3' ends of contaminant sequences is much more complex than the flat pattern previously described in some Neandertal contaminants. Although much research on samples with known contaminant histories is needed, our results suggest that endogenous and contaminant sequences cannot be distinguished by the fragmentation pattern alone.
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