Rice awn reduction: not a domestication trait

In a recent paper in Economic Botany, Svizzero, Ray and Chakraborty (2019) ask whether awn reduction is really part of the domestication syndrome of rice or instead a crop improvement trait. It is true that I once listed this as part of the domestication syndrome traits in cereals (Fuller 2007): awn/appendage reduction, but I don't think I really pressed for this to a be central part of domestication. It was only meant to identify a tendency that recurs across most cereals. I would now agree that this post-domestication and varietal improvement trait. That this should be regarded as post-domestication/improvement trait is clear from the fact that it affects only some lineages of rice (most temperate japonica, many indica, but few tropical japonica or circum-aus, and mostly not Oryza glaberrima). Many cultivars have awns of varying length. The authors usefully illustrate diagrammatically how economy (foraging, pre-domestication cultivation, agriculture), harvesting methods and the evolution of some morphological traits (like the awn) are not synchronous changes. These are part of what makes domestication a protracted and entangled process.

In the case of rice, the presence of awns may have actually been necessary during the early stages of cultivation! This is the implication of recent work by the Kobe rice genetics group (Ishii, Ishikawa and colleagues), who have recently published data identify three interacting loci in rice (Amarasinghe et al 2020 in Rice) . They have worked the slow processingf of backcrossing indica genetic components into a population of wild rice, and are able to document the additive effects of 3 loci on reducing the awn length. The reason that awns are important in wild rice has to do with seed dispersal-- like in other cereals awns help to propel spikelets across and into the soil, and in the case of rice they likely also play a role in dispersal across water. But the reason they would have been important to early rice gatherers and the first rice cultivators is that awns mean that grains, even after they have shattered, to get stuck within the rice panicle, making them more readily gatherable by people. This goes hand in hand with a key domestication trait, previously identified by work at Kobe, namely the closed panicle morphology (controlled by the OsLG1 mutation, also called SPR3, published in Nature 2013). This closed panicle trait would make the more compact panicles easier to harvest, especially with long awns that allow shattered spikelets to get caught. Indeed, the data in Ishii et al (2013), allows us to estimate an increased in return rate on harvested rice, with just this mutation of about +50%. This actually implies that awns were selected for during earliest phases of cultivation, but would have lost selection advantages (in terms of harvest) once non-shattering became dominant.  Thus, as concluded by Amarasinghe et al 2020,  after domestication it became reasonable to selected for reduced awns. Without awns harvested spikelets take or less space and plant would not have needed the same degree of metabolic investment in producing awns. The reduction of awns is also common in many varieties of wheats, barley, oat, but I suspect it was not actually part of the initial domestication in these either. Thus the conclusion of Svizzero et al (2019) may well have relevance to many cereals beyond rice.

However, Swizzero et al are wrong that this trait can not be studied archaeologically, even if it really hasn;t been so far.  We are able nor to recover lemma apex remains and determine these as awned or awnless (as in the example at left from work by Cristina Castillo at Khao Sam Kaeo, Thailand). In recent years work by Castillo, myself, and others has increasingly recovered these from flotation samples. They are lightly smaller than spikelet bases, less common than spikelet bases but nevertheless can be reognized as either complete apices (with a beak like end) or torn (like the one at left) indicating that they were awned. Thus there is potential to study this archaeologically. The example shown here is part of a dataset that indicates the predominance of awned japonica rice in Thailand upto at least the Iron Age. In waterlogged material from the Lower Yangtze it is clear that early rice, even non-shattering ones are awned. More work to be done on recognizing when and where awnless rices became common. Reduced awn or awnless rices appear to be present at Roman era sites on the Red Sea soast of Egypt (at Berenike and Quseir al-Qadim), at which time they are presumably being imported from somewhere in southern or western India (published in the books by Rene Cappers, and Marijke van der Veen).

Rice domestication was slow, and post-domestication varietal diversification, including the reduction of awns in some varieties, took even longer. And there is much we still don't know about this history-- but a history of varietal and geographical diversification starting to be unravelled in part through genomic history (but that should be a post for another time).

Using big machines to look at the finer aspects of seeds

This year has seen three studies on high resolution x-ray computed tomography applied to archaeobotany, one using ct-scanning to recovered chaff hidden in ceramics (see Finding Rice Domestication in Clay), and two using a synchrotron to peer inside seeds, including soybeans and horsegram.

This past summer, I published with colleague Charlene Murphy, a Scientific Reports article on domestication of the Indian crop horsegram. While this article represents an important contribution on the domestication history of a major crop in India, and evidence for evolution of morphological change during that crops domestication in South India (see also our GRCE paper, reviewing all that is known about horsegram origins), this is really more significant for the methodological contribution to the archaeobotanical documentation of domestication. We were able to put our small archaeological seeds in a very large machine, the Diamond Light synchrotron (shown at left). which allowed us to non-destructively capture the the internal structure of the entire seed (not as straightfoward as it sounds as it takes a lot of computing time). And from this we could measure seed coat thickness on any of the 1000s of cross-section slices through our seeds (like that below/right)

One of the well-known domestication syndrome traits in pulses is the thinning of the seed coat, tied to loss of germination inhibition. But it has been difficult to document this archaeologically. Seed coats are often destroyed in charring, but even if preserved they study on charred seeds would require destructive breaking of seeds. And even if damaged, it might only be possible to document the seed coat thickness in one or two places with an SEM or high powered normal microscope. As a result this has been rarely documented, which has lead to a fair degree of speculation on the evolution of thin-seedcoat, readily germinating pulses, as the result of conscious selection of the readymade mutants in the wild (although none have been documented in the present day)-- the domestication before cultivation hypothesis applied to lentils-- or positing a rapid conscious selection by those who initiated cultivation-- lets call this the pea breeding before agriculture hypothesis. The truth appears to be, however, a gradual evolutionary process as seed coats thinned over time, much like the evolution of increasing seed size or the non-shattering in cereals-- at least in horsegram. This can be seen in the chart below showing the thinning seed coat along side a trend in seed size increase in horsegram. Further work is needed on additional pulses to see if this pans out as typical of the pulses domestication processes, or whether there was variation, or indeed any cases of plucking domesticated types from the wild-- of which I am doubtful. At least now we have a method for approaching this.

This is actually, quite logical: established stands of pulses could be maintained and wild-type dormant seeds would constitute an established seed, and would recurrently add new plants to the the stand over a series of years. But due to annual human harvests mutations that reduced dormancy would get selected, and would be particularly important for any new populations planted in areas without existing wild populations. In this context we can expect the gradual evolution for thinner coated, more easily germinating seeds through selection across what are presumably multiple loci, as is evident in our archaeological horsegram data (shown left).

Soybean oil content in charred seeds?
The claim for earliest use of a synchrotron to look at charred archaeological pulse seeds, however, goes to our colleagues in China, in collaboration with Prof. Gary Carwford, Shandong archaeobotanist Xuexiang Chen. They argue that soybean underwent selection for increased oil content in prehistory during domestication-- undoubtedly true-- and that this can be tracked archaeological through a change in the number and size of pores visible on the inside of charred soybeans viewed through the synchrotron and High-Resolution Computed Tomography. I remain unconvinced on this last point, and although the paper reports on examination of modern soybeans and, other oily crop seeds, and experimentally charred seeds none of these are illustrated or really described so as to support this interpretation. The authors infer that more small pore is a product of more oil whereas large pores represent burned out protein, but is this true. The differences look to me more like artefacts of carbonization processes, and not a good proxy for the internal anatomy of the original uncharred soybeans. As the few illustrated example suggest larger and irregular pore are present in seeds with more distorted external surface anatomy (e.g. c), whereas small pores are more evident in better preserved examples (e.g. f).

Unfortunately, the central claim in this paper does not really add up, or at least are not well justified and explained in the text. This makes me very nervous about accepting the main conclusion of the paper, i.e. that the authors have demonstrated an increase in oil content in soybean during domestication by measuring the quantity of bubbles (voids) of different sizes in charred archaeological soybeans. Small voids are attributed to oil content and large voids to protein—but this is never demonstrated (for example in modern and experimental charred examples) or backed up by citations on soybean anatomy, as to why these voids should differ between oil and protein. That soybeans are oily, in contrast to most pulses is clear, but this also has major implications for the nature of archaeological finds. Most carbonized archaeological soybean are poorly preserved, distorted, full of large voids and small voids and very shiny on their interior. This is contrast to pretty much every other pulse I have seen archaeobotanically, from Vigna spp. to lentils and peas to Lablab. Even in the Chinese samples, presumably subjected to similar formation processes Vigna angularis seed present typical features of carbonized pulses, including a dense charred matrix with distinct cotyledons. In Glycine cotyledons are rarely evident and their interiors are heavily distorted by voids and bubbles. The obvious deduction is that this state of things is the result of the oil content in soybeans, and of course many other oily seeds, from cotton to sesame, also tend to show similar levels of bubbling and porosity when charred. If large voids in soybean are due to protein burning up during carbonization then surely one would expect to see this in any pulse, all of which have at least 20% protein content. It is true that the oil in soybean is contained in fresh seeds in many small droplets/sacs but upon charring things are likely to end up being very different. Oils are going to burn to more readily to gas than carbohydrates or proteins and thus create more bubbles and explosions of expanding gas. As this progresses and cracks to the outside of the seed allow penetration of gas (and some oxygen) from the exterior, one would expect this to speed up. The persistence of small voids then might be predicted to be the result of less oxidation, less temperature and perhaps other variables of charring conditions of a given seed. Cracking and penetration of gases into the charring seed may indeed be affected by aspects of domestication—thinning of seed coat, increase in seed size. Indeed, larger seeds seem likey to leave larger parts of their interior cotyledons unexposed to exterior cracks and oxygen; and in this context would be expected to preserved more small oil bubbles as a side effect of seed volume increase: i.e. the difference over time would reflect preservation artefacts rather than selection for genetic change. It is hard to see how at this stage we can deduce difference in underlying phenotype and genetics from this sort of data—at least until we have much better grasp on who charring conditions affect the distribution of seed contents, and this calls for some systematic experiments.

Undoubtedly soybeans were selected for oil content, but when and how this took place in relation to other domestication traits remains sadly unclear. I find I have to reject to conclusions of Zong et al., although their paper doe illustrate the potential analytical power of using a synchrotron to peer inside archaeological seeds

In Memoriam, Professor David R. Harris (1930-2013)

It is with a heavy heart that I report the passing of David Harris during the holiday period, Professor Emeritus of Human Environment at the Institute of Archaeology (UCL) and former director of the institute (1989-1996). Our sympathies go to his widow Helen, their children and grandchildren. He also leaves a hole in the intellectual community of the Institute and wider research community on domestication and agricultural origins. For a few generations of archaeologists he was an influential teacher on past subsistence, drawing on a global and encyclopaedic knowledge of ethnographic subsistence systems and world archaeology. Through his writings, edited volumes, and conference organization, and no doubt peer-reviewing, he influenced generations of environmental archaeologists, especially archaeobotanists, and he promoted a comparative and world approach to the transition from forager to farmer. While I was not a student of his in the classroom, I was heavily inspired by his writing on tropical and savannah cropping systems [e.g. 1967, 1972, 2006, 1980 book], on the spectrum transitional subsistence systems that included pre-domestication cultivation (while he did not coin this term, he probably did more than anyone else, to promote its use and to clarify the concept, in part through a series of highly influential and reproduced diagrams-- e.g. Harris 2007, or this 2007 derivative). He was also a dedicated and knowledgible historian of the Institute of Archaeology (e.g. 1997), of Gordon Childe's work, and their influences on the development of Neolithic research.

David Harris studying swidden farming in the upper
Orinoco River, Venezuela, 1968 (from AI 9)

When I joined the institute, David become a mentor, friend and frequent discussant; he informed my ideas, the direction of my research, and always made me look wider, inter-regionally. In many ways he was a unique figure because he adopted archaeology, having moved to the Institute as Professor of Human Environment in 1980 after some two decades teaching in Geography (in UCL Geography from 1964). He had long had predilections for archaeology, indicated by his involvement in the Ucko and Dimbleby conferences on "The domestication and exploitation of Plants and Animals" and "Man, Settlement and Urbanism". His papers on tropical agriculture and the importance of vegeculture were highly influential in encouraging the development of tropical archaeobotanies, from the Neotropics to Africa to New Guinea. His recruitment of Gordon Hillman led an fruitful and extremely influential partnership, both for research, synthesis (their jointly edited book, Foraging and Farming, remains in many ways unparalleled). His contributions were in many world regions, from early work in the Caribbean and Neotropics (e.g. 1962, 1971), the American Southwest (e.g. 1966), to the Torres Straits islands (e.g. 1995), the Fertile Crescent and his more recent work on Djeitun in Central Asia (e.g. 1997;  2010 book). He is well-known for his clear working definitions of slippery concepts, and his monumental syntheses, often streamlining what was the best current knowledge of the origins of agriculture in various regions, often including the Near East and China , along tropical regions.

David photographing tea cultivation in
Zhejiang, Sept. 2010

Several colleagues have written to express their gratitude to and memories of David. Andy Fairbairn points that he was “ great advocate for our work and was a major influence on taking archaeobotany from a minor sideshow to a discipline in its own right”. Keith Dobney recalls “some rocking seminars with him and others on domestication.” Ehud Weiss remembers him as influential teaching, “amazed by his knowledge”. Several more have written to me about how he was inspirational on their work.

Please do leave further memories and observations in the comments on this blog.

I will append some addition photos below. Feel free to submit others.

Visiting the Harvard arboretum in Boston (2008): Dorian Fuller, Ksenija Borojevic, David Harris

 

At the excavation of the Liangzhu city (ca. 2500 BC) wall, outside Hangzhou: Liu Bin, Zheng Yunfei, Qin Ling, Helen Harris, David Harris (Aug/Sept. 2010).

Peking University archaeologist Ling Qin discussing Liangzhu ceramics with David Harris and Helen Harris (Aug/Sept. 2010)

Visiting Hemudu archaeological site museum, Aug. 2010: DQ Fuller, Ling Qin, Helen and David Harris.

Victor Paz, Lewis Binford, Dorian Fuller, David Harris, Lazslo Torok (Cambridge, 1998).

David Harris in conversation with Prof. Barbara Pickersgill and Dr. Mark Nesbitt, Linnean Society of London 2006.

Gordon Hillman, Mary Anne Murray, David Harris, and Sue Colledge, in office 311, UCL Institute of Archaeology 1998/99.

Origins of Rice Podcasts

Last week, before typhoon tragedies hit the Philippines, I joined about 700 geneticists and plant breeders working on rice for the Rice Genetics 7 symposium, organized by IRRI. and I was very proud to present our current archaeological picture on the origins and spread of rice in Asia to a packed auditorium the first morning. I also had the opportunity to take part in an IRRI radio podcast on the "Origin of Rice" for a ~5 minute version also featuring Prof Sudan McCouch go here . For the extended 14-minute version on archaeobotany try this link.

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

More contributions on rice, linguistics and genetics

More papers from the Cornell meeting on rice, linguistics and cultural spread continue to come out on-line. This includes my own attempt ("Pathways to Asian Civilizations") to integrate historical linguistics hypotheses, current archaeobotany and recent genetics (including some considerations of issues blogged a few weeks ago).

Perhaps more importantly it includes a updated  assessment of the comparative lingusitics of rice vocabularies by the CNRS linguist Laurent Sagart, who favours an early historical linkage between Sino-Tibetan and Austronesia: for him this relationship is genetic but I wonder whether an early situation on contacts and loans (including millet and rice) makes more sense? An earlier study by Blench collecting rice vocabulary, published in 2008 [available here],  deserves to be considered alongside this paper for its extensive tables across several language families. There is updated overview by Peter Bellwood of his language/farming dispersal hypothesis in its Island Southeast Asian hearth, which includes some important new revisions (such as an early migration eastwards to micronesia and shift in line of newer views of Chinese rice domestication as being later). A rice-driven spread of rice through Indonesia looks less and less plausible, and even though there was some early (late 3rd Millennium BC?) from a few sites it may never have really taken hold: i.e. there was a failed "revolution" in grain culture. In a forthcoming article by Huw Barton on the rice versus sago in Borneo, he makes the case that "Rice appears to be an illogical crop choice in the rainforests of Borneo" by comparison to the higher yielding forest staple Sago (see his yield estimates chart below). Serious and persistence rice agriculture may be much more recent (although I guess before the Malay period when rice was moved from this region to Madagascar).

In relation to Austronesian origins, there is also a paper on rice in Taiwan, which mainly reports some genetic data on local land-races, but also provides the best illustrations yet of some archaeobotanical evidence from the site of Nankuanli (including rice and foxtail millet).

There are also some papers of a more palaeoenvironmental flavour on rice. Quaternary International has a second special issue on "Agricultural activities and rice cultivation in East Asia [Part 2]" coming out. Judging from the editorial, we can expect several pollen  studies from around East and northeast Asia which detect human farming impacts on vegetation, but little that is likely to change views on the origins and spread of rice, nor on archaeobotany. Part 1 was an issue in late 2010, had a few highlights, such as expanded data and discussion of the vegetation, vegetation burning in relation to the early cultivation site of Kuahuqiao (Shu et al), and Li et al's  palynological assessment of vegetation and forests during the Liangzhu period-- worth looking at alongside Fuller & Qin's Environmental Archaeology paper on the environmental context of rice (Dec. 2010). Although it should be noted that Li et al repeat some old mis-identifications from Qianshanyang repeated by non-botanical archaeologists in 1960! Notably "peanut" (introduced via Europeans in the 16th century, see the classic study by Ho 1955) and sesame (probably not older than the Han dynasty: see Fuller 2003)-- the latter certainly is melon (Cucumis melo) which is widely encountered. It pains me to see wrong and unreliable identifications repeated....

More important still is an on-line article by Gary Crawford "Early rice exploitation in the Lower Yangzi: what are we missing?" for a forthcoming issue of The Holocene also on early rice and palaeoenvironment (that I expect to also be an issue that is mainly palynological and sedimentological). It is a thoughtful and provocative paper, partly meant to update Crawford and Shen (1998) and partly meant to be critical of recent work in the Lower Yangtze (including mine), with extended discussions of the issue of immature grains and spikelet base criteria (but without any substantive new suggestions)-- true these criteria are not as straight forward as an either or division, but they still work pretty clearly for characterizing the big trends and transitions. He also summarizes in English a new Chinese proposal (by Gu and Zhao) for morphometric formulae for determining from grain measurements the percentage of rice that was wild or domesticated (although I expect the reliability of such an over-precise formula is dubious). He muddies the definition of "domestication" somewhat by taking a catholic list of "DRT" (domestication-related traits) from the genetics literature-- some of which have little to do with basic crop origins at the beginnings of agriculture, despite their appeal to breeders or the importance in some cultures (like waxiness or white grains). This article includes important critical comments on alleged Pleistocene claims for wild rice, whether from the South China see or Yuchanyan

One of Crawford's main points is to emphasize that we must understand more than rice, that rice "casts a long shadow" on consideration of other resources. (I fully agree, this was the starting point for my original Hemudu critiques [2007, 2008], that 1000s of acorns should not be ignored). He argues consider landscape management for taxa such as oaks and peaches, points I would certainly agree with. He pushes for nut-managers or niche constructors, while characterizing my interpretation as one of "nut-gatherers who became cultivators", which failed to consider other "crops". Perhaps there was management for nuts like acorns (which I suggested in Fuller&Qin 2009), but the problem is that we are hard pressed to see any evidence for this. And if landscapes were managed for nuts (likely to at least some degree) I doubt whether this can be seen as somehow fundamentally different in the Holocene from the kinds of practices that characterized early modern humans in the later Pleistocene (as argued in Fuller, Willcox and Allaby in World Archaeology), since they knew how to manage vegetation through burning and to plant and transplant if desired (as indicated by bottlegourds that must have been cultivated since the Pleistocene beyond Africa) rice cultivation is fundamentally different-- the management for habitats for annual plants rather than landscapes of perennials. A key shift in rice is from perennial ancestors to more productive annuals, a point he touches on as well. And the creation of rice cultivation systems that could select for this and for domestication traits like non-shattering was fundamentally different in outcome and commitment than whatever landscape and tree management that had come before. 

Crawford flirts with the Hayden hypothesis that rice cultivation developed because rice was the first luxury food. While the prestige of risking labour in rice probably is relevant to many cases of secondary adoption, as Huw Barton suggests for rice cultivation in sago-rich Borneo, I am less convinces this is true for the for the sparse early Holocene/terminal Pleistocene Neolithic of Yangtze China. Instead domesticated rice, and its intensified use (from ca. 4500-4000 BC onwards) correlated with material culture evidence from craft specialization and artefactual prestige-goods (see Fuller and Qin 2010). Hayden's speculation (in the recent volume edited by Barker & Jakowski) would be that competitive feasting and prestige battles are there to be found and we just need to keep looking (perhaps in submerged coastal areas which Crawford suggests may hold many secrets). I prefer to focus on the evidence we do have rather than speculate about what is under the sea or alluvium.  Domesticated rice, in the morphological sense, was later than had long been assumed, and created new opportunities for wealth production and demography: it was a game changer, at least in its native Yangtze heartland. Morphological domestication and how rice was cultivated is not an unimportant detail, but central to understanding a major economic and landscape transition which made later Neolithic societies onwards fundamentally different from those that had existed for much longer before in the Early Holocene or Pleistocene... In any case, clearly a paper that deserves reading and thinking about.

rice genetics watch: structure in Chinese rices but not domestication genes?

• In the Oct. 2009 issue of Theoretical and Applied Genetics, a large Chinese research group (Zhang et al.) looked Genetics structure among Chinese rice landraces, with over 3000 Chinese rice populations. They find clear population structure, not just between indica and japonica as expected, but also within each of these. Interesting they report that the structure in indica seems to relate to flowering time (early, middle or late flowering varieties), which suggests that early differentiation after indica originated may be focused on seasonality (and constraints of seasonal land and water availability). In the case of japonica (primarily temperate japonica one presumes), seasonality is pretty much always restricted to the warm wet summer, as China has dry, cool winters that are not conducive to rice. Instead structure seems to divide Chinese japonica landraces on the ground of soil and water adaptations, and whether they are best grown ion paddies or on upland rainfall. Indeed, as predicted from the archaeology the earliest ecological efforts in rice domestication in China are likely to have focused on water manipulation (see Fuller & Qin in World Archaeology), while early dispersal must have also seen diversification in rainfed and less labour intensive systems of cultivation. On the whole an interesting approach that one would like see extended beyond China.
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• Another paper also with Zhang et al. authorship (but a different Zhang), that came out at the end of the summer in New Phytologist looked in more detail at the phylogeny of sh4 and qsh1 non-shattering (domestication) genes, and provides a coallescent model of their origin in terms of fixation time. Their estimate this trait should have been fixed in ~100 years seems a throwback to the kind results that models produced a decade ago, now at odds with the archaeobotanical evidence on domestication rates. The authors are at odds to explain this by positing thhat the now universal(?) sh4 domestication gene evolved after initial domestication and then diffused throughout rice (and replaced some earlier domestication genes). Not a particular elegant, nor historically/archaeologically compelling model. I am forced to assume that something is amiss in the math or the assumptions of the model. Can an apparent rapid bottleneck be artefact of another process in the way the apparent monophyly can (as per Allaby et al 2008). I also note that the phylogeny that relate domesticated sh4 to wild populations the same or a close gene, on the surface suggests an origin of sh4 from a Lao rufipogon or an Indian nivara-- but surely these wild taxa, and the indica and japonica types deriving from them should not group together in a population phylogeny when they have different chloroplast genomes (with a common ancestor in excess of 70,000 years ago!). Of course a Neighbourjoining tree, however much bolster by bootstraps and Montecarlo methods is still just a cluster analysis that is not a particularly logical or robust way to look for phylogenetic relationships within a species that hybridizes. Thus the method employed here denies the reticulate evolution which is so clearly a part of evolutionary story of rice, as so elegantly argued in earlier papers by Sang & Ge or more robustly in the recent papers of Kovach et al or McNally et al. I am therefore provisionally not at all sure what this sh4 data is actually telling us.

Review on lentil domestication

A recent review article by Sonnante, Hammer and Pignone (2009) " From the cradle of agriculture a handful of lentils: History of domestication" in the rather obscure Rendiconti Lincei of April reviews the archaeology and genetics of Lentil domestication. It provides a useful overview, including a wide range of neutral genetic evidence that confers with the orthodoxy (e.g. of Zohary and Hopf) of a single Lentil domestication somewhere in the Levant, although the authors note the possibility that pre-domestication cultivation began with more than population of Lentils, but in the end only one was domesticated. They also provide a tabulation of the identified domestication-related genes in Lentil, which have generally received less attention than those in peas or Phaeseolus, and discussion of the morphological domestication syndrome in Lentils. They some speculation on why/how people came to cultivate lentils, which remains something of mystery for this and other pulses, in which seed germination rates of wild types are so low as to make them unlikely candidates for domestication. They concur the early Near Eastern agriculture including that of Lentils did not come from a dump-heap origin, but they still suggest that wild lentils might have occurred as weeds in early cereals and thus been a co-domesticate. Given what we know of wild lentil habitats this hypothesis seems little stronger than a dump-heap model, and I must favour some sort of intentional interest in Lentils and other pusles (perhaps for their protein content, or taste, or storability) which lead early cultivators to persist in their efforts despite initially low germination rates.