Assessing the fidelity of ancient DNA sequences amplified from nuclear genes

Ancient DNA and Evolution Group, Centre for Ancient Genetics, Niels Bohr Institute, University of Copenhagen, Denmark.
Genetics (Impact Factor: 5.96). 02/2006; 172(2):733-41. DOI: 10.1534/genetics.105.049718
Source: PubMed


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.

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    • "The disparity between mtDNA and nuDNA mean fragment length is in agreement with recent studies of vertebrates from permafrost and sediment deposits (Schwarz et al. 2009; Allentoft et al. 2012), which suggest that nuDNA degrades at a faster rate than mtDNA. This may be due to the circular configuration of mtDNA making it less accessible to exonucleases (Allentoft et al. 2012), the double membrane of the mitochondrion offering additional protection (Schwarz et al. 2009) or the interaction of nuDNA and histones facilitating strand breaks (Binladen et al. 2006). "
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    Molecular Ecology Resources 05/2014; 14(3):606-615. DOI:10.1111/1755-0998.12205 · 3.71 Impact Factor
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    • "Both as typical members of the " Coelodonta-Mammuthus Fauna " in late Pleistocene, the woolly rhinoceros and the woolly mammoth have received unequal attentions at the molecular level. The phylogenetic position of the woolly mammoth has been fully resolved by multiple sampling locations (Yang et al., 1996; Noro et al., 1998; Lister et al., 2001; Debruyne et al., 2003; Krause et al., 2006; Rogaev et al., 2006; Yang et al., 2006; Gilbert et al., 2008; Miller et al., 2008; Enk et al., 2009), whereas DNA studies on Coelodonta antiquitatis were focused only on very limited sampling sites in Europe and northern Asia (Orlando et al., 2003; Binladen et al., 2006; Willerslev et al., 2009; Lorenzen et al., 2011). Among the interested issues of the woolly rhinoceros, the close phylogenetic relationship between this species and the modern Sumatran rhinoceros was accepted by previous ancient DNA studies (Orlando et al., 2003; Willerslev et al., 2009). "
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    Science China Earth Science 03/2014; 57(3):388-396. DOI:10.1007/s11430-013-4702-6 · 1.49 Impact Factor
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    • "This supports the notion that post-mortem miscoding lesions are a negligible source of error in historical specimens [20], [25]. Although we used organellar DNA to assess damage, the sequence error rates in organelle and nuclear genomes have been observed not to differ [32] and, therefore, we expect that our organellar genomic results should be representative of those for nuclear genomes. Whilst the observed sequencing errors are like random noise and unlikely to produce a phylogenetic signal given sufficient read depth coverage, our data could be used for high-confidence genotyping, and selection of SNP and indel-rich coding regions that will allow for genome-scale genetic diversity and phylogenetic analyses. "
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    PLoS ONE 07/2013; 8(7):e69189. DOI:10.1371/journal.pone.0069189 · 3.23 Impact Factor
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