ArticleBMC biology2018
Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences.
Article in BMC biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed.
- Genomic data from the extinct California brown bear suggests a source population for reintroduction to California.The Journal of heredity · 2025Article
- The genomic footprints of migration: how ancient DNA reveals our history of mobility.Genome biology · 2025Review
- Article
- Statistical Distributions of Genome Assemblies Reveal Random Effects in Ancient Viral DNA Reconstructions.Viruses · 2025Article
- Improving data archiving practices in ancient genomics.Scientific data · 2024Article
- Unravelling reference bias in ancient DNA datasets.Bioinformatics (Oxford, England) · 2024Article
- Genome sequences of 36,000- to 37,000-year-old modern humans at Buran-Kaya III in Crimea.Nature ecology & evolution · 2023Article
- Deep-time paleogenomics and the limits of DNA survival.Science (New York, N.Y.) · 2023Review
- Historical RNA expression profiles from the extinct Tasmanian tiger.Genome research · 2023Article
- DNA and protein analyses of hair in forensic genetics.International journal of legal medicine · 2023Review
- Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections.Biodiversity data journal · 2023Article
- 4000-year-old hair from the Middle Nile highlights unusual ancient DNA degradation pattern and a potential source of early eastern Africa pastoralists.Scientific reports · 2022Article
- A theoretical analysis of taxonomic binning accuracy.Molecular ecology resources · 2022Article
- GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species.BMC bioinformatics · 2022Article
- The genetic identity of the earliest human-made hybrid animals, the kungas of Syro-Mesopotamia.Science advances · 2022Article
- Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- MTaxi: A comparative tool for taxon identification of ultra low coverage ancient genomes.Open research Europe · 2022Article
- Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics.Proceedings. Biological sciences · 2021Review
- Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets.BMC genomics · 2020Article
- Reconstructing double-stranded DNA fragments on a single-molecule level reveals patterns of degradation in ancient samples.Genome research · 2020Article
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3 authors.
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Abstract
backgroundThe study of ancient DNA is hampered by degradation, resulting in short DNA fragments. Advances in laboratory methods have made it possible to retrieve short DNA fragments, thereby improving access to DNA preserved in highly degraded, ancient material. However, such material contains large amounts of microbial contamination in addition to DNA fragments from the ancient organism. The resulting mixture of sequences constitutes a challenge for computational analysis, since microbial sequences are hard to distinguish from the ancient sequences of interest, especially when they are short.
resultsHere, we develop a method to quantify spurious alignments based on the presence or absence of rare variants. We find that spurious alignments are enriched for mismatches and insertion/deletion differences and lack substitution patterns typical of ancient DNA. The impact of spurious alignments can be reduced by filtering on these features and by imposing a sample-specific minimum length cutoff. We apply this approach to sequences from four ~ 430,000-year-old Sima de los Huesos hominin remains, which contain particularly short DNA fragments, and increase the amount of usable sequence data by 17-150%. This allows us to place a third specimen from the site on the Neandertal lineage.
conclusionsOur method maximizes the sequence data amenable to genetic analysis from highly degraded ancient material and avoids pitfalls that are associated with the analysis of ultra-short DNA sequences.
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