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.

Grapes from the Tarim Basin

Jiang, Hong-en a young archaeobotanist at the Institute of Botany in Beijing, has been working on plants remains from dessciated tombs in the Tarim Basin in western China. He has been progressively expanding of list of archaeological plants from the region, often one species at a time, and the contribution has been published in the Journal of Archaeological Science (for July2009, but now online). As with his previous studies, this find is meticulously documented with excellent plant anatomical images, in this case anatomical thin sections. This is the first true domesticated grape vine (vinifera), in China, although native wild grapes (Vitis spp.) were widely used since the Neolithic in central China.

Previously Jiang has published a number of articles, each devoted to the careful documentation of single species, from the tombs at Yanghai or those at Sampula (both cemeteries of late centuries BC in the Tarim Basin, Xinjiang).

• Jiang, H.E., et al., 2008. A consideration of the involucre remains of Coix lacryma-jobi L. (Poaceae) in the Sampula Cemetery (2000 years BP), Xinjiang, China. Journal of Archaeological Science 35, 1311–1316.
  
• Jiang, H.E., et al 2007a. The discovery of Capparis spinosa L. (Capparidaceae) in the Yanghai Tombs (2800 years B.P.), NW China, and its medicinal implications. Journal of Ethnopharmacology 113, 409– 420.
  
• Jiang, H.E., et al., 2007b. Fruits of Lithospermum officinale L. (Boraginaceae) used as an early plant decoration (2500 years BP) in Xinjiang, China. Journal of Archaeological Science 34, 167–170.
  
• Jiang, H.E., et al. 2006. A new insight into Cannabis sativa (Cannabaceae) utilization from 2500-year-old Yanghai Tombs, Xinjiang, China. Journal of Ethnopharmacology 108, 414–422.

The latter study, of Cannabis, has some particularly nice SEMs. The botanical side of this work is impeccable...

Nevertheless, I must express some frustration with the archaeological part of this work, as we lack any sense of assemblages, of which species are occurring together in which tombs, or how many tombs have been sampled and how often do various things occur. Was the Cannabis a one-off or routine? Were wheat or barley or millet finds part of the standard offering? Doing a quick tally from Jiang's papers, we can conclude that the taxa-lists are as follows, (but I suspect these are very imcomplete lists!)

Sampula Cemetery (reported by Jiang): Coix lacrhymajobi (job’s tears used as beads), Amygdalus persicus (peach), Armeniaca vulgaris (apricot), Panicum miliaceum, Hordeum vulgare var. nudum, Jugland regia, and Elaengus. Previous work reported wheat (recorded in a secondary source, Mallory & Mair Tarim Mummies)

The Yanghai tombs (reported by Jiang): Capparis spinosa, Cannabis sativa, Lithospermum officinale (used as beads). Wood and bedding materials include Populus, Salix and Phragmites

Earlier reports from other cemetery sites in the region include Wheat (presumably hexaploid, but one would like to see this confirmed with rachis remains ?) further north at Tort Erik and Chong Bangh, both cemeteries perhaps as old as 1500 BC. Of interest is the apparently exclusive presence of wheat on these two earlier sites, although barley is reported from Qizilchoqa (the only source for these, in English, so far as I know is the passing notes in the Mallory and Mair’s Tarim Mummies book, 2000).

So, we still have some waiting to do before the archaeobotany of westernmost China can be grasped in a holistic sense.