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?

Dating archaeobotanical treasure troves from Armenia and Peru

The arrival of a new issue of Antiquity is always a welcomed event. The issue that arrived in my mail box this week a particular trove of treasures of an archaeobotanical sort. Not so much for archaeobotanical reports as such (the only such is the study by Willcox and  Strodeur on the details of Jerf el Ahmar), but for tantalizing new information of sites that have exceptional plant assemblages, or that one expects will in the future, like the Han era Pompeii, Sanyanzhuang (blogged below). Two sites, which are well-known for exceptional preservation are the Areni-1 cave complex in Aremenia (Areshian et al in Antiquity), left, and Huaca Prieta mound in coastal peru, below right (Dillehay et al.). 

     Areni made the news a couple of years ago for its early leather footwear, from ca. 3500 BC (Pinhasi et al in PLOSone), but it also has dessicated plant remains of many sorts: emmer and free-threshing wheat and barley, of course, but also lentil, grasspea, grapes, plums, walnuts, almonds and pears. How many of these fruit and nuts represent species that were available wild in the region, were under cultivation or introduced as cultivars still needs to be clarified. The site has produced features indicating on-site wine production, so presumably grapes were cultivated, from at least, from around 4000 BC. 4000 BC is associated with the earliest material reported so far, but the site still has much to yield to excavation, presumably including earlier material. Late samples from the past 2000 years include cotton and textiles.

     Huaca Prieta also boasts exceptional archaeobotanical preservation, and with a long sequence it provides information that suggests the chronology of cultivar introductions in this region. Few plants are likely to be native here and so their introductions point earlier cultivation and domestication elsewhere. This includes Cucurbita sqaush, avocado and lima bean at 7000-5500 BC, and thereafter the appearance of chillis and bottlegourds. Cotton cultivation was established around 4800 BC, and after 4500 BC maize was added to the repertoire. This is some of the best dated and documented early maize in South America, detailed of which were published earlier this year (see previous blog). Peanut, sweet potato and quinoa also come from later levels. Full details are not yet published but some summary can be found in the on-line supplement. This site has also produced coca leaves, indicating the long traditions of chewing this drug plant. Dillehay and colleagues reported the earliest for use of this drug, back to ca. 6000 BC, from elsewhere in northern Peru about a year and half ago, also in Antiquity. Intriguingly this drug plant, plausibly from across the Andes, appeared to already have domestication features at this date.

The rapid spread & differentiation of maize: new Peruvian data

New finds from the N. Peruvian coast report clear evidence for an earlier arrival of maize the region than previously thought (Grobman & al., PNAS), and with wonderful dessicated preservation indicating that they are popcorn varieties, but flourly varieties are also present. That there is a popcorn indicates quite rapid early varietal diversification, and these show already traits of South American rather Mesoamerican varieties. A direct AMS date puts these back to at least 4500 BC, so still a few millennia after perhaps 7000 BC date for the earliest maize in its Mesoamerican place of origin. The macro-remains are augmented by phytolith analyses and strach grains extracted both from the maize cobs and tools. Of methodological interest is the apparent discrepancy between dates on dessicated and dates on carbonized material, with the dessicated stuff being way to young. This may mean the dried stuff may sometime get contaminated with young carbon in some way (whereas the charred stuff has it true carbon fixed nicely by carbonization). Also of note is that maize is apparently not the most common plant find, and was not the dietary staple, although the present PNAS article focuses on the details of maize and we will have to await another forthcoming publication in Antiqiuty for more on the chillis, beans, squash and wild plants. Another discussion of this paper can be found in ScienceDaily news report from a couple of weeks ago.

Recent commentaries: the surge of archaeobotany

These have been a busy few months for the archaeobotany of domestication, or at least those keeping up with reading new publications. (The hard work producing the data was no doubt also busily spread out over the past few years). Since December we have seen new data on early foods in Peru, Maize in Mexico, North American crops, new thoughts on the wild food use at the start of Near Eastern domestication (Willcox et al., in The Holocene [or GCW's site]), new early evidence for Panicum miliaceum cultivation in Gansu, and then even earlier dates in central China at Cishan, and the evidence on the evoution of domesticated rice from Tianluoshan. Well-preserved granaries (the oldest) from the PPNA of Jordan when cereals were still morphologically wild but probably cultivated, have also been noted (blog here). The vast majority of these studies appeared in big impact journals (PNAS, Science), and these have of course, attracted some wisened commentaries. Here are some links to those commentaries but (without any particular further comments on them).

T. Douglas Price, commenting on Smith & Yarnell, in PNAS 106 (16): 6427-6428

Gary Crawford, commenting on Lu et al , in PNAS 106 (18): 7271-7272

Martin Jones & X. Liu in Science (8 May 2009), commenting on Tianluoshan, and early Chinese millets.

New World Archaeobotany Watch: early dates for maize and other centres

Rio Balsas Maize, 6700 BC. New data pushes back maize earlier in Mexico than outside mexico and in the right part of Mexico, but notice that it is already domesticated, which means the beginnings of cultivation are earlier. This has a ScienceNOW post by Michael Balter, and the artilce by Piperno et al in PNAS (March 2009), "Starch grain and phytolith evidence for early ninth millennium B.P. maize from the Central Balsas River Valley, Mexico," needs to be read with the Ranere et al PNAS paper in the volume on the archaeological context., "The cultural and chronological context of early Holocene maize and squash domestication in the Central Balsas River Valley, Mexico".

North Peruvian Early Agriculture. Starch grain data from human teeth confirms the consumption og Phaseolus beans, squach (Cucurbita cf. moschata) and peanut at ca. 6000 BC, as reported in the recent (Dec 2008) PNAS paper by Piperno and Dillehay. The confirms the evidence of macrobotanical remains reported by Dillehay et al in 2007 in Science, in which AMS dates pushed cultivation in this region back to 7000-8000 BC. While all this may be suggestive of this area being an early focus of agriculture (and it featured as possible centre 3c in the recent Purugganan and Fuller map in a Nature review), some of this crops (certainly peanut) and arguably squash (?) were probably not native this particular region, implying that their start to cultivation was somewhere else and even earlier!

North American Early Crops. The latest installment on the evidence for indigenous domesticates of the later Mid-Holocene of Eastern North America is represented by the Smith and Yarnell report on the Riverton seed assemblage in PNAS 7 April 2009, which includes some of the classic 'lost crops' of North America such as Hordeum pusillium and Chenopodium berlanderi