Earlier sorghum in Sudan

I have recently been made aware of a small report in Nyame Akuma on Kasala (northeast Sudan), where Italian researchers have restarted research which can be regarded as following on from the 1980s survey headed by R. Fattovich. The new work has included the study of some plant impressions in ceramics published as "Sorghum exploitation at Kasala and its environs, North Eastern Sudan in the Second and First Millennium BC" by Alemseged Beldados and Lorenzo Constantini in Nyame Akuma vol. 75. As its title indicates this study does confirm the present of Sorghum bicolor, plausibly (but not definitively) domesticated, in ceramics from the site of Mahal Teglinos and some from near by survey collections. It reports examination of 25 sherds of which 11 from Teglinos and 11 from survey have sorghum.

As many will know I have been critical of some previous sorghum identification from impressions, in particular coming out the lab in Rome (most infamously those from Oman and Yemen). As a result, in various tallies of early sorghum I have always regarded the 1980s report of Sorghum of the Kasala region survey as requiring a big question mark next to it (e.g. "The economic basis of the Qustul splinter state"). The sorghum here, at least in fig 4, looks legitimate. The suggestion that grains shape (narrow versus wide) can be used to identify both wild and domesticated sorghum is more problematic. Meroitic Umm Nuri produced very very thin but apparently domesticated sorghum (published by me in Sudan and Nubia 2004).What is really needed is clean views of spikelet bases (for wild versus domesticated hulled forms) or evidence for still attached rachillae (especially in free-threshing forms).

I now believe that sorghum is there in Kasala, dated by ceramics (Mokram group) and association to 1500-500 BC. This is important news, as it takes sorghum earlier probably than any of the find in the Nile Valley, which are mainly Meroitic, and with possibly earlier Napatan sorghum at Kawa (in Sudan and Nubian 2004). This is a relief given that it is India before this time by at least a couple of centuries, and maybe more (for an updated review of early African crops in South Asia see by papers in Nicole Boivin, either that in J. World Prehistory on Arabia, or the Etudes Ocean Indien paper [in English]).

Some of the other identifications, notably cowpea (Vigna unguiculata) reported from one impression remain unconvincing, at least as photographed, and I really cannot except them on this sort of evidence. I would also expect pulse seeds to make poor temper for pottery. While we might expect this species in this region and period, as it was in cultivation prior to 1500 BC in West Africa and had arrived in India too by this time, I'll await more convincing evidence.

It is a pity high quality imaging, especially SEMs, were not made of the casts as, then one could see finer details of morphology like characteristic hairs, etc., that really clinch an ID. (See, for example the unicellular  e.g. w&v in the images from the Essouk archaeobotanical report, also a rachis stalk which suggests it is domesticated).

Also tantalizing is the evidence for millet, Setaria, impressions in 3 sherds. As illustrated, one could also propose a Bracharia and we really need better resolution SEMs and husk comparisons to get this to species level. Nevertheless it is plausibly a fit for S. sphaceleata, which is of particular interest as the  "lost" millet of Nubia,which we have evidence for cultivation of from Napatan to Medieval times (Kawa, Qasr Ibrim, Nauri). The origins and history of this lost millet of Nubia really needs to be chased down. It has gone extinct from Nubia in the past millennium, replaced by Setaria italica.

(Thanks to Mike Brass for bringing this paper to my attention)

Unravelling agricultural packages

Two recent studies, one for the west and and one for the east, illustrate how crop packages unravel and become less diverse as they spread. The spread of agriculture is so often presented as a processing of unfolding, like a blanket being stretched from the point of origin outwards. This is especially true of the spread of Near Eastern agriculture, a truly diversified crop package of cereals (multiple kinds of wheat and barley, pulses, flax, plus livestock). But when the spread of agriculture is examined in detail, it is clear that crop species and varieties drop out along the way, and those which do make it probably become less genetically diverse. A recent database analysis of Neolithic Ireland illustrates the extreme western edge of Neolithic dispersal from western Asia. Published by Meriel McClatchie (whose PhD hails from here at UCL) and various collaborators (including UCL colleague, Sue Colledge), has been published in Journal of Archaeological Science, "Neolithic farming in north-western Europe: archaeobotanical evidence from Ireland" . This study demonstrates the clear pattern of quantitative reduction in most crops in Neolithic Ireland compared with elsewhere in Europe. Emmer wheat, virtually no einkorn (and one has to ask how securely identified any einkorn was), naked barley and a bit of flax-- that pretty much sums up Neolithic Ireland, in contrast to the 8 "founder crops" that are meant to characterize the start of agricultural dispersal from the Near East. 

A similar barley and wheat (with a dash of flax) characterizes the UK early Neolithic, which like Ireland see the dramatic introduction of cereal farming shortly after 4000 BC. As recently suggested in the study of radiocarbon dates from the UK (Stevens and Fuller in Antiquity, Sept 2012). One looks forward to further Irish Analyses to see whether the collapse of Neolithic cereal farming that Chris Stevens and I see in the England and Scotland cereal data also held true in Ireland.

This parallels what we see in the East, in India for example, which has recently been mapped in the paper I co-wrote with Nicole Boivin and Alison Crowther, "Old World Globalization and the Colombian Exchange: comparions and contrast." In South Asia wheats (including glume and free-threshing), barley, several pulses and flax, all seem to be important on the Indus Valley, but this package becomes less frequent and less stable as one moves into "inner" India. Sure enough wheat and barley make it both eastwards to Bihar and south to Karnataka, but generally with a strong preference for barley few or no pulses. In China only select wheat, and rarely barley, makes any showing at all, and there wheat is quantitatively negligible. This highlights that in some cases the caloric and subsistence needs are not likely to be served by the introduced cereals from the Near East. Some years ago I made the case (Antiquity 2005) that wheat and barley in Southern India might also have been status crops, used perhaps for beer, rather than as staples. One can ask the question as to what extent some the westernmost spread of cereals in Europe was as much about preferred foodstuffs rather than subsistence necessity when wild sources like hazelnuts were still so readily used and available?

There are broad similarities but also differences in the outward spread of crops from the Fertile Crescent. While in India and China this spread is seen largely in terms of the adoption of crops by local populations, in western Europe there is evidence for a greater role of migration. While in India we tend to attribute this to the local importance of other crops, Brachiaria ramosa and mungbean in the south or rice in the Ganges, that was clearly not the case in Ireland. So I wonder if we are seeing both the effects of crossing ecological frontiers, perhaps quicker than some crops can adapt, or beyond which some crops just can not adapt. Northern Europe certainly presented great challenges to agriculture, highlighted in its extreme margins such as Norway, but also in Britain by the apparent abandonment of cereals in the later Neolithic, perhaps as temperature retreated somewhat (Stevens and Fuller 2012). Monsoon Asia was not the most suited to the Near Eastern crops either, which also points towards social rather than caloric drivers in crop spread. In another parallel with distant Britain the agriculture and sedentism in parts of the Deccan, most clearly in western Maharashtra, where wheat and barley were quite prominent, appear to have collapsed and possible were abandoned over a wide area (in this case around 1200-1000 BC at the end of the Jorwe period).

Both of these studies show the importance of larger regional datasets, in which broad patterns are often visible even with simple quantification. This broad patterns raise questions that in turn call for more intensive sampling and local studies to work out wheat is actually happening at the periods of intial adoption or abandonment. What is missing currently is more usable data from the middle, Central Asia, the Iranian plateau, etc., so that archaeobotanical databases can become truly continental across all of Eurasia.

A genome map that is not a map of origins (Rice Genetics Watch returns)

Last week Nature ran an article (Huang et al) with the headline that " A map of rice genome variation reveals the origin of cultivated rice." I here to report that this paper does not do what is says. There is nothing obviously relevant to locating where rice was first brought into cultivation, and the claims in the article are misleading and misguided. This is apparently one of most read Nature papers at the moment, so no doubt we will have to face lots of additional confusion over rice domestication-- and I thought there was already enough confused and misguided info out there. I have had several queries on this over the past week, so below is my quick response.

 There is some important data here and details, and much for further critical analysis. BUT: This study changes nothing. Its stated conclusions are misleading, making false unstated assumptions and arriving at unreasonable and unbelievable conclusions.  In a way this mistake was inevitable and obvious. The authors have concluded the the closest wild ancestors to cultivated rice are living wild populations in the  Pearl River basin. The problem is that rice was domesticated not from living populations but from past populations almost certainly from regions where wild rice is now extinct (technically, we would say, extirpated). This study demonstrates that big science and lots of resources do not inevitably produce answers, but that nuanced analysis and critical thinking, and in this case some knowledge of Chinese history, are necessary to direct analyses.

It is clear that wild rice (O. rufipogon) formerly occurred much further north, through much of the Yangtze valley and even as far north as the Shandong peninsula and lower Yellow River basin. This is clearly attested from Chinese written sources of the Song Dynasty (i.e. about 1000 years ago). Even by that period it is likely that wild rice distribution was greatly reduced by the impact of China’s huge human population and agricultural expansion which took place between 6000 years ago and 1000 years ago. More so than anywhere else on earth central China (from the Yellow river  to the Yangtze) has supported massive human populations and suffered the corresponding habitat loss. In the late Bronze Age (Zhou dynasty), they were hunting elephants on the banks of the Yellow river (for a wonderful book on Chinese environmental history that takes this as representative of the broader sweep of Chinese history, see the Retreat of the The Elephants by Mark Elvin 2004). These would certainly not be represented in a genetic study of living elephant populations! (as blogged previously these may actually be an extinct elephant species with straight tusks)

Although reference 2 in the article is to a paper I co-authored (Fuller et al 2010), this study clearly did not take on part of the fundamental implications of the maps and discussion early in that paper about the past distribution of wild rice, which has been modified both by major climatic change since the wetter and warmer early Holocene and by the impact of habitat destruction by Chinese farmers since the Neolithic. Areas that could support wild rice made excellent areas for agricultural reclamation: domesticated rice replaced wild rice over much of its original range in central China, which had the highest human populations. Even clearer, I think, is the paper I published in the journal Rice in 2011, which includes maps and a phylogenetic diagram illustrating the fallacy of using modern extant wild rice to represent the full diversity of past wild rice. By making this assumption in pinpointing a pearl river origins for rice pretty much all the authors subsequent conclusions are inevitably problematic. The  only way oin which genetics is going to advance pinpointing the number and location of domestication events in rice is through the recovery of ancient DNA. The fallacy an approach that relies purely on the modern time-frame of sampling is well-illustrated with European pigs and boar genetics, in which only via recovery of ancient DNA is it possible to see that the first Neolithic pigs were derived from Near Eastern boar and pigs but were later replaced by genetics from European wild boar (see: Larson G, et al. (2007).

That modern populations of Oryza rufipogon are not the direct ancestors of japonica rice is implicit in the data in fact. The “obvious genetic distinction between japonica and Or-IIIa (Fig. 2a)”, implies that domestication rice and South Chinese rufipogon are in fact not really so close, just the closest available in linving populations. The intermediates found with Or-1 and indica are because Indian wild rice have been less decimated by the combination climatic changes and human impacts. Indeed this pattern is not new, but was already evidence some years ago, especially in the study of Cheng et al 2003. (Polyphyletic origin of cultivated rice: Based on the interspersionpatterns of SINEs). —this is discussed on the basis of the more detailed Ohtsubo et al paper or 2004 in my 2010 paper and various earlier articles in the archaeological literature). It is nice to see a much larger dataset in the this new paper re-affirm the results of the  p-Sine study, but there is not really anything new accept that the present authors have tries to grab a headline by claiming a Pearl River  origin for rice. It is the populations that bridge the gap between OR-IIIa and japonica which are crucial and these must be extinct populations of Oryza rufipogon that were brought into cultivation in the earlier Holocene. Geographically, this points back towards the north and the Yangtze.

The authors have found more extensive evidence that most domestication genes were selected in japonica and then entered indica through hybridization. Some geneticists, like the Japanese scholar Y-I Sato, or Susan McCouch at Cornell have been discussing this for years, and evidence for this has been mounting—you will also find discussions in the "rice consilience paper" or the "pathways to Asian civilizations" paper. It is misleading, however, to speak of this as “introgression” which implies that pollen flow from domesticated japonica into wild populations in India created indica. What is missing here, and clearly absent from this study, as it was from the Molina et al PNAS paper last year (see previous blog), is consideration of the chloroplast genome. This is older work, but really key, because chloroplasts are not carried in pollen. The Chloroplast (cpDNA) genome of indica and japonica are completely different. Thus introgression by pollen flow from japonica into wild rices is a very convoluted way to account for this hybridization as it would require domestication genes to then persist in wild population that were then re-domesticated. More reasobale in the model I have been promoting as the “proto-indica”model in which wild ancestors of indica (with indica chloroplasts) were under early cultivation or management and the were improved by hybridization with introduced japonica. This does not require domestication gene to somehow persist in wild population where they would be selected against (actually I would expect such introgression to lead to the evolution of weedy rices by "de-domestication": see this blog: ). It also implies a role for human agency in this hybridization process. This means that there were separate starts to cultivation (the human behaviour) for indica and japonica even if the domestication syndrome was shared and evolved one time. 

Does genetic evidence on its own trump fossil evidence? No. Archaeological evidence, which is a fossil record of past rice and past human activities, has once again been simply ignored! Archaeologically early farming societies, with sedentism and villages and evidence for rice cultivation and rice undergoing morphological changes of domestication are found only in the Yangtze valley, as you probably well know. There is no equivalent evidence from Guangdong/ Pearl River. In fact when rice in the Lower Yangtze is showing morphological evolution under cultivation, i.e. between 5000 and 4000 BC, in the Pearl River and South China there are only sparse populations of hunter-gatherer fishers, represented mainly by coastal shell midden sites. These sites provide the earliest evidence for ceramics in the coastal zone (more than 10,000 years later than pottery in the Yangtze!). The first agriculture, based on rice, was introduced between 5000 and 4000 BP, although finds remain few and focused on the southern mountain slopes and north of the Pearl River delta. By this time the Lower Yangtze support urban sites, such as Liangzhu, support by extensive paddy field systems and intensive cultivation of fully domesticated rice. It makes no sense for rice domestication to be placed in the Pearl River region

Archaeobotanist returns

After a summer with fieldwork in Kurdistan, Ethiopia, Turkey and Kurdistan in that order. but I am now back in full teaching mode and getting caught up on the latest publications!


Above, at excavations in the Gamo-Baroda Project in Southern Ethiopia, directed by Kathryn Arthur, John Arthur, and Matthew Curtis.

My son Peter enjoying the excavations at Catal Hoyuk (Turkey).

A new project at the famous Neolithic site of Jarmo, Iraqi Kurdistan, pilot excavations Sept. 2012.

IWGP 2013 website

The International Work group for Palaeoethnobotany, the only major international meeting in archaeobotany (every 3 years), has its next conference in about a year's time in Greece. Its website it now live. In general this conference has a Eurasian focus. For those with African interests, there is the smaller IWAA, also every three years, and meeting this July.

Weed evolution by de-domestication: the case of rice

The study of weed origins and evolutionary history is the poor cousin of the archaeobotany of crop domestication. Archaeobotanists can potentially do much more on this, and undoubtedly should. To provide some inspiration it is worth considering some recent insights from genetics, to do with weedy rice. While it is surely the case that rice's wild progenitors may act as weeds in the crop, it now appears that much weedy rice is descended from the crop and not directly from the wild progenitor. A recent paper in Genetic Resources and Crop Evolution by Zhang et al. explores the variation in weedy rices in southern China (Guangdong) and northeast China (Liaoning). In Liaoning there are no wild progenitor populations so it is cultivated fields or their margins which provide the only real habitat for spontaneous rices. In Guangdong by contrast there are populations of wild O. rufipogon. Based on microsatellite markers they show that weedy rice in each region clusters with crops, which represent indica and temperate japonica rices, and the weedy rices are distant from true wild populations. They take this to support the hypothesis that weedy rice is secondarily derived from the crop.

Last year this hypothesis also got support from an anatomical study of weedy rice in the USA, by Thurber, Kepler and Caicedo in BMC Plant Biology which shows that the abscission layer which leads to shattering is clearly distinct from non-shattering domesticated rice but also differs from shattering wild rices in terms of its timing in development: it breaks down sooner leading to earlier shattering than in wild rice. This presumably is an useful adapation for beating the farmer to it and getting into the seedbank before the rice harvest. Thurber et al conclude that this points to unidentified regulatory genes that allowed weedy rice, derived from the crop, to reacquire wild-type shattering. (Whether one might be able to tell weedy from wild rice on the physical remains of spikelet bases is another matter, but surely worthy of investigation by an archaeobotanist!). What is more,  genetic characterization (Thurber et al 2010 Molecular Ecology) found that these weedy rices all possessed the sh4 mutation that characterizes domesticated non-shattering rices! This points unambiguously to the acquisition of a different novel mutation that allows shattering. A few years ago Londo & Schaal (in Molecular Ecology) did some haplotyping of American weedy rices and found mutliple origins, with haplotypes from japonica, indica and aus rices (as well as some hybridization).

So rice has a proclivity to weediness, as with many other crops, and the wild progenitor per se may be less to blame. Contrast this with crops that have been domesticated from weeds (oat, rye, kodo millet) and we can begin to think about alternative pathways to and from being a weed.

When there is no blog

No one has time to blog all the time or to blog every new archaeobotanical study that deserves it, or relevant genetic study. Some I have set up some scoop.it pages to stash links to sources and citation of interest when I simply don't have time to blog, or have not gotten a chance to read them. Suggestion of sources are welcome. One scoops page that I have been trialling for a while is one rice origins and culture history, and the other is more general on archaeobotany and domestication. I also do one on Nubian archaeology, since I teach in this area.... By the way, for those wondering the image at the left is a waterlogged Euryale ferox seed from Tianluoshan (Neolithic Zhejiang, China).