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.

Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany

“…Instead, we find surprisingly high levels (15-46%) of endogenous DNA preservation in 15 of 19 fish bone specimens up to 1,300 y old from five different archeological sites. Notwithstanding the use of a recently developed extraction protocol aimed to maximize endogenous DNA (54), this rate of success compares favorably to results from mammalian bones whereby the majority of samples-excluding petrous bonestypically yield a few percent endogenous DNA at most (55). Our positive results agree with studies using PCR-based methods that have reported successful amplification from fish bones (56)(57)(58)(59)(60) in some cases up to 10,000 y old (61).…”

“…DNA from ancient samples was extracted in a dedicated aDNA laboratory at the University of Oslo by following strict precautions (79, 80) using a combined bleach and predigestion (BleDD 2 ) protocol (54). Ancient DNA libraries were created by using a blunt-end ligation protocol (81) with minor adjustments (20) (SI Materials and Methods).…”

An environmental (pre)history of European fishing: past and future archaeological contributions to sustainable fisheries

“…In methodological terms, archaeological research demonstrating the trade of a widely distributed species such as G. morhua depends on recent advances in aDNA analysis (Boessenkool et al, ; Star et al, ) and the creation of baseline isoscapes to which stable‐isotope data from archaeological specimens can be compared (Barrett et al, ; Barrett et al, ; Hutchinson et al, ). Early developments in the isotopic provenancing of fishes emerged from within archaeology but are now being augmented greatly by isotope ecologists to trace predator migration and to source marketed fish products (St. John Glew et al, ; Trueman et al, ).…”

Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments

“…In this study, we evaluate whether using a modified version of the Method D protocol (henceforth Method H), with an initial EDTA wash and an extended digestion and decalcification step, results in improved endogenous aDNA recovery. In addition, because the majority of development in aDNA extraction protocols has been conducted with samples from temperate or cold contexts (Barlow et al, 2016;Boessenkool et al, 2016;Dabney et al, 2013a;Gamba et al, 2016;Gamba et al, 2014;) but see (Damgaard et al, 2015;Pinhasi et al, 2015;Tromp et al, 2017), this work focuses on protocol optimization with tooth and petrous portion samples recovered from tropical sites. Here we examine raw DNA yields and endogenous reads, recovered after shotgun Illumina sequencing from parallel, paired extractions and characterize differences in base pair composition, sequence read complexity, post-mortem damage profiles, and average read lengths recovered between the two methods.…”