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Combining bleach and mild predigestion improves ancient DNA recovery from bones
Abstract
The feasibility of genome‐scale studies from archaeological material remains critically dependent on the ability to access endogenous, authentic DNA . In the majority of cases, this represents a few per cent of the DNA extract, at most. A number of specific pre‐extraction protocols for bone powder aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750–1350 cal. years before present. Using high‐throughput sequencing, we show that combined together, bleach wash and predigestion consistently yield DNA libraries with higher endogenous content than either of these methods alone. Additionally, the molecular complexity of these libraries is improved and endogenous DNA templates show larger size distributions. Other library characteristics, such as DNA damage profiles or the composition of microbial communities, are little affected by the pre‐extraction protocols. Application of the combined protocol presented in this study will facilitate the genetic analysis of an increasing number of ancient remains and will reduce the cost of whole‐genome sequencing.
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“The methods may also be combined 42 , but both approaches also result in varying degrees of endogenous aDNA loss, and therefore aggressive cleaning should be viewed as a trade-off that is subject to diminishing returns.”
From Ancient DNA analysis (2021) · cites this paper as [42]
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“Specific chemical treatment of bone powder, for example with bleach 40,42 , can reduce the exogenous DNA fraction and may be attempted in cases of repeated failure due to contamination; however, such treatment can also artificially age modern contaminant DNA, and so authentication of bleachtreated samples should be performed with care.”
From Ancient DNA analysis (2021) · cites this paper as [42]
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Metadata
- Authors
- Boessenkool, S., Hanghøj, K., Nistelberger, H. M., Der Sarkissian, C., Gondek, A. T., Orlando, L., Barrett, J. H., & Star, B.
- Affiliations
- Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo PO Box 1066 Blindern N‐0316 Oslo Norway
- Centre for Geogenetics Natural History Museum of Denmark University of Copenhagen Øster Voldgade 5‐7 1350 Copenhagen K Denmark
- McDonald Institute for Archaeological Research University of Cambridge Downing Street Cambridge CB2 3ER UK
- Venue
- Molecular Ecology Resources
- Publisher
- Wiley
- Published
- 2016-12-15
- Volume
- 17
- Issue
- 4
- Pages
- 742-751
- ISSN
- 1755-098X
- 1755-0998
- Cited by
- 124
- References
- 11
- Language
- en
- Funders
- Norges Forskningsråd (#230821/F20, #203850/E40, #221734/O30)
- Leverhulme Trust
- Natur og Univers, Det Frie Forskningsråd (#4002‐00152B)
- Université de Toulouse
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