The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils

Allentoft, Morten E.; Collins, Matthew J.; Harker, David; Haile, James; Oskam, Charlotte L.; Hale, Marie L.; Campos, Paula F.; Samaniego, José A.; Gilbert, M. Thomas P.; Willerslev, Eske; Zhang, Guojie; Scofield, R. Paul; Holdaway, Richard N.; Bunce, Michael

doi:10.1098/rspb.2012.1745

Cited by 493 publications

(490 citation statements)

References 65 publications

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“…Figure 3d shows no correlation, either for direct or relative dates. For non-UDGtreated libraries, Sawyer et al [41] and Allentoft et al [42] explored a wider range of dates and found a correlation.…”

Section: Results (A) Library Constructionmentioning

confidence: 99%

Partial uracil–DNA–glycosylase treatment for screening of ancient DNA

Rohland

Harney

Mallick

et al. 2015

Phil. Trans. R. Soc. B

430

441

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The challenge of sequencing ancient DNA has led to the development of specialized laboratory protocols that have focused on reducing contamination and maximizing the number of molecules that are extracted from ancient remains. Despite the fact that success in ancient DNA studies is typically obtained by screening many samples to identify a promising subset, ancient DNA protocols have not, in general, focused on reducing the time required to screen samples. We present an adaptation of a popular ancient library preparation method that makes screening more efficient. First, the DNA extract is treated using a protocol that causes characteristic ancient DNA damage to be restricted to the terminal nucleotides, while nearly eliminating it in the interior of the DNA molecules, allowing a single library to be used both to test for ancient DNA authenticity and to carry out population genetic analysis. Second, the DNA molecules are ligated to a unique pair of barcodes, which eliminates undetected cross-contamination from this step onwards. Third, the barcoded library molecules include incomplete adapters of short length that can increase the specificity of hybridization-based genomic target enrichment. The adapters are completed just before sequencing, so the same DNA library can be used in multiple experiments, and the sequences distinguished. We demonstrate this protocol on 60 ancient human samples.

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Section: Results (A) Library Constructionmentioning

confidence: 99%

Partial uracil–DNA–glycosylase treatment for screening of ancient DNA

Rohland

Harney

Mallick

et al. 2015

Phil. Trans. R. Soc. B

430

441

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“…feathers, bones, mummified remains, egg shells) are attributed to them [18][19][20]. Because of the availability of exceptionally preserved specimens, DNA recovered from various moa specimens has been used to differentiate species [20,21] and estimate rates of DNA degradation [22]. However, few complementary studies of moa proteins have been attempted [3,23].…”

Section: Introductionmentioning

confidence: 99%

Biologically and diagenetically derived peptide modifications in moa collagens

2015

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The modifications that occur on proteins in natural environments over time are not well studied, yet characterizing them is vital to correctly interpret sequence data recovered from fossils. The recently extinct moa (Dinornithidae) is an excellent candidate for investigating the preservation of proteins, their post-translational modifications (PTMs) and diagenetic alterations during degradation. Moa protein extracts were analysed using mass spectrometry, and peptides from collagen I, collagen II and collagen V were identified. We also identified biologically derived PTMs (i.e. methylation, di-methylation, alkylation, hydroxylation, fucosylation) on amino acids at locations consistent with extant proteins. In addition to these in vivo modifications, we detected novel modifications that are probably diagenetically derived. These include loss of hydroxylation/glutamic semialdehyde, carboxymethyllysine and peptide backbone cleavage, as well as previously noted deamidation. Moa collagen sequences and modifications provide a baseline by which to evaluate proteomic studies of other fossils, and a framework for defining the molecular relationship of moa to other closely related taxa.

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“…Depurination affects the stability of the DNA backbone and leads to nicks and single-strand overhangs of the DNA fragments (2). Consequently, most free DNA fragments in the environment are <100 bp in size (3)(4)(5)(6)(7)(8). Deamination particularly affects cytosine, creating uracil residues that can lead to cytosine-tothymine exchanges, which result in DNA sequencing errors (9).…”

mentioning

confidence: 99%

Bacterial natural transformation by highly fragmented and damaged DNA

Overballe‐Petersen¹,

Harms

Orlando³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

171

142

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DNA molecules are continuously released through decomposition of organic matter and are ubiquitous in most environments. Such DNA becomes fragmented and damaged (often <100 bp) and may persist in the environment for more than half a million years. Fragmented DNA is recognized as nutrient source for microbes, but not as potential substrate for bacterial evolution. Here, we show that fragmented DNA molecules (≥20 bp) that additionally may contain abasic sites, cross-links, or miscoding lesions are acquired by the environmental bacterium Acinetobacter baylyi through natural transformation. With uptake of DNA from a 43,000-y-old woolly mammoth bone, we further demonstrate that such natural transformation events include ancient DNA molecules. We find that the DNA recombination is RecA recombinase independent and is directly linked to DNA replication. We show that the adjacent nucleotide variations generated by uptake of short DNA fragments escape mismatch repair. Moreover, doublenucleotide polymorphisms appear more common among genomes of transformable than nontransformable bacteria. Our findings reveal that short and damaged, including truly ancient, DNA molecules, which are present in large quantities in the environment, can be acquired by bacteria through natural transformation. Our findings open for the possibility that natural genetic exchange can occur with DNA up to several hundreds of thousands years old. microbial evolution | horizontal gene transfer | DNA degradation | early life | anachronistic evolution

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The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils

Cited by 493 publications

References 65 publications

Partial uracil–DNA–glycosylase treatment for screening of ancient DNA

Partial uracil–DNA–glycosylase treatment for screening of ancient DNA

Biologically and diagenetically derived peptide modifications in moa collagens

Bacterial natural transformation by highly fragmented and damaged DNA

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