Friday, 21 September 2018

Pearl Millet genomics and domestication centre

Modern genomes have the potential to reveal alot about evolutionary history and past geography of a crop. Of course there are some limitation to the degree that it hard to account for extirpated past populations, such as the wild rice that used to grow in central China or the wild pearl millet that used to grow what is now the Sahara. A new study of pearl millet (Pennisetum glaucum) by Bugarella et al (2018) provides a convincing set of deductions from genetic history that infer an origin of the crop in the western Sahel/Sahara around what is today northern Mali/northeast Mauretania (map at left), followed by early differentiation between those of the far west (Mauretania/Senegal), and the eastern Sahel (e.g. Sudan) from those in the core zones of western Africa. Based on spatial simulations that take into account a few archaeological data points they also estimated the onset of the expansion of pearl millet as crop out of its centre of origin a starting ca. 4800-4900 years ago. This fits nicely with current archaeobotany. The earliest, already domesticated, pearl millet is from northeastern Mali in the lower Tilemsi valley between 2500 and 2000 BC. Perhaps a parallel trajectory of dispersal is represented by the Tichitt Tradition of Mauretania (from ca. 1700 BC). What remains an open question is whether these two area represent distinct domestication trajectories (a point suggested by MacDonald et al 2009; Manning and Fuller 2014), much as we see the West Asian Fertile Crescent as a mosaic of domesticators across the region as more or less the same time ( or there ). The zone delimited by the genetic study could well represent a sort of "West African Fertile Crescent" in which more than cultural groups were in the process of cultivating and domesticating pearl millet during the middle Holocene. The differentiation of a far western genetic groups would then represent dispersal first through the Tichitt-Oualata traditions of Mauretania and onwards to the Sengal valley- which fits with Brunken, De Wet and Harlan's old taxonomic differentiation of a western race leonis (Economic Botany 1977). A rapid and early spread easterns to the eastern Sahel, which was followed by local introgression with local wild populations, is also implied in this genetic analysis, and fits with the albeit limited archaeobotanical evidence for pearl millet (both morphologically domesticated and wild) alongside cultivated sorghum in the Kasala region of eastern Sudan around 1850 BC, just recently published by Beldados et al. (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?

Improved methods for looking at plant remains in pots

I have previously highlighted the potential of ct-Scanning and synchrotron imaging to look inside archaeological seeds, or seeds inside archaeological pots. And wanted here to highlight the publication of a more detailed protocol for ct-scanning bits of pottery for looking at inclusions, recently published by Barron and Denham in Journal of Archaeological Science: Reports. We have, of course, been looking at impression of plant temper on the surface of sherds from a long time, since the days of Hans Helbaek in the 1940s. It seems unlikely that the utility of casting  and studying impressions on sherd surfaces will go away, as it remains something that is easily carried out in bulk across large sherd assemblage with relative speed and low cost-- providing among other things our best current evidence on sorghum domestication. Nevertheless, the beauty of ct-scanning lies in the ability to see a much larger sample of impressions below the surface, including those that are potentially much better and more completely preserved than those just on the surface. The example of the rice spikelet pictured at left from a sherd from Loc Giang, a Neolithic site in Vietnam is a nice case in point. 

The spikelet bases from this site and sherds from nearby An Son leave no doubt as the domesticated status of rice in this part of Second Millennium BC Vietnam. Interestingly, imaging also found a wild Lemna (duckweed) seed in a sherd from An Son. What remains an open question, however, from a single specimen like this is whether this should be interpreted as a weed of wet rice, or merely a component of clay gathered from a wetland. The weight of archaeobotanical evidence at present points to Neolithic rice in Southeast Asia being large rainfed (see published discussion in "Pathways of Rice Diversification..."), which would not create conditions suitable for Lemna, so I would favour seeing this as a component of the clay. Also of note is the identification of pebble inclusions in sherds from the hunter-gatherers site Con Co Ngua-- such pebbles are the kind of inclusions that have from time to time been mistaken for seeds in pottery...