Abstract
The majority of archaeological plant material is preserved in a charred state. Obtaining reliable ancient DNA data from these remains has presented challenges due to high rates of nucleotide damage, short DNA fragment lengths, low endogenous DNA content and the potential for modern contamination. It has been suggested that high-throughput sequencing (HTS) technologies coupled with DNA enrichment techniques may overcome some of these limitations. Here we report the findings of HTS and target enrichment on four important archaeological crops (barley, grape, maize and rice) performed in three different laboratories, presenting the largest HTS assessment of charred archaeobotanical specimens to date. Rigorous analysis of our data – excluding false-positives due to background contamination or incorrect index assignments – indicated a lack of endogenous DNA in nearly all samples, except for one lightly-charred maize cob. Even with target enrichment, this sample failed to yield adequate data required to address fundamental questions in archaeology and biology. We further reanalysed part of an existing dataset on charred plant material, and found all purported endogenous DNA sequences were likely to be spurious. We suggest these technologies are not suitable for use with charred archaeobotanicals and urge great caution when interpreting data obtained by HTS of these remains.
Highlights
Advances in DNA extraction methodology and sequencing technology have allowed for the field of plant archaeogenetics – DNA analysis of archaeological plant remains – to flourish over the last decade[1,2]
We have combined the results of independent studies of four domesticated plant species Hordeum vulgare L, Vitis Vinifera L, Zea mays L and Oryza sativa L using a combination of shotgun sequencing and target enrichment in order to assess the utility of High-throughput sequencing (HTS) in ancient DNA (aDNA) studies of charred plant material
Given that aDNA damage patterns were only observed in those samples that were sequenced together with ancient grape samples, we investigated if these damage patterns could originate from reads that were falsely assigned to the charred samples, i.e. due to “sample bleeding”
Summary
Advances in DNA extraction methodology and sequencing technology have allowed for the field of plant archaeogenetics – DNA analysis of archaeological plant remains – to flourish over the last decade[1,2]. Ancient remains have the added disadvantage of DNA degradation accumulating over time[13] Despite such damage, several studies have reported successful extraction and amplification of DNA from charred plant material from a range of species including peas[3,14], wheat[6,15,16], rice[17], grapes[18], maize[19] and radish[20]. We further re-analysed a study that has reported endogenous DNA from charred cereal grains over 3000 years old[8]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
