Friday, 21 September 2018

Ancient DNA in charred grains? More bad news.

No one can have missed the massive impact that ancient DNA has been having on the history of human populations and those of several domesticated animals. Bones, at least some of them, provide a nice venue for the preservation of old genomes. Plants have featured much less in this story, with estimates of 200 C) for sometime (many hours)-- does not do DNA any favours. This who have worked on ancient DNA have tended to focus on desiccated plant remains- from dry desert contexts.

A  new report on ancient DNA extraction from archaeological grains (Lundstrom et al 2018), in this case barley, from Medieval and Late Medieval Sweden, reports some good success from some dry grains from a 17th century's Bishop's burial, some success from waterlogged specimens but no success from 46 charred grains. This replicates similar attempts to get aDNA out of charred Finish barley (Lempaiainen-Avci et al 2018) and methodological trail of Nistelberger et al. 2016 who tried High-Throughput Sequencing ("shotgun sequencing") on various charred archaeological grapes, maize, rice and barley (Pictured at right), including rice provided by my lab from India, Thailand and the Comores. Nistelberger et al. concluded that charred material is likely to rarely yield sufficient reliable genetic data, a conclusion re-iterated by two Scandinavian studies.

The open question is what does this entail for older aDNA results, using "old-fashioned" methods, i.e. targeted PCR, to extract chloroplast DNA, which appears to sometimes be quite successful in differentiating indica from japonica rice for example (Castillo et al 2016), or which was used in the early days of aDNA in the 1990s to separate tetraploid from hexaploid wheats (e.g. Allaby et al 1997). Estimates then were that maybe 5% of charred grains might have some aDNA in them, but maybe those were generous over-estimates? Are we now supposed to reject such earlier work and methods out of hand? Or does it mean that methodologically, there is something about current high-throughput methods that has not solved the problem of dealing with the highly fragmented and sparse DNA that is thought to be preserved in a minority of charred remains? Reading the fine print, Nistelberger did identify a small amount of ancient DNA reads, but they regarded them as so few as to be "inconsequential". But if little is all we are left with maybe we need to change our aims to make these consequential through the questions we ask of them?

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