ArticleGenetics2006
Assessing the fidelity of ancient DNA sequences amplified from nuclear genes.
Article in Genetics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
45 citing papers in PubMed, 120 citations in OpenAlex.
- Co-mutation Based Genetic Networks to Infer Temporal Mutation Dynamics in Ancient Human Mitochondrial Genomes.Journal of molecular evolution · 2026Article
- Neanderthal and Denisovan Glutamate Dehydrogenase 2 Evolution and Clinical Significance.International journal of molecular sciences · 2025Article
- Ancient mitogenomes reveal a high maternal genetic diversity of Pleistocene woolly rhinoceros in Northern China.BMC ecology and evolution · 2023Article
- Historical RNA expression profiles from the extinct Tasmanian tiger.Genome research · 2023Article
- Test of the FlashFREEZE unit in tissue samples freezing for biobanking purposes.Cell and tissue banking · 2023Article
- Whole-genome sequencing of artificial single-nucleotide variants induced by DNA degradation in biological crime scene traces.International journal of legal medicine · 2023Article
- Genetic Diversity Analysis of MitochondrialLife (Basel, Switzerland) · 2022Article
- New Insights Into Mitochondrial DNA Reconstruction and Variant Detection in Ancient Samples.Frontiers in genetics · 2021Article
- Article
- Review
- Genome Sequencing of Ancient Plant Remains: Findings, Uses and Potential Applications for the Study and Improvement of Modern Crops.Frontiers in plant science · 2018Review
- Organellar Genomes from a ∼5,000-Year-Old Archaeological Maize Sample Are Closely Related to NB Genotype.Genome biology and evolution · 2017Article
- Resurrecting the Dead (Molecules).Computational and structural biotechnology journal · 2017Review
- Odintifier--A computational method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing.BMC bioinformatics · 2015Article
- Proxy comparison in ancient peat sediments: pollen, macrofossil and plant DNA.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2015Article
- Screening ancient tuberculosis with qPCR: challenges and opportunities.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2015Article
- The First Attested Extraction of Ancient DNA in Legumes (Fabaceae).Frontiers in plant science · 2015Review
- Molecular analysis of ancient caries.Proceedings. Biological sciences · 2014Article
- Ancient DNA damage.Cold Spring Harbor perspectives in biology · 2013Review
- Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens.PloS one · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 6 institutions in 5 countries.
Funding
Abstract
To date, the field of ancient DNA has relied almost exclusively on mitochondrial DNA (mtDNA) sequences. However, a number of recent studies have reported the successful recovery of ancient nuclear DNA (nuDNA) sequences, thereby allowing the characterization of genetic loci directly involved in phenotypic traits of extinct taxa. It is well documented that postmortem damage in ancient mtDNA can lead to the generation of artifactual sequences. However, as yet no one has thoroughly investigated the damage spectrum in ancient nuDNA. By comparing clone sequences from 23 fossil specimens, recovered from environments ranging from permafrost to desert, we demonstrate the presence of miscoding lesion damage in both the mtDNA and nuDNA, resulting in insertion of erroneous bases during amplification. Interestingly, no significant differences in the frequency of miscoding lesion damage are recorded between mtDNA and nuDNA despite great differences in cellular copy numbers. For both mtDNA and nuDNA, we find significant positive correlations between total sequence heterogeneity and the rates of type 1 transitions (adenine --> guanine and thymine --> cytosine) and type 2 transitions (cytosine --> thymine and guanine --> adenine), respectively. Type 2 transitions are by far the most dominant and increase relative to those of type 1 with damage load. The results suggest that the deamination of cytosine (and 5-methyl cytosine) to uracil (and thymine) is the main cause of miscoding lesions in both ancient mtDNA and nuDNA sequences. We argue that the problems presented by postmortem damage, as well as problems with contamination from exogenous sources of conserved nuclear genes, allelic variation, and the reliance on single nucleotide polymorphisms, call for great caution in studies relying on ancient nuDNA sequences.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.