J Binladen
Assessing the fidelity of ancient DNA sequences amplified from nuclear genes
Binladen, J; Wiuf, C; Gilbert, MTP; Bunce, M; Barnett, R; Larson, G; Greenwood, AD; Haile, J; Ho, SYW; Hansen, AJ; Willerslev, E
Authors
C Wiuf
MTP Gilbert
M Bunce
R Barnett
G Larson
AD Greenwood
J Haile
SYW Ho
AJ Hansen
E Willerslev
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.
Citation
Binladen, J., Wiuf, C., Gilbert, M., Bunce, M., Barnett, R., Larson, G., …Willerslev, E. (2006). Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics, 172(2), 733-741. https://doi.org/10.1534/genetics.105.049718
Journal Article Type | Article |
---|---|
Publication Date | Feb 1, 2006 |
Deposit Date | Jul 1, 2009 |
Journal | Genetics |
Print ISSN | 0016-6731 |
Electronic ISSN | 1943-2361 |
Publisher | Genetics Society of America |
Peer Reviewed | Peer Reviewed |
Volume | 172 |
Issue | 2 |
Pages | 733-741 |
DOI | https://doi.org/10.1534/genetics.105.049718 |
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