Friday 30 December 2011

Olduvai plant fossils taphonomy

Although it is not, strickly speaking, archaeobotany I am interested to note a recent palaeobotanical study on Olduvai Gorge, which provides a new additional line of evidence on the environmental mosaic in which early hominins (Australopithecus etc.) lived published on-line for Quaternery International by Marion Bamford. Perhaps no surprise that it points to a dry savanna type environment with localized wetlands and apparent wet-dry cycles over the long-term. The interest in the paper, which does not even attempt identification beyond monocoit vs. dicot, however is in it taphonomic approach to how fibrous monocots (sedges, grasses, culms and rhizomes)  versus woody dicots weather in the open air versus in water before the fossilizing deposition. There are some principles of wider applicability to plant remains of other period I suspect, and some of the systematic differences between waterlogged versus desiccated archaeobotanical remains relating to plant parts and states of preservation.

Some on-line sources on Indian forest/ forestry history

Just a few links I have been coming across to some of the old classics on Indian forestry, especially during the 19th century. More and more primary material is coming on-line! My own version of how this fits together with a broader history of plant ecology and vegetation classification can be found as Chapter 2 in Asouti & Fuller Trees and Woodlands in South India (2008 US edition; 2010 Indian edition).

Hugh Cleghorn's Forest's and Gardens of South India (1861) is available from google ebooks or the internet archive. As it's title even implies this book does not make an idealistic distinction between natural forests and human used/managed woods, but treats both together under subjects like shifting cultivation firewood and charcoal production, and teak plantations although it was not conceived and written as coherent book but collects various shorter reports and letters as well as appendices of 19th century forest rules, etc. Cleghorn's discussion of shifting cultivation (kumri) drew upon the earlier descriptions from Buchanan's 1807 Journey  from Madras through the countries of Mysore, Canara and Malabar also available for download. (For a longterm perspective on shifting cultivation in India, see the recent article with my student Ellie Kingwell-Banham for Quaternary International.)

Deitrich Brandis' Illustrations for the Flora of North-west and Central India (1874 London) includes about 70 illustrations [on-line or as PDF]

Cleghorn and Brandis were the foresters who first established forest conservation guidelines for British India which in turn were fairly influential on conservation approaches throughout the empire on the development of forestry as a scientific discipline. See this web article on the colonial origins scientific forestry.

VS Rao's (1961) history 100 Years of Indian Forestry is free on the Internet Archive.

JD Hooker's (1855) Introductory essay on Flora indica which includes the first real overview of climatic and vegetation zones in the subcontinent.

Some more classic sources of Indian botanical illustrations that are available digitally:
Hortus malabaricus.

Wight's Icones plantae Indiae oreintalis.  Wight's illustrations of Indian Botany

William Roxburgh's Plants of the Coromabdel Coast

Wednesday 21 December 2011

Concatenating rice and language phylogenies: a recipe for single origins?

The literature has been and remains split on singular or multiple origins for rice. The discussion of whether or not all Asian rice can be traced to a single domestication event and a single cultural origin of cultivation continues, and there have been major arguments in favour of it this past year including the high profile genetic modelling paper by Molina et al published in PNAS in May, and a recent contribution on the historical linguistics front. I remain in favour of multiple origins [as per the "rice consilience" paper of last year] -- at least in terms of multiple starts of cultivation of wild rice even if not all of these starts lead on real domestication (in morpholoigcal adaptation terms) or to rice lineages still with us today. Increasingly I am coming to think that modern time-plane sampling, such as modern germplasm or modern minority language vocabularies, is biased by missing out on past diversity-- extinct landraces and wild progenitor populations, lost language diversity. Less diversity sampled will surely tend towards simpler historical reconstructions. Both disciplines also have a predilection for simplifying relationships as trees, which tend to favour single origins. Is there a sense in which genetics and historical linguistics together will tend to be biased towards identifying single points of origin? If so, then when there is evidence to contrary it should surely be given extra weight. A clearly there is an important role for archaeology to try to reclaim some of the lost diversity of the past.

Linguistic homeland for rice?

The new article on "the ethnolinguistic identity of the domesticators of Asian rice" has been published linguist George Van Driem, one of the foremost experts of Himilayan languages many highly obscure and dwindling, especially of the Tibeto-Burman language family has made numerous stabs at the contentious prize of correlating rice agricultural dispersal with historical linguistics, and its inferred history of population movements. In general it provides useful overview of the Austroastiatic and Hmong-Mien reconstruction relating rice and arguments about the homelands of these reconstructed proto-languages. Most archaeologists are probably more familiar with the hypotheses of Peter Bellwood and Charles Higham focused mainly on the Austronesian and Austroasiatic languages in Southeast Asia. (For two recent summary papers by Bellwood, from 2011, see Current Anthropology and the journal Rice). However, there has been considerable recent debate over how Sino-Tibetan (or Tibeto-Burman) languages fit in. The French Linguist Laurent Sagart, an the the instigator of a recent  Cornell conference on the rice and language, has argued in recent years for a shared ancestry of Sino-Tibetan and Austronesian, with an outward migration of rice and millet (Setaria) farmers from central-Eastern China. Van Driem tends to have more of an emphasis on Southwest China through Assam/Burma as a focal area, although he also postulates southwards migrations of  early Hmong-Mien speakers--  likely domesticators of rice (perhaps along the Middle Yangtze). Domestication of  rice by Austroasiatic speakers could have been separate although he seems to tend towards wanting a single origin. As for these Austroasiatic domesticators he places them  somewhere like Assam-- "the Northern Bay of Bengal littoral" (but I presume he does not intend of coastally adapted culture?). In this article Van Driem points to the recent Molina paper as simplifying matters of rice origins, allowing for early cultivation in India to be dismissed. In general the Molina paper and the earlier Londo et al (2006) map are used to suggest a northern Southeast Asia/NE Indian focus for rice domestication, while archaeology is cited mainly for failure to have worked in the required areas. While I would be the first to argue that we need archaeobotanical sampling across Southern China, Burma and Assam I think this paper put too much stock on modern time place samples (languages and genes) and lacks a full engagement with the material constraints that archaeology already provides-- good dates for a domestication process in the Yangtze, good dates for when cereal agriculture, fully formed, arrived in Thailand or Sichuan (e.g. recent blog). These make a dispersal into the Yangtze from a single origin elsewhere impossible, and a dispersal of early rice use into India unlikely (although later introduction of domestication genes is another matter). I do regard as plausible, even likely that there was a separate domestication pathway in the unsampled area, perhaps associated with Austroasiatic, but this must have been in addition to what was happening in the Yangtze and the Ganges. There is a likelihood to would related to the aus-rices-- a group not incorporated in the Molina et al model.

Maps based on modern/recent distributions are a recurrent weakness in the paper. Modern wild rices, like those mapped following Londo et al (or Sampled by Molina et al) are of course biased towards the more tropical South as wild rices are not extant in most of the Yangtze nor in eastern China, but this is a product of environmental change both climatic and anthropogenic-- the extirpated wild rices of the Lower Yangtze, Huai, southern Shandong are of course missing from modern sampling, but archaeobotany has the potential (and is) putting this on the map. Much of the paper  considers the linguistic paleontology for the homeland of  Austroasiatic, in the case of the latter providing a series of maps of fauna that reconstruct to Proto-Austroasiatic, which point towards a southeast Asian (or Southernmost China) distribution. While these provide an important starting point they are also biased towards modern geography rather than early/middle Holocene geography. To take two examples consider water buffalo and elephants, both mapped as going as far north as southern fringes of the Yangtze. But both are species that we know used to range into and north of the Yellow River valley at least through the Bronze Age (i.e. until perhaps 1500-1000BC). Hoffpauir's (2000) excellent chapter on the Water Buffalo in the Cambridge World History of Food provides a good map while a more schematic map occurs in my 2007 paper on non-human genetics, agricultural origins and linguistics in South Asia [pdf]. As for the elephant its former northern occurrence apparently even for Shang royal elephant hunts, provides the leitmotif and title for an excellent long-term environmental history of China,

Mark Elvin's The Retreat of the Elephants. Compare Van Driem's map (top/left) and Elvin's retreat map (lower/right)

[note added 30 Dec. 2011: I have just come across the study by Li et al. (in press in Quaternary International) which has identified Early-Middle Holocene and Bronze Age "elephants" of northern China as the extinct Palaeoloxodon straight-tusked elephants rather than modern Asian elephants (Elephas maximus) but the point still stands since either could the be referent of an early etymon.

As for the genetic single origin (of Molina et al.)

Molina et al (2011a) carried out analysis of demographic history by attempting to model demographic parameters from several phylogenetic datasets using the new generation of collascent models (BEAST and DADI) which allow for multiple branches, bottlenecks and populations. This represents an important step away from single bottleneck models (e.g. Zhu et al 2007; Zhang et al 2009) which only attempted to estimate the correlation between early population size and length of the domestication (bottleneck period) of a single hypothetical origin. They conclude that single domestication of japonica is likely with indica derived from a subsequent bottleneck (underlying grey image below left), their discussion later hedges this with raising the importance of hybridzation/ introgression in indica, although the headline that most take away from this paper is still the idea of a single origin, single domestication event. However origin (start of cultivation) and domestication may not be the same thing.
 This study, however, does not sway me from my conclusion about the evidence for a proto-indica exploited in India before the introduction and hybridization with improved japonica, but reinforces the need for a fossil record. They are unable to sample and model the full range of diversity in all the lineages that have ever been cultivated, however briefly, over the past 8000 years. Their work focused on nuclear genetics, undoubtedly the most informative about evolutionary history in general, but they over overlooked the chloroplast. The chloroplast, which is maternally inherited, differs fundamentally between indica and japonica, nivara and rufipogon, such that there are shared characters between indica and nivara which differ with those of japonica and rufipogon, while other characters in indica are unknown in the wild. This set of chloroplast relationships is indicated in the color overlay in Figure. While they conclude that introgression, which I take to mean pollen flow, from wild rice (into the crop) in India might account for some of the genetic diversity in indica not seen in japonica, it cannot account for the chloroplast diversity, since chloroplasts are not carried in pollen. Thus pollen from wild Indian rices introduced to japonica is insufficient explanation. Instead one would have to posit pollen flow from crops into wild populations (with some nivara-related traits and some now extirpated traits) and that those wild populations retained domestication traits and were subsequently brought back into cultivation. Instead it seems still easier to posit proto-indica cultivation into which cultivated japonica , with a suite of valuable domestication traits, was brought into contact. The genetic background was largely indica into which japonica was the source of introgression, i.e. pollen flow.   I also worry the discernment between their alternative models is not very clear; comparing visually the differences in predicted outputs and actual data (Figure S4 of Molina et a 2011a) it is hard to see much of a dramatic difference between either predictions or fit. In the end I worry that they are forcing us to choose a false dichotomy between common ancestry and gene flow for explaining similarities between indica and japonica, and favouring shared ancestry on the basis an averaged phylogenetic tree across several datasets which may favour a single origin for domesticates much as is true of the neighbour-joining analysis of neutral genetic variation (Allaby et al 2008 or Allaby et al  2010 ).

Something that can certainly be remedied in the next round of models is the exclusion of temperate japonica, which was excluded from the sample set of Molina et al. As we see in the spread of rice in China, it enters the temperate zone of North China already by 3800 BC (based on a direct AMS at Nanjiaokou), where the short-grained is already evident. Based on environment and grain morphology then, we can infer the temperate japonica evolved (through its own post-domestication bottleneck) quite early. It is also from this region (the Yellow River) that diffusion westwards to central Asia and Northwest India is most likely. Therefore I would envision an early form of temperate japonica making the first hybrids with proto-indica. The sequence of bottlenecks associated with rice dispersal event was surely more than two, and some of these may have been associated with quite strong selection pressures (such as for or against photoperiodicity) as rice adapted to new ecologies: just two bottlenecks is unrealistic.  

Nevertheless Molina et al provide what probably a more realistic molecular clock estimate than has been possible before, with an initial domestication placed at 8200 BP (upto 13000), and the indica bottleneck at ca. 3900 BP. The former fits quite well with current archaeobotanical evidence for the beginnings of morphological change in Yangtze rice, and the later  date is spot on for the first appearance of the “Chinese horizon” in Pakistan and Northwest India. If this study is taken as representing the main stream of fully domesticated rice then it seems to be closing on elements of reality.

I would regard many of the problems identified above as conceptually relevant to historical linguistic hypotheses. Linguistic reconstructions inevitably work backwards from a modern time plane (although some may benefit from old texts too), towards a reconstructed common ancestor. This is like the domestication bottleneck in that while its form may be inferred from the modern data (given certain simplifying assumptions), lost side lineages, may be overlooked, and shared ancestry may therefore be easier to see than parallel developments. The dominance of the single japonica narrative found by Molina et al. (2011a) is much like the dominant Austronesian paradigm in its downplaying of substrates and language levelling processes. Indeed, recent perspectives on the later history of Southeast Asia, such as James Scott's (2009) The Art of Not Being Governed, have emphasized that ethnic affiliation has been flexible and that disgruntled overtaxed rice farmers have recurrently taken to the hills and joined the shifting-cultivator tribes, switching identity and language (at least for the past 1000 years). This is probably one factor contributing to the remarkable typological convergence across Southeast Asian language families and this may obscure early history. I find this conceptually similar to the observation that over time domesticated crop varieties come to resemble each other more than any resemble wild progenitor populations, leading to false ascertainment of monophyly (Allaby et al 2008; 2010).

. . .
My own working hypotheses on how rice phylogenetics and especially historical linguistics can be fit together within the framework of evidential constraints provided by archaeobotanical evidence, should be published soon in a special issue of the journal Rice [on-line here] arising from the Cornell conference....let the discussion continue and may it inspire new archaeobotanical sampling and genetic modelling. 

Monday 19 December 2011

From domestication to Global Warming: the Early Rice Project in Archaeology International

2012 is the 75th anniversary of the founding of the London Institute of Archaeology (which is now part of UCL), and semi-popular journal Archaeology International has just launched a bumper double in honour of this. This also marks a reformatting of the journal and launch of an on-line edition, which is fully open access. In addition back issues are now available digitally for free, the three most recent are on-line already, and other should follow. This issue includes retrospectives from former students who have gone on to other lines of work and fame, retrospectives on past members of staff (e.g. the recently deceased John Evans), an introduction to our new satellite campus in Qatar, as well as article reporting on a small selection of research projects, from Neolithic Catal Hoyuk to Anglo-Saxon political landscapes, from the 14th century capital of Mali (Sorotomo) to early silverworking in the Andes. It also includes a summary of my Earl Rice Project (Fuller and Alison Weisskopf) including an up to date summary of rice domestication evidence from China, and our phytolith assemblage approach to reconstructing rice cultivation systems, which Alison in pioneering.

Here is our abstract: 
The Early Rice Project, at the UCL Institute of Archaeology, is clarifying the origins of Asian rice agriculture. In the Lower Yangtze region of China, we have found the tipping point when domesticated forms first outnumber wild types c.4600 BC. Investigations of assorted weed flora are also revealing how the cultivation of rice changed over time, with early cultivation in small, irregular, dug-out paddy fields in the Lower Yangtze from c.4000 BC, providing a means for the careful control of water conditions. We also work on early rice cultivation in Thailand and India. By better characterising how rice was cultivated across its entire range, we aim to model the ancient output of atmospheric methane from wet rice fields, as this was a potential contributor to the long story of human-caused global warming

The article and PDF are open access: here

Friday 9 December 2011

De-centering the fertile crescent

The Near Eastern "fertile crescent" is the classic centre of origin for domesticated plants. Although when James Breasted coined the term (1906) he was thinking about the beginnings of agrarian civilizations in Egypt and Mesopotamia. The term become subsequently linked to Gordon Childe's notion (1935) of the "Neolithic Revolution" and with Vavilov's "centres of origin" idea, and the Fertile Crescent became, in archaeological argot, the centre of agricultural origins par excellence. In another classic paradigm-setting paper Jack Harlan used the Fertile Crescent as representative of a "centre" of origin, a focused area in which a package of crops was domesticated together, opposed to his notion of a "non-centre" of diffuse origins of crops that were not-packaged and spread out in domestications in space and time, of which the sub-Saharan savannah was perhaps the classic Harlanian exemplar. Within "centres" the Neolithic was meant to be a revolution, domestication rapid, and hunter-gatherers transformed to village farmers in one process. However, the evidence for this has been gradually unravelling for the Near East, with domestication-- the evolution of domestication syndrome traits in crops-- taking place quite slowly (3000-4000 years), and taking place not in a focused area, as a package of crops, but spread out and with as many dead-end proto-domesticates as paths into the crops and farming systems we know for later prehistory or history. In other words, there was no Neolithic Revolution as such but evolutionary processes, in the slow Darwinian sense, in which many incremental changes and transformations only added up to something revolutionary in retrospect, after millennia (some 150 to 200 human generations) of small steps.

You can find the case for this made in the December World Archaeology in my joint paper with George Willcox and Robin Allaby "Cultivation and domestication had multiple origins: arguments against the core area hypothesis for the origins  of agriculture in the Near East" which is a companion piece with our in press paper in the Journal of Experimental Botany  "Early agricultural pathways: moving outside the ‘core area’ hypothesis in Southwest Asia". Both are responses precipitated by publication late last year by Abbo et al. of a re-iteration of the "core area" view of  a tightly focused area where a single package of "founder crops" was domesticated rapidly. Such a view requires the assumption that archaeobotanical evidence is false fossil record, a poor reflection of actual domestication processes, i.e. that the gradual changes that appear in systematic archaeobotanical evidence, are somehow misleading or mistaken. I find this hard to accept-- perhaps because I am a practicing archaeobotanist and regard the preserved grains and rachises of prehistoric crops as our most material record of what these plants were like and how they were used in the past-- but also because recent years have seen increasing sampling and sample size and it is the increase in these data, and the detail with which they have been studied, that most points to the more gradual evolutionary processes. In addition, the "core area" view delimits a smaller number of founder crops and sets aside (or even rejects implicitly) the presence of past cultivars and domesticates now extinct, from the Abu Hureyra rye, 2-grained einkorn, the "new type" emmer ('striate emmeroid'), or the Gilgal oats-- all species which are the product of careful efforts of archaeobotanists to document the material remains of past crops and not to assume that all crops that ever were must still exist today. These constitute the "lost crops" of the Fertile Crescent just as much as Iva annua is a lost crop of the American midwest.  Coupled with the genetics of known crops that support multiple "domestication pathways" (such as in barley, emmer, pea, probably one-grained einkorn), the Fertile Crescent as a whole was host to something like 20 domestication "events," only a fraction of which can be localized in any one sub-area of the Fertile Crescent or can be expected to be present in modern germplasm collections. With this number of domestications and their diffuse nature across the Near East, the Fertile Crescent as a whole starts to look like a Harlanian "non-centre". On the level of individual crops and domestication events there may well be many centres of origins but in terms of regions it look increasingly like all were non-centres. The closer one looks for a core centre, the blurrier it becomes. 

Last year I declared in General Anthropology, a paradigm shift in agricultural origins research. Perhaps rather pretentious, but it remains the case that domestication appears to be a slower process as we gather more evidence, and there is evidence for more places of domestication around the world (North America, South India, separate North and South China, various parts of Africa, New Guinea, to name a few). This year I have put my money where my mouth is, and brought out a number of contributions looking at domestication processes in the Near East in particular and in comparison to the best documented crops from elsewhere (mainly in the Old World). This includes attempting to objectively calculate rates of domestication in terms of phenotypic units, the darwin and haldane, reported in terms of more general conclusions-- that domestication was slow and not somehow special compared to other forms of evolution-- in the journal Evolution (Purugganan and Fuller), and unpacked with more consideration of the variation across crops in the Near East and elsewhere in Vegetation History and Archaeobotany (Fuller, Asouti, Purugganan). See also the updated rachis data of Tanno and Willcox (2011)phenotypic change may differ in adjacent geographical contexts, and in particular that there appear to be in island effects on Cyprus, where grain size change was sped up (Lucas, Colledge, Simmons & Fuller). A careful consideration of the hard evidence, such as the essay assaying the southern Levant (Asouti & Fuller), shows that even for the Fertile Crescent we still lack the evidence we need to be clear about domestication processes in particular micro-regions, early cultivation or when agriculture emerged (keeping in mind that cultivation, domestication and agriculture are really different things from among the many transitions that gradually came together). We also note that there is alot more work to be done on the species that were important wild food stuffs, which were abandoned as cereal agriculture took off, the small-seeded grasses and legumes, wild nuts and nutlets-- evidence in other new archaeobotanical datasets such as that from Jordan (el-Hemmeh) of White et al. (which reports important evidence for how barley was harvested prior to domestication) or 3 sites from the northern and eastern Fertile Crescent (SE Turkey and Iran) of Riehl et al.. Of course as the role of many wild foods along side pre-domesticated cereals gains recognition, the difficulty of being clear what was a likely weed as opposed to gathered become acute-- an issue discussed in a short paper by Willcox on early weeds. Another recent paper out of London (Wollstonecroft, Hroudova, Hillman & Fuller on Bolboschoenus) illustrates an example of challenges that still confront archaeobotanical identification, and the the potential ecological and dietary implications of refining these to species level, in this case for the sedge Bolboschoenus glaucus.
 Most of these papers, now available on-line for a forthcoming Vegetation History and Archaeobotany issue on the Near East which will illustrate the revised (and more diverse) understanding of the precursors of Fertile Crescent agriculture: the tides seem to have turned on the simpler core area paradigm!

Tuesday 6 December 2011

More on rice and millet in South China and Southeast Asia

Some new publications highlight new research and new researchers working on the archaeobotany of parts of China and Southeast Asia. Three recent papers all from among a new generation of archaeobotanists report and review evidence for archaeological rice and foxtail millet (Setaria italica) in the parts of China and in Thailand. Recently published in Archaeological and Anthropological Sciences, is a paper by Nasu et al. on "Land use change for rice and millet at Chengtoushan" a Daxi era (4500-4000 BC) site in Hunan province. This reports in detail the weed flora, mainly indicative of wet rice cultivation (on , as well as discussion of probable rainfed foxtail millet, the earliest South of its probably northern Chinese areas of origin, as well as plausible Perilla and melon (Cucumis melo) cultivation. Two papers have also appeared in the journal Rice from a conference on agriculture and language-spread held at Cornell in September, both by PhD students. One by Jade Guedes, who is carrying out new primary archaeobotanical research in Sichuan province, reviews "Millets, Rice, Social Complexity, and the Spread of Agriculture to the Chengdu Plain and Southwest China." The other, by one my PhD students at UCL, Cristina Castillo, reviews the archaeobotanical record from Thailand: "Rice in Thailand: The Archaeobotanical Contribution". Both also discuss weed flora, including evidence for wet rice cultivation in the case of the Chengdu Bronze Age and dry, rainfed rice in the case of Iron Age southern Thailand.

Soybean archaeobotany: multiple origins and not coincident with cereals

A important paper on Soybean domestication (subtitle "Does size matter?") was published last month in PLOSone by G-A. Lee, Gary Crawford and colleagues. This reports details on the morphometrics of more than 900 archaeological soybeans across 22 sites in (northern) China, South Korea and Japan, including 7 directly dated by AMS. This provides the first really good archaeological dataset for making inferences about soybean domestication, and includes a summary of the soybean metrics from Wangchenggang published in a Chinese monograph in 2007 by Zhao Zhijun (and in more detail his 2010 book collection) , previously suggested to indicate some size increase by the Longshan period (i.e. 2500-1900 BC). The data reported here suggests large, truly domesticated soybeans present in middle Jomon Japan Shimoyakebe (near Tokyo), from the Third Millennium BC. These are significantly larger than those from the Yellow River valley oif similar age, the Longshan period, which are also probably enlarged by selection under cultivation (at least the population from Wangchengang appear enlarged while some other Longshan samples still fall in the wild type range). In Korea a measured population form the Middle Chulmun is perhaps marginally enlarged while those of the later Mumum had clearly undergone selection for size increase. The overall impression that selection for seed size increase in soybeans was a protracted process and one that was uneven in different regions, and it may be that in some areas wild population continued to be exploited or proximity of wild populations and early cultivation methods did not lends themselves to selecting for larger seed size. This then complements data emerging from several crops for a protracted process of evolution of domestication traits (see previous, for example my articles in Annals of Botany or Evolution, and for a discussion of protracted domestication processes in the New World tropics see the recent Current Anthropology by Piperno). It also strongly points to a Jomon domestication independent from that in northern China, and one in which seed size evolved more quickly. While genetic publications present a cacophony of single versus multiple domestication models for the soybean, those favouring a single genetic origin tend to rely on genome-wide-markers and simple tree-building, or bottleneck models, e.g. Guo et al 2010 (which has been shown to be problematic, e.g. by Allaby et al. 2008 and 2010), and those favouring multiple origins, including a separate Japanese origin seem more realistic and have support from chloroplast polymorphisms, e.g. Abe et al 2002; Xu et al 2002).

For those looking for generalizations about agricultural origins, East Asian soybean has long been taken as an east Asian equivalent of the pulses and beans of Near Eastern, as the legume component of cereal-legume package of early agriculture. Proponents of a single centered origin of agriculture in the northern Fertile Crescent of the Near East, for example Abbo et al (2010), point to the overlap zone of wild wheats, barley, lentil, pea, chickpea, as the core area of domestication in part on the assumption that this package of crops must have originated together. I am among those who disagree (e.g. in World Archaeology or J. of Experimental Botany), and see this as a package that came together piecemeal and gradually. In East Asia, there is now systematic archaeobotany that points to no initial linkage between soybean and early cultivated millets of the north nor rice of the Yangtze. Soybean were a later addition, gathered wild by some and cultivated by some some, perhaps not much earlier than the third millennium BC. 

See also this news piece from the University of Oregon. See also the excellent overview on Korean archaeobotany by Lee in a recent Current Anthropology, which also has reviews on Japan by Crawford, and China by Zhao Zhijun.

Friday 18 November 2011

International Workshop for African Archaeobotany

The 7th international workshop for African Archaeobotany, and important small gathering every 3 years, now has a website for its next meeting, next summer in Vienna. Looking forward to it.

Korean seed atlas discovered

Not sure how long this has been available but new to me is the on-line seed Atlas of Korean wild plants, which should be of use for in generally for archaeobotanical work in East Asia.

Friday 28 October 2011

New online Phytolith reference collection

A new searchable database of l phytoliths images has been made available by the Barcelona lab GEPEG (Research Group for Palaeocological and Geoarchaeological Studies). Find it here: GEPEG phytolith database. I have not  had a chance to explore it in detail, but it will doubtless prove useful. It has about 185 images in it, so it by no means comprehensive, and it includes archaeological as well as modern reference material. (And it reminds me that our UCL phytolith on-line gallery needs updating, as I have let in languish for a few years without additions).

Monday 10 October 2011

Recognizing immature millets

Recently published on-line is an highly significant, but rather unassuming paper, about variation in millet grains due to immaturity. Motuzaite-Matuzeviciute et al from the Cambridge archaeobotany lab report on "Experimental approaches to understanding variation in grain size in Panicum miliaceum" in Vegetation History and Archaeobotany.  One of the major conclusions is that immature grains are likely to preserve archaeologically and contribute small grains to samples, and their recognition is important for archaeobotanical interpretation. This study vindicates the recognition and quantification of immature millet grains, indeed both immature Setaria italica and Panicum miliaceum have been recognized and reported from recent work in China (starting from Fuller and Zhang (2007)'s report on Ying valley survey samples [pdf from here], although it did not provide adequate illustrations). Immature grains have often is overlooked or lumped with other small grasses, such as Digitaria sp. as indeterminate "panicoids". Examples can be found in illustrated reports, such as the the two at the right, in which the modern grain at the top is a 8-day-old grain from the new Motuzaite-Matuzeviciute paper and the other two are from Huizui and the Yiluo reports (published by Lee et al in Indo-Pacific Prehistory Bulletin and PNAS in 2007). I do not mean here to single out any lab as worse than any other, all or most archaeobotanists were failing to deal adequately with highly immature millet grains-- indeed I suspect I need to go back through samples from Neolithic South India sorted during my PhD to check for mis-counted immature Brachiaria ramosa grains. The important thing is for practice to change. Immature grains are important for the recognition of crop-processing stages in millets (as discussed in Fuller and Zhang 2007). In addition, a shift from more to less immature grains harvested might be expected to take place with domestication, much as was the case with rice, i.e. morphologically wild panicles needed to be targeted on average more green to avoid grain loss to shattering. (This issue I raised in relation to rice domestication a few years ago, for example in Antiquity 2007).  

Wednesday 15 June 2011

Early Agriculture & Anthropogenic Climate

A quick note on the publication of the updated rice archaeology database and a model effort based on it examining the spread of rice with an attempt to test its hypothesized contribution to rising global methane levels between 3000 BC and 1000 AD. This was a team effort involving students and post-docs with Early Rice Project (Kingwell-Banham; Castillo; Weisskop; Qin Ling) collaborators from abroad (Sato (Kyoto); Hijmans (David)) and some nice GIS modelling work by Jacob van Etten (Madrid). Some maps wet rice distirbution in selected  time-slices are shown left; but for more details read the paper.  This article "The contribution of rice agriculture and livestock pastoralism to prehistoric methane levels" is available ahead-of-print on-line from The Holocene.  Our key conclusion is that by 1000 AD perhaps 80% of 'anomalous' methane could be attributed to rice cultivation but also at 2000 BC rice is still not that significant and other sources should be sought such as the rapid spread of pastoralism around this period especially through the savannas of Africa and South Asia.

I have previously blogged the rice-part of the Ruddiman (Early Anthropogenic) hypothesis i.e. that early rice framing (and its spread) contributed enough extra methane to the atmosphere to make a global impact from sometime just after 3000 BC. I did raise some questions about the quality of the data: how many early rice finds actually represent cultivated rice (not wild) and how many represent flooded or paddyfield rice rather than upland rainfed rice? Also what role did the spread of cattle pastoralism over the Old World play in contributing to Mid-Holocene methane levels? So this new paper is an attempt to address some of these questions. We make a first stab at mapping the areas over which pastoralism spread in addition to modelling the spread of rice and the land area under wet rice cultivation. For rice at least we are able to estimate methane output but further work is needed for an equivalent calculation from cattle. I think we also would all admit that our estimate from rice remains imperfect and there is a lot of additional work to do! Collecting better quality archaeobotany (and more of); more zooarchaeology; and more sophisticated modelling...

A recent summary of the Early Anthropogenic Greenhouse Gas hypothesis has been published on-line by Bill Ruddiman at It has attracted a lot of discussion. Essentially this provides a preview to some of the results due out in the August issue of the journal The Holocene (although many of the paper are already available on-line). This issue has also received attention in Nature in their News section (in March) and was one of the issue debated at the AGU Chapman conference in Santa Fe in March.

Thursday 9 June 2011

Short rice: another domestication trait (for Early Japonica)

New genetics work on rice from a Japanese team indicates that the mutations SD-EQ1, which makes rice plants shorter, was strongly selected early on in the process of rice domestication, at least within the japonica sub-species, which is presumed to be that domesticated in the  Neolithic Yangtze. This article bu Matsuoka et al, published in PNAS, has been highlighted in Science magazine's on-line news. A transcript of my full comments and initial thoughts, are provided here.

This study by Asano et al on the SD1 gene, which shows strong selection for shorter rice plants in domesticated japonica, adds to a growing list of genetic evidence for the different origins of indica and japonica rices and for the differing cultural ecologies in which these crops were first cultivated. Subsequent hybridizations transferred some domestication-selected genes, but selectively from japonica to indica, probably around 3800-4000 years ago (see, e.g. Fuller & al. 2010, Archaeological & Anthropological Sciences). Deductions from the modern ecology of wild rice varieties and archaeobotanical evidence (e.g.  Fuller & Qin 2009; p. 147 in  Fuller & Qin 2010) points to a important role for human manipulation of the water conditions of early japonica rice cultivated in China with necessary adaptations in the growth habit of rice and shift towards a more annual seasonal pattern as opposed to the wild-type perennial pattern. Wild O. rufipogon is a perennial, which prefers growing in more less permanent water or areas that only dry up for short periods. It can produce extremely tall, long culms in order to grow in deeper water, While deeper water reduced competition from other plants it also reduced productivity since growth is focused on vegetation tissues (leaves and culms), and as long as water conditions are fairly staple plants with reproduce vegetatively and produce few seeds. Early cultivation of rice in the Yangtze region of China clearly focused on wetlands margins (for example at Kuahuqiao, 6000-5400 BC, or Tianluoshan, 5000-4300 BC) in Zhejiang. The pollen and microcharcoal data from Kuahuqiao, published already by Zong et al 2007 (for further details see this 2009 paper) already indicated the manipulation of wetland margin environments by 5700-5400 BC. While these sites, especially the evidence from Tianluoshan (which we published in Science in 2009) indicates selection for non-shattering rices over this period, it also suggests a change in the ecology in which the rice was growing. Accompanying weed seeds indicate a shift away from a predominance of perennial, and taller, sedges (Cyperaceae) towards a wider diversity of shorter annual grasses and dicot weeds (summarized inFuller & Qin 2010, but only published in detail in Chinese this past month in a Tianluoshan monograph; English papers still to come!). This suggests that there were also developments for how (and where) rice was grown. This would have involved manipulating the soils and water depth in which rice was grown. One reason for this is that in order to promote annuality and higher seed production the rice plants need to water-starved, i.e. subjected to drought like conditions, when they are starting flowering: the drought conditions  lead to increased grain output, a strategy that would be suitable for true drought but also would increase yields for early farmers. Thus more productive early rice required humans to create seasonal drought like conditions; genetic adaptations to these conditions would then be selected for.

Subsequent to Tianluoshan, at around 4200-3800 BC, other sites in the Lower Yangtze regions, such as Caoxieshan and Chuodun (see discussion in Fuller and Qin 2009), show increased human efforts at managing water levels in very small paddy fields some with adjacent channels and water 'storage pits', which would allow these small fields to be drained. Such systems would have strongly selected for changed in rice plant architecture towards less spreading grow habits (based on the gene Prog1, published in by Tan et al in Nature Genetics 2008; some discussion for the selection of this which is parallels in other cereals is provided in Fuller, Allaby and Stevens "Entanglements...", in World Archaeology). Shorter rice plants might also have been favoured here, if not already at the early wetland margin cultivation of Tianluoshan, since human manipulation of water would remove the need for taller plants, which would be prone to falling over (i.e. lodging) and would produce fewer grains (since metobolism was being invested in more culm rather than more seeds). An interesting question would be to know whether shorter plants (SD1) or less branching (Prog1) was selected first.

Once japonica was introdouced into areas with proto-indica, selection for these traits would be well-finished, and shorter growth habits may have been unnecessary and unattractive to South Asian cultivators. Thus in early India there was a selection process of crossing japonica to indica to acquire some, but not all, domestication related traits.

Sunday 8 May 2011

Journal Issue on Food Processing

The latest issue of Archaeological and Anthropological Sciences (Volume 3(1)), is a themed issue on food processing studies in archaeobotany and ethnobotany. It has a range of case studies I can recommends, geographically from Argentina to Germany to Greece to Japan, and in age from the Palaeolithic to the European Iron Age and the South American Inka. This is definitely an important for archaeobotanical thinking and research, and it provides a framework that cuts across the usual divide between hunter-gatherers and farmers. The guest editors, Aylen Caparelli, Soutana Valamoti, and Michele Wollstonecroft deserved congratulations.
 >>>Editorial: After the harvest: investigating the role of food processing in past human societies<<<  Aylen Capparelli, Soultana Maria Valamoti & Michèle M. Wollstonecroft. [link]
 >>>Staple or famine food?: ethnographic and archaeological approaches to nut processing in East Asian prehistory<<<  Leo Aoi Hosoya [link]
 >>>Ground cereal food preparations from Greece: the prehistory and modern survival of traditional Mediterranean ‘fast foods’<<<  Soultana Maria Valamoti [Link]
 >>>Early Iron Age and Late Mediaeval malt finds from Germany—attempts at reconstruction of early Celtic brewing and the taste of Celtic beer<<<  Hans-Peter Stika [link]
 >>>Traditional post-harvest processing to make quinoa grains (Chenopodium quinoa var. quinoa) apt for consumption in Northern Lipez (Potosí, Bolivia): ethnoarchaeological and archaeobotanical analyses<<< Laura M. López, Aylen Capparelli & Axel Emil Nielsen [link]

 >>>Recognition of post-harvest processing of algarrobo (Prosopis spp.) as food from two sites of Northwestern Argentina: an ethnobotanical and experimental approach for desiccated macroremains<<<   Aylen Capparelli & Verónica Lema  [link]
 >>>Elucidating post-harvest practices involved in the processing of algarrobo (Prosopis spp.) for food at El Shincal Inka site (Northwest Argentina): an experimental approach based on charred remains<<< Aylen Capparelli [Link]
 >>>The possible influence of post-harvest objectives on Cucurbita maxima subspecies maxima and subspecies andreana evolution under cultivation at the Argentinean Northwest: an archaeological example<<< Verónica S. Lema [link]
 >>>Investigating the role of food processing in human evolution: a niche construction approach<<<  Michèle M. Wollstonecroft  [link]

No more nano-diamonds

As many know, in the last few years the Younger Dryas (or, Greenlanf Interstadial 1, if you prefer) has received quite a bit of attention as a potential mega-catastrophe, and impact of extraterrestrial asteroid, conveniently hitting the arctic ice sheet so as to not leave behind a crater, but nevertheless being alleged to have left behind nano-diamonds around the world, climate change and extinctions in its wake (and the origins of agriculture). It made the news in Nature [pdf], was written up in PNAS in 2007, and started a race to find archaeological and palaeoecological evidence of nano-diamonds. Doug Kennett came to London to search through the archive archaeobotanical samples from Abu Hureyra in hopes of finding some with sediment that might contain these alleged forensic evidence for the devastating impact. Well, this hypothesis, despite all the hype, has quite roundly and thoroughly dismantled, through numerous studies, but which are all drawn together in a nice "requiem" by Pinter, Scott, et al., in the recent issue of  Earth Science Reviews ( For more online summary see the discussion of this article on

As an archaeologist interested in the Younger Dryas for its local impacts on ecosystems and cultural adpatations, this was only ever a distraction. That there was a climatic event remains clear, and we can return to looking critically at how this is reflected locally in archaeological and palaeoenvironmental evidence. Indeed, recent focused studies on Near Eastern archaeobotany have begun to question to relevance of the YD as the key event in the origins of agriculture. Did cultivation actually start in the YD at Abu Hureyra, or can patterns on the plant remains be more parsimoniously explained as shifts in foraging? For example, an detailed rethink of the nitty-gritty of the Abu Hureyra data, has been recently published by Sue Colledge & James Conolly in Environmental Archaeology, Dec 2010. As archaeobotanical evidence increasingly points towards a slow evolutionary process of domesticated plants in the Near East as elsewhere, and a dispersed process both in space and time around the fertile crescent, it makes less and less sense to see a few potential plots of cultivated rye in the Younger Dryas as somehow dictating the direction of all changes towards agriculture over the subsequent 3000-4000 years in the greater Near East. So we need to get back the work of looking at regional environmental impacts and cultural sequences.

(on the slow domestication in the Near East and elsewhere, one might have a look at these paper from the past year:
Purugganan & Fuller. Archaeological data reveal slow rates of evolution during plant domestication. Evolution 65(1) [2011]
Allaby, et al. (2010) A simulation of the effect of inbreeding on crop domestication genetics with comments on the integration of archaeobotany and genetics Vegetation History and Archaeobotany 19(2)
Fuller (2010) An Emerging Paradigm Shift in the Origins of Agriculture. General Anthropology 17 (2): 1, 8-12 [pdf])

[posted from Jinan, Shandong]