title: 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.
authors: Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO Box 1066, Blindern, N-0316, Oslo, Norway.
authors: Sanne
authors: S
authors: Boessenkool
authors: Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.|Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, University Paul Sabatier (UPS), Toulouse, France.
authors: Kristian
authors: K
authors: Hanghøj
authors: Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO Box 1066, Blindern, N-0316, Oslo, Norway.
authors: Heidi M
authors: HM
authors: Nistelberger
authors: Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
authors: Clio
authors: C
authors: Der Sarkissian
authors: Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO Box 1066, Blindern, N-0316, Oslo, Norway.
authors: Agata T
authors: AT
authors: Gondek
authors: Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.|Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, University Paul Sabatier (UPS), Toulouse, France.
authors: Ludovic
authors: L
authors: Orlando
authors: McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK.
authors: James H
authors: JH
authors: Barrett
authors: Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO Box 1066, Blindern, N-0316, Oslo, Norway.
authors: Bastiaan
authors: B
authors: Star
mesh_terms: D000818:Animals; D001842:Bone and Bones; D000072441:DNA, Ancient / Q000302:isolation & purification*; D048389:Gadus morhua; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D006736:Horses; D017422:Sequence Analysis, DNA; D012973:Sodium Hypochlorite / Q000737:chemistry*
chemical_list: D000072441:DNA, Ancient; D012973:Sodium Hypochlorite
keywords: Atlantic cod; DNA extraction; ancient DNA; contamination; high-throughput sequencing; horse