Wednesday, 17 October 2012

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.

Monday, 16 April 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.

Tuesday, 3 April 2012

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 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).

Eastern Mediternnanean database back on-line

Simone Riehl's database of Eastern Mediterranean and Near Eastern Plant Remains has been offline for a while due to a server change. But tt is now online again under:

Tuesday, 27 March 2012

IWGP session topic on archaeogenetics

We have another session proposal for the next IWGP. The title of the session is:

Plant archaeogenetics and archaeogenomics

Session organizers are Angela Schlumbaum, Basel and Terry Brown, Manchester. Those interested in contributing please contact the session organisers.

This can be added to two earlier proposed thematic sessions: 

(Proposal for a thematic session at IWGP 2013, Greece) By Dorian Q Fuller and Soultania Valamoti

Food Globalization in Prehistory Across Eurasia. Chair of a session: Prof. Martin K. Jones

The conference website is now live (but has not been formally announced): it includes a list of session topics.

Monday, 19 March 2012

Predomestication cereal processing and storage

The latest Antiquity includes a detailed treatment by Willcox and Strodeur of Large-scale cereal processing before domestication during the tenth millennium cal BC in northern Syria at Jerf el Ahmar. The archaeobotany of Jerf has featured large in discussion in recent years on Near Eastern domestication, with apparent evidence for an early arable weed flora (see Willcox 2012 for latest), some grain size increase (reported in Willcox 2004, discussed further in Fuller 2007), but with wild-type shattering rachides, mostly of barley and rye. Jerf has been one of the major datasets contributing to a "slowing down" of domestication, from how fast we thought it was before, and of a "de-centring of the fertile crescent." So it is important to understand just how the archaeobotanical evidence fits with the archaeology on this site, and there are some important details to digest. In this paper the present some more details on the spatial patterning of finds, especially rye and barley in relation to crop-processing (mainly later stage dehusking and preparation for grinding), and argue for possible storage in the 'public' multi-room round building in the the site. There is also discussion of rodent dropping, mainly mice (Mus), which argues for on-site cereal stores, the key context for the evolution of commensal rodents.

South Indian aridification press release

The Woods Hole Oceanographic institute has put out a press release on the palaeoclimatic data for India aridification over the late Holocene, based on the GRL paper published a few weeks ago and blogged previously.

Friday, 16 March 2012

Wood charcoal papers online

It recently came to my attention that last year's meet of archaeological charcoal analysts (mainly European), has a nice set of extended abstracts (or short papers) published freely on line as a special number of the Spanish periodical Saguntum. The wood charcoal papers are here, amongst which are number of interesting study, including a Irish study on quantification issues attempting to identify saturation points, the fragment count at which taxa diversity in a sample stops increasing: for Ireland this appear to be around 20 taxa. A French study develops the Dufraisse model for using charcoal ring diameters to model the size of fire wood being collected as a way into human behavioral patterns in wood exploitation (image at left). Eleni Asouti explores the wood charcoal from Catal Hoyuk which fits neither with a straight forward model of climate-driven change in taxa or anthropogenic over-exploitation models. Meanwhile a burnt down building from PPNB Qarassa in Syria provides a glimpse into the construction material used in early villages in the Levant. You can also find a small, but pioneering study of charcoal from Chinese flotation samples taken in a region survey, an analysis of some Yanghao-Longshan charcoal from the Ying valley in Eastern Henan-- which provides evidence for the dominance of oak forests, oak as fuel source, despite a seed record that is dominated by cultivated millets, lacking evidence for acorn consumption. Although we lack good earlier archaeobotanical evidence from this particularly region, it does still suggest a contrast with the earlier predominance of acorns elsewhere in China. By the Yangshao period agriculture had pretty much taken over and wild foods were in decline, although the Yangsaho period still shows a higher range of wild fruits than we find in subsequent periods in the Ying (see Zhang et al in J. Arch Sci 2010).

And there are many other charcoal studies there I have yet to explore.

Friday, 9 March 2012

Pre-axumite wheat and barley preference: isotopic evidence

I seem to have overlooked this last year, but was excited to see some stable isotope results, (published last year in J. Arch Science by D'Andrea et al), from northern Ethiopian pre-Axumite  and Proto-Axumite sites (i.e. 800-100 BC). This indicate a strong tendency in human bones towards predominantly (but not necessarily) exclusively C-3 plant diet, i.e. such crops as wheat and barley, but with limited C-4 input. This is of interest since Sorghum, tef and finger millet, all of which might expect to have been around are C-4 plants. So the mystery deepens as to the antiquity of these taxa in agriculture in this region-- or at least they were not very important. If memory serves there is some evidence for tef from around this period (but mainly later)-- treated in some detail by D'Andrea (and blogged previously), where as the earliest finds of finger millet and Sorghum are later and Axumite Also there is an important contrast with the domestic fauna, which have a distinctly different diet form the people. Cattle and donkey have a strongly C4 signature suggesting grazing or foddering mainly from the savannah grasslands. Sheep, goat and gazelle fall in between suggesting C4 grazing mixed with browsing of C3 shrubs etc.

Thursday, 8 March 2012

Domestication of Plants in the [western] Old World, revised.

No doubt all students and researchers of plant domestication and archaeobotany will be pleased to hear that the revised 4th edition of Zohary and Hopf's Domestication of Plants in the Old World (now Zohary, Hopf and Weiss) is hot off the presses in Oxford. I have not seen a copy yet myself but previous editions, the last in 2000, remains the standard reference work on the crops of the Near East and Mediterranean, their wild progenitors and early archaeobotanical evidence. An updated treatment is only to be welcomed.

Wheat museum

It was hard to resist the image at right, of a museum dedicated to wheat, designed with an ear on top. This web site, of an old press release (July 2005), was just brought my attention by a colleague. It claims to celebrate "the earliest known wheat culture" (well that was not in Turkmenistan) the Anau culture (which is pretty late in the Neolithic), and the archaeology of Pumpelly (turn of the last century), who is credited with the first explanatory model of agricultural origins that attributed agricultural origins to climatic change. Good to have that immortalized somewhere. Later announcements indicate that this museum was also to become a national germplasm bank for wheat, which seems a good thing.

Does starch evidence push back foxtail millet domestication?

A recent article in PNAS, by Yang Xiaoyan et al., on starch grains (and some phytoliths) from two early Holocene sites in northern China (approx. 9500-7500 BC), pushes back evidence for the early cultivation of foxtail millet. This builds on recently reported identification criteria for millet starch.  This paper is an important contribution to the earlier prehistory of grass and millet exploitation in Northern China and provides important new evidence for the discussions and debates about the timing, areas and processes of millet exploitation and initial cultivation. For on thing it highlights the importance of grasses, including a large proportion of millet grasses, in the subsistence of later hunter-gatherer, or cultivator transition, northern China. This hints at a contrast with nut-hungry and acquatic-focused south (Yangtze). These new data make foxtail millet exploitation, and possible cultivation, at least as early, if not earlier, than the claimed early Panicum from Cishan (although in the latter case, hard evidence for cultivation rather than gathering remained elusive). Phytolith data indicates the occurrence of Panicum miliaceum types only from late Donghulin. Taken with other recent finds this is suggestive that Panicum and Setaria were not brought into cultivation together, perhaps each more than once, and separately, in different parts on northern China. The bringing together of these two crops, fully domesticated, in an integrated system, would seem to be a key transition, yet to be identified, but which must have happened by the time of the emergence of the Early Yangshao tradition in the first half of the 5th Millennium BC.

The trends that Yang and colleagues have found, towards more of the larger Setaria italica like starches are suggestive a subsistence shift, and potentially as the authors argue, of changes evolving in foxtail millet, as part of the domestication process. More data from more sites and periods are needed, however, to confirm whether this a real trend. It would also be nice to see what these kinds of ratios look like on later sites with clear macro-remains of domesticated foxtail millet.

Nanzhuangtou and Donghulin as early Holocene/terminal Pleistocene transition sites with early pottery are often cited as the precursors of more typically Neolithic miller cultivators but have lacked much of any archaeobotanical evidence. These findings will take on an obvious significance to those interested in the early Holocene or early agriculture in Northern China. This study is also a good example of careful archaeological starch research, and is therefore wider methodological interest. Although starch grain research has become increasingly popular in China, some studies have been rather unconvincing, especially with regards to methodologies for identification and for being clear about uncertainties. That is not the case here, where a clear methodology for identification of millet-type starch grains has been employed which is in part qualitative and in part quantitative and it includes a clear recognition of some of the uncertainties in secure species level identifications, especially of smaller and less fissured starch grains. It is also clear that the reference collection of modern material that has been studied is the most extensive to date for Chinese grasses and this increases greatly the likelihood of their reported identifications. The inclusion of control samples of sediment and loess from Donghulin to check for contamination is also methodologically very important, since modern contamination will always be a concern in starch studies. It is also good to see consideration of the presence of immature starches, since immature millet grains are a significant component of charred assemblages, and significant present on immature/unfilled spikelets has been noted in Chinese agricultural texts throughout history, since records in the Han Dynasty. The recognition of carbonized immature Panicum grains has recently been bolstered by an experimental study blogged previously.

Wednesday, 7 March 2012

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.

Monday, 5 March 2012

Han period 'Pompeii' includes farmland

In the latest Antiquity Kidder, Liu and Li report on Sanyanzhuang, a settlement buried by catastrophic Yellow River floods around AD 23. This is a essentially a central Chinese Pompeii but without the burning. So far little of the settlement occupation area has been excavated but it appears that field systems around the site were preserved as well. Some exceptional preservation includes leaf megafossils (leaf casts), in this case of mulberry and elm trees. The report is basically descriptive and notes sampling for pollen. One can hope that in the future systematic flotation and phytolith sampling will be carried out, because a site like this provides an amazing opportunity to ground truth the reliability and biases of the (limited) textual sources on Han agriculture. Despite the fact that written sources refer to "row crop cultivation" (p. 46), as found here.

20,000 yr old huts from Jordan

This report on Kharaneh IV, published in PLoSone  a couple of weeks ago, has a lot of people excited: well-preserved hut features from the early epipalaeolithic of the southern Levant, over 20,000 years old, are a pretty uncommon archaeological find. Most sits of such age provide a bunch of chipped stone, some animal bones and if one is lucky some wood charcoal. Of course, this period has already produced the remarkable Ohalo 2 over in Israel, with amazing plant preservation in burnt down huts of similar age, partial details of which were published in J. Arch Science by Ehud Weiss et al in 2008. One of the problems of Ohalo 2 has been there is so little to compare it with, apart from sites of much later periods. Now there is the opportunity. No plant evidence from Karaneh IV has been reported yet, although colleague here in London are working on it, Sue Colledge on the flotation samples, and a PhD student Monica Nicolaides is working on phytoliths and starch samples. We can expect some important results id due course, although it is unlikely to come close to Ohalo in terms of quantity and preservation in macros, but supplemented by much more systematically collected micros. Other exciting work on the faunal remains is taking place down the hall here, by Lousie Martin, Liz Henton, and Anna Spyrou, which will provide insights into mobility and seasonality.

The archaeology of this site has received plenty of media attention on-line already, and a useful summary at

Sunday, 4 March 2012

Permafrost anceint DNA

One of the most remarkable, and unusual, pieces of archaeobotany I have seen lately is the report of bringing back to life Pleistocene campion (Silene) flowers, published by Yashina et al in a recent PNAS. Ancient seeds did not themselves germinate, but their genetic material, from immature fruits, was cultured in vitro and then propagated clonally. So the images at right are clones of a plant that was trapped in frost some 31,800 years ago. It is not strictly archaeological, there is no report of a human site there. Direct AMS dates put fruits, apparently from ancient rodent (squirrel) burrows back to over   30,000 years old. 

There are of course periodic reports of extremely old seeds germinating, although in most cases is unlikely that seeds of more than about a century or so, with germinate. See, for example, Barbara Youngman's old review on the germination of old seeds (in Kew Bulletin 1951). "Mummy wheats" are a myth. In general,  longevity may decrease rapidly for many seeds after a decade or so. But natural ice mummy seeds, would appear to be a reality, or at least a source of genetic material that might be propagated by lab methods. As seed banks have learned freezing temperatures can keep seeds longer, slowing down all manner of  enzymatic and decay processes-- part of the rationale for Norway's Svalhard ice burrowing seedbank. 

Will such approaches become more common place? Elephantid phylogenetics have certainly been aided by the ancient DNA from frozen remains of mammoths (see Alan Cooper's 2006 "Year of the Mammoth" in PLOSone): is there is a similar set of phylogenetic surprises in store as more permafrost Pleistocene plants are dug up? Of course permafrost regions are too far north for much in the way of agriculture to be practiced-- taking crops north was a challenge as the archaeobotany of Norway reveals-- so  there is unlikely to be much in the way of agricultural crops.

Early plant cords in rock art?

In the lastest Antiquity project gallery, "fibre technology depicted in archaic art" is a re-interpretion of some rock art from Borneo, as depicting a twisted cord, presumably of some plant fibre, with frayed ends. The image is more than 8000 years old, and also includes human and apparent orangutan figures. Rather than being some sort of symbolic pathway, Judith Cameron, suggests that it represents something material, and she can point towards, admittedly later, evidence for plant cordage from Neolithic burials at Niah Cave. Of course, throughout the Palaeolithic, or at least the later Palaeolithic associated with modern human use of plant fibres, cordage, weaving of baskets must have been quite widespread. In addition to rare finds of actual cordage, such as at Ohalo 2 at >21000 years BP, other plant finds that suggest the use of plant cordage may be seen in the phytolith record: phytoliths of palms and from wild banana (Musa) leaves occur throughout the sequence at Batadomba-Lena rock shelter in Sri Lanka by to 36,000 BP [Perera et al. 2011 People of the Rainforest...]. And as phytolith sampling, and some exceptional examples of preservation, at Catal Hoyuk demonstrate there silica skeletons can provide evidence for Plants as material culture (Ryan 2011 in J. Anthro. Arch.), and so it is not too much of a strecth to think about phytolith, such as those from palms, Musa and many other fibrous monocots, as likely to represent past human gathering for raw materials, perhaps even more so than use as food.

One is reminded of Karen Hardy's impassioned plea for giving more consideration to the importance of string in early evolution on human technology ("String Theory" in Antiqiuty 2008). This reexamining of rock art appears to be step in that direction.  

Wednesday, 22 February 2012

Wild plant use in archaeobotany: a new networking site

A new Groupsite, a kind of private 'facebook' for thematic sharing and networking has been started for the study  the "Ancient Wild Plant Economy", with a group blog and other networking potential. Visit or join at:

Something similar, I came across recently in, which provides networking for the archaeobotany of Asia, Australia and Oceania.

Millet ethusiasts and gerbil enthusiats

At first it seems an unlikely place to look for basic information on millets, but it turns out that gerbil enthusiasts also care about millets (e-gerbil). The information is basic, but this website at least includes info on some of the more obscure millets like Browntop millet (Brachiaria ramosa-- they use the Urochloa name); that is more than can be said for wikipedia. They still missed out the Taiwanese oil millet, and some some of the other hypoer-locals, like Digitaria cruciata or the West African fonios. Still, millet enthusiasts are to be encouraged.

Tuesday, 21 February 2012

Weeds of Australia database

Just found this. Some basic info on a wide range of "weeds," often with seed images. Includes a bunch of things exotic to Australia that most of us would not regard as weeds, like olives and peaches(!), but it may be a useful resource:

Friday, 17 February 2012

new book: Biodiversity in Agriculture Domestication, Evolution, and Sustainability

Apparently just out from Cambridge University Press. I haven't seen the final form yet, but it contains 8 or 9 archaeological (archaeobotanical, zooarchaeological, ethnobotanical) papers, some modern genetics and  studies of recent agrobiodiversity:  Biodiversity in Agriculture Domestication, Evolution, and Sustainability


I just came across the on-line Fruitpedia, a compilation of basic information and photos of edible fruits from all over the world. Looks like a useful resource:

Tuesday, 14 February 2012

Bay of Bengal ardification data and South Indian agricultural adaptation

A new article, out this week in Geophysical Research Letters, "Holocene aridification of India", by, Ponton, Giosan, an others, presents important new, and quite high resolution, data on past monsoon dynamics and vegetation of peninsular India spanning the whole Holocene. This research, lead by researchers from the Woods Hole Oceanographic Institute, analyzed evidence from a Bay of Bengal sediment core, which captures discharges from the large Godavari river system. The core data comes from carbon isotopes of leaf waxes, reflecting the amount of arid-adapted/ savannah vegetation in the Godavari catchment, and oxygen isotopes from a marine microfossil that record salinity. This points to a general aridification trend over the course of the middle and late Holocene, supporting what we already would infer from pollen data in Rajasthan or monsoon proxies in the Arabian Sea, but this time providing more direct evidence from South India. My own involvement in this work came in the form of trying to think about how this might be correlated with archaeological evidence for settlement, agriculture and population in South India-- where the archaeological record suggests increasing sedentism, population and agriculture in response to, or despite, aridification, a contrast from the Indus region for example where the long-term trend of population depletion as aridification proceeded. This suggests long term cultural adapatation processes to aridification in peninsular Indian agricultural practices.

To quote from part of our conclusion: "The significant aridification recorded after ca. 4,000 years ago may have spurred the widespread adoption of sedentary agriculture in central and south India capable of providing surplus food in a less secure hydroclimate. Archaeological site numbers and the summed probability distributions of calibrated radiocarbon dates from archaeological sites, which serve as proxies of agricultural population, increase markedly after 4,000 BP in peninsular India [discussed in detail in the electronic supplementary text]...In contrast, the same process of drying elicited the opposite response in the already arid northwestern region of the subcontinent along the Indus River. From 3,900 to 3,200 years BP, the urban Harappan civilization entered a phase of protracted collapse. Late Harrapan rural settlements became instead more numerous in the rainier regions at the foothills of the Himalaya and in the Ganges watershed."  Most of the archaeological information is summarized in the electronic supplement, Section 4., and included an attempt to sum Neolithic/Chalcolithihc radiocarbon dates (as limited as they are) and to tally known site numbers through the Iron Age. 

This work complements recent sedimentary studies of the Indus river system, such as the Clift et al Geology paper, blogged earlier.

Saturday, 11 February 2012

Expanding Indus fibre crops

Two recent articles in Archaeological and Anthropological Sciences, report new evidence for species used in Harappan fibre work. Rita Wright and colleagues have reported evidence for jute textiles (Cochorus capsularis), based on analysis of fibre impressions preserved in ceramics. As with work done on plant impressions in pottery, this demonstrates that quite fine detail can be preserved in impressions, recorded in casts and studied with SEM. While we have perhaps long suspected jute, which is native to South Asia, was grown in the Indus period, seed finds from sites such as Rojdi (Weber 1991) were ambiguous as whether this species was cultivated, and processed for fibres.  Processing  involves retting (rotting in water), something I encountered a few years ago in the Son valley. My photo below shows a stack of harvested jute which is about to be weighed down with stones (visible in the water behind) for a week or two, before it is pounded to remove the fibres.
Posing for a photo with recently harvested jut that is about to retted  in the side channel of the Son river behind.

 Finds of textiles from eastern Iran published a few years ago by Irene Good, in the book  Ancient Textiles: Production, Craft and Society, included a couple examples of jute, as well as many of sunn hemp (Crotalaria juncea), which were also presumed to have been imported from the Indus to the east. Unfortunately as a small-seeded legume, recognizing the presence of sunn hemp in seed assemblages, especially as this crop and not a related weedy species, is not yet really possible, and could prove intractable. Taken together with evidence for flax seeds, and cotton in the Indus Valley [see my 2008 review pdf], as well as wild silk production (from the Assam silk moth), reported by Good & al. from Harappa in Archaeometry 2009, the Harappan civilization was quite the centre of textile crop diversity in the Bronze Age (compared to apparently only flax cultivation in contemporary Egypt or Mesopotamia). This adds weight to the notion that Indus exports, including those of the textually known Meluhha merchants of the Persian Gulf, included a range of cloth types.

Wild fibre sources were also important, and spun and woven net material from Shahi Tump, has also been reported recently by Thomas, Tengberg et al. in AASc. In this case, they appear to be using the local dwarf Mazari palms (Nannarrhops ritchiana). One of the excellent components of the paper is comparative study of palm phytoliths (admittedly of the limited taxa range that might be found in Pakistan), but which shows clearly that there is significant and taxonomically-informative variation in the spikey silica balls that palms produce. The next challenge will be doing more work on this variation and it taxonomic interpretation in the palm-rich tropics.

Another IWGP theme:Food Globalization in Prehistory Across Eurasia

Another proposal for  a thematic session at IWGP 2013, Thessaloniki, has come through. This is not from me, but from Cambridge so interest should be sent as appropiate to some of the Cambridge archaeobotanical post-doc (website), Geidre Motuzaite Matuzeviciuit or Liu Xinyi. This lab has been active on the research of temperate millets for a while (previous blog), including recognition of immature Panicum.

This topic obviously relates to the discussion article that this group published in the last World Archaeology, on food globalization in prehistoric Eurasia (which I have not gotten around to commenting on previously in this blog.

Here is the precis for their session: Food Globalization in Prehistory Across Eurasia. Chair of a session: Prof. Martin K. Jones

 A variety of crops that originated in China or central Asia, such as the Chinese millets and buckwheat, had appeared in Europe by the 5th millennium BC, while by the end of the second millennium BC, the south-west Asian crops, wheat and barley, had reached several parts of China.

There are some striking features of that early phase of food globalisation, features that relate both to the crop plants themselves and to the societies that utilised them. A series of later episodes of globalisation, from the Classical period onwards, involve exotic fruits, vegetables and spices. The earlier phase, however, is manifested in evidence for staple sources of grain starch, the cereals, and the 'pseudo-cereal' buckwheat. 

We would like to invite papers or poster on current archaeobotanical and genetics studies that aim to establish when and how that early globalisation of staple foodstuffs happened, what it meant for human societies in very different parts of Eurasia, and what it meant for the plants upon which they relied for food.

Friday, 10 February 2012

Archaeobotany of Near Eastern domestication: new special issue

The latest issue of Vegetation History and Archaeobotany (Feb. 2012) is a special issue on Near Eastern origins: From collecting to cultivation:transitions to a production economy in the Near East. Some of my own contributions to this discussion have been blogged previously. But as a whole issue there is a lot of important new data, and discussion herein. Although Current Anthropology has a recent volume on "origins of agriculture: new data, new ideas" I actually think there is a lot more new data, and ideas, in this specialist journal. Of course it is only about the Fertile Crescent, and we need more equivalent work on other world regions.

seeds & chaff from Iran and SE Turkey (Riehl et al)
As for what is in the issue, best to quote from the editorial by Willcox, Nessbit and Bittman: "The selected articles in the current issue throw new light on our understanding of how Homo sapiens became caught in the agriculture trap in the Near East. They are the outcome of the session entitled ‘Origins of agriculture in the Near East’ held at the 15th IWGP conference in Wilhelmshaven 2010. The subject is constantly being revised as new information and more refined analyses become available, so these papers provide a state of the art in 2010/2011. Each major discovery adds complexity to what has become a multi-faceted puzzle with data being drawn from disciplines as wide apart as archaeology and genetics, plant biology and palaeo-climatology. In this issue papers concentrate on results obtained from charred plant remains and their interpretation.".... " with hindsight simple hypotheses are no longer plausible given the archaeological and environmental diversity within the Fertile Crescent. This complex diversity is exemplified by the vast geographical area where transition sites are located, which spans different climate and vegetation zones. Thus, sites in the north of the Fertile Crescent are 1,000 km from those in the south and likewise in the east–west direction. Archaeological diversity is exemplified by the extended chronological range of transition sites. We can trace the use of wild cereals back to about 23,000 years ago when habitations consisted of simple brush huts to villages with sophisticated architecture associated with the earliest domesticated cereals 12,500 years later."

On a personal note, this issue marks a major foray into thinking about the dynamics of domestication is what remains the best archaeobotanically studied region of agricultural origins, but even here we still have a quite patchy dataset to work with.

Here's the contents list.