Sunday, 5 January 2014

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. 19621971), 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.

Thursday, 14 November 2013

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.

Monday, 15 July 2013

The eastern fertile crescent returns

The recent paper in Science by Riehl et al. on  the evidence for Chogah Golan has rightly garnerd wide attention (e.g. Science news; commentary by Willcox). This is a highly significant paper, which shows that the beginnings of cultivation were indeed mutlicentric within the fertile ccrescent, and it suggests that there was an independent domestication process for emmer wheat in the eastern fertile crescent in addition to that in the western fertile crescent. 

Are there surprises? Yes. The big surprise here is the emmer wheat domestication, as many have argued on biogeographical and modern genetic grounds that there should have been and eastern and western barley domestication, but this has been little considered for wheat. This is mainly because the modern distribution of wild wheats does not extend that far east and south, and thus the data from the Chogha Golan, especially the lower levels indicates that the distribution of wild wheats at the start of the Holocene/end of the Pleistocene was indeed different and more extensive than modern wild wheats. This further implies that some starts to cultivation and domestication events could have drawn on wild population that are extirpated today and therefore are not reflected in modern wild germplasm collections. Modern collection used in genetic studies are only a fragmentary representation of the past, although geneticists often fall into the trap of assuming that good wild sampling in the modern day means they have captured the wild diversity from which domestication began.

What this what we/ I suspected? Yes. I am one of a number of scholars who have been arguing for a multicentric process of parallel starts to cultivation and parallel, and protracted, domestication processes around the Fertile Crescent, i.e. De-centering the Fertile Crescent. Mostly we have argued this on contrasts between the Southwest and the north/central fertile crescent and the contrasts between morphological diversity in archaeological samples and that in modern germplasm. As the authors here note with their triticoids, they are dealing with a wild wheat type not well represented in modern collections; this is equally true of early domesticated wheats in Syria/Anatolia and even in Neolithic Europe. In the Neolithic there are extinct genetic lineages, that are morphologically distinct, that are not found in modern landraces. In other words there are several lost crops of early agriculture. 

Were things really synchronous? This remains a little unclear. The lower levels seems to have pre-domestication cultivation of barley and lentil and lost wild wheat in the equivalent of PPNA/ EPPNB time periods-- this is indeed the same period that we see this in Jordan, Israel, north and south Syria. However in the Chogha Golan there is then a break and a large minority of domesticated type emmer appears. But this is mainly in the Late PPNB (ca. 7800 BC)! By this period domesticated crops are well established at higher frequencies (usually 60-70% non-shattering spikelet bases) in western fertile crescent assemblages (mainly of einkorn wheat or barley). Emmer at Tell Aswad in Syria is ~23% non-shattering at 8300 BC and at Tell el-Kherkh in NW Syria it is 44% at ca. 8400 BC. This evolution of non-shattering (a key domestication trait) appears  slightly ahead in the west. This could mean the that 25%-domesticated assemblage at upper Chogha Golan has spread from early cultivated population elsewhere that were undergoing the gradual selection for non-shattering, or it could indicate a local process, maybe not at Chogha Golan, but nearby that simply got started a bit later. 

I would note in passing, that there was one previous suggestion of eastern emmer domestication, many years ago by Hans Helbaek in the 1960s based on rather poor samples collected by the Braidwood expedition at Jarmo in Iraqi Kurdistan in the 1950s, in which Helbaek reported intermediate types and mixtures of wild and domesticated emmer. These data were never quantified nor fully published but would potentially fit with the Chogha Golan finds. So a return to Jarmo may yet have some important archaeobotanical contributions to make.

On the whole, however, these new data offer strong support from a new dataset and a different research group for what I have been championing as a paradigm shift in agricultural origins research. From the paradigm of a rapid and singular agricultural revolution to a paradigm of protraction and entanglement that was messy and non-centric. (See, e.g. refs 2 and 19 cited by Riehl). 

Tuesday, 7 May 2013

Used Planet

Last week saw the publication of "Used planet: a global history" in PNAS [pdf] in which I teamed up with some land use and palaeoenvironmental modellers to offer an alternative synthesis of the evidence for human environmental modification. Much of the time in studies of land use and environmental change it is assumed that major environmental change and destruction is quite new, something brought on by the industrial era in the last few hundred years. Land use models like the HYDE model illustrate this, with something that approximate the projection of modern population: land use ratios backwards to periods when very few people were around. The key authors of the original HYDE model were part of this paper, and are quick to point out the many uncertainties and flaws in the HYDE dataset and its application (as in this recent paper). This is illustrated by the graph on the left (above) with most of the transformed land (in light purple) only dating to the past few centuries). By contrast in a model that assumes landuse intensification fewer people used land more extensively and only more intensively as rising population forced them to (the right hand charts above). Comparing maps of these different models, makes it look like "two different planets"  (to quote the blog of lead author Erle Ellis). Whereas archaeologists and anthropologists have debating and modifying Boserup's intensification concept or the notion of "agricultural involution" of Geertz for decades, this seems to have came rather late to global climate and land use modelling studies. Intensification in the use of all sorts of things has been a hallmark of human prehistory, from the broad spectrum revolution, the development of post-harvest intensification, in the use of grinding stone and other cook techniques (explored elegantly by Wollstonecroft 2011), the development of pre-harvest intensification (i.e. cultivation), improved yields through the evolution of domestication traits (with its own new labour demands, a kind of intensification too, see, e.g. my "domestication as innovation" paper), and agricultural intensification as it is normally defined (on which, see Morrison 1994). That our review of these two planets, which fairly clearly comes out in favour of one in which transformations by people are old and intensification processes are long-term, catches some sort of zeitgeist, is suggested both by the press coverage of this paper in New Scientist, Scientific American and The, and a session devoted to the same theme at last months SAA (summarized by Michael Balter). Of interest is that the latter two take the younger "impact" date of 3000 years, while the former takes 5000 years (I guess on my suggestion). One of the things that came up in discussions that lead to this coverage is what kind of impacts were there and when should we put the start of the "Anthropocene." 

From Early Holocene impacts to the Anthropocene

Should we replace "Holocene" with "Anthropocene"? Some might tend towards this view, since the start of Holocene is afterall when cultivation began, i.e. human "niche construction" intensified. My own view was that while that was a watershed in human behaviour, it was a long time before cultivation got underway in most parts of the world, or even in those early centres, before it developed into true agriculture, cultivation at the scale that impacted landscapes and made economies that were basically dependent on domesticates, leaving little subsistence space or time for wild foods. Early impacts were not early Holocene but notably middle Holocene from around 6000 BC-1000 BC, and with increasing intensity.

To the put the early impacts into chronological perspective, I would make the following points. 8000 years ago represents the approximate point at which agriculture was established and agriculturally-supported permanent villages appeared in several parts of the world. This is the period of the first villages in China, focused on millet cultivation and with domesticated pigs on the North Chinese loess plateau and the Yellow river valley. This appear in several places from Gansu to Hebei to inner Mongolia. By this period there is clear evidence fo established cultivation of domesticated maize and squash in southern Mexico, and various crops being farmed on the northwest coast of Peru, peanuts among them, and these had there origins in Amzonia east of the Andes. In West Asia this is the period of well-integrated agroo-pastoral systems with a whole suite of crops (wheat, barley, flax, pea, lentil) and animals (cow, goat, sheep horse). This period (9000-8000 years ago) see the rise of not just permanent villages around the Near East but large "mega-sites", for example Catal Hoyuk in central Turkey, which supported permanent population in the 1000s (~6000 is one estimate of site's size). This may not sound big in modern terms, but when you consider that hunter-gather bands are on the scale of 30-40, with large seasonal gatherings at maybe twice or 3 times that at most (i.e. there were unlikely to ever be more than 100 people in one place at one time for even for a seasonal festival for the 150,000 or so years of Homo sapiens history prior to that), then a few 1000 people living together in one place, supported by local agriculture, is a big difference. 9000-8000 years ago is when farming started to spread from the Near East reaching Turkmentistan, Pakistan in the east by 8000 (which big permanent villages established in those areas) and reaching in SW Europe (Greece, and Balkans. The establishment of agriculture on several continents means sustained transformations of local landscapes and ecosystems. Of interest is that this roughly the time point at which some, such as Bill Ruddiman, have inferred that global carbon-dioxide level just start to divert from the expected interglacial trend (see his recent Earth & Planetary Sciences review paper and his Real Climate blog post). This lends extra importance to the 8000 BP landmark. Our paper is not about the greenhouse gas story, which involves lots of complicated factors of the carbon cycle, but we are certainly with Ruddiman in as much as one needs to factor human activities into the equation at that time when considering global carbon issues since 8000 years ago.

Another landmark for me is in the 5000 BP sort of timeframe. This is the period which sees the beginning of tropical savannah farmng, in subsaharan  Africa, inner India, also the central and eastern USA, mainland SE Asia. This sees the major spread of rice out of China and into SE Asia (see my previous blog), and the land area in the Old World (Africa and Asia) that support pastoralism (sheep, goat, cattle) doubling. This period sees the spread of agriculture with llama-keeping to high elevantions in the Andes, and by about 4500 BP the establishment of maize-beans-squash farming in the American southwest. In these more marginal environments the impact of early farming on erosion and local flora may have been more severe than in naturally better-watered regions. In the established agricultural centres (Mesopotamia, Egypt, the Yellow River, southern Mexico) this is the period in which the urbanism get establish (slightly later in Mexico perhaps) with all sorts of new demands on agricultural intensification and specialized production to support urban populations that do not carry out their own subsistence. The rise of major textile and metal industries at this time, especially well documented in Mesopotamia and Egypt, means larger herd of sheep that were not for eating, land for flax that was not for eating, and increase wood fuel demands for bronze furnaces (and new materials like Faience or in China proto-porcelains). Bronze is a bit later in China and SE Asia (after 4000-3500 years ago), but still falls into this time horizon generally. There is a new scale in deforestation to go along with the establishment of agriculture on all continents and subcontinent (except Australia or the polar regions). In Ruddiman's Greenhouse gas story this period is when global methane is meant to diverge from expected interglacial trends. In other words after 5000 BP both the greenhouse gases have started to look unnatural. He has hypothesized that this was to do with the spread of wet rice, and elsewhere (in a Holocene paper) I have argued that one also must count the cattle which spread like wildfire through the tropical savannahs of Africa, India and perhaps SE Asia at this time (see previous blog). This is also roughly the dairying revolution in Europe, not when people first used a bit of milk, but when people began to herd cattle to specialize in milk production (and European people evolved adult lactase enzymes): this may have also been a upturn in animal herd density. How human activities translate into greenhouse gases is complicated, because of interacting carbon sinks and sources, and not the point of the "Used Planet" paper, but the implication of out paper is that human activities should not be ruled as a contributing to global processes

By 3000 BP or so it is hard to deny human impacts, although I would put the significant shift earlier. In archaeological terms 3000 BP roughly corresponds to the Iron Age. The thing about Iron is that is much more egalitarian than copper alloys, in as much as Iron ores are really widespread and found in all regions. Mesopotamia had import copper from Oman or distant parts of Turkey, and time from Afghanistan. Africa south of Egypt and Nubia never really had a bronze age, nor did southern India, but they all took to Iron because iron ores were available. Everybody had iron ore on their doorstep. But iron smelting requires twice as much wood fuel (at least) as copper. One set of wood fuel just to turn wood into charcoal, and then charcoal represents a second set. So a upturn in wood demands and deforestation. There is no Iron Age in the Americas but Peruvian and Mexican metallurgy (copper, gold) are full swing by this time. The other thing about the centuries after 3000 BP is the upscaling and cities and the first empires. Think Assyrians, followed by Persians. The Qin emperor of China may not unify China until the 3rd c. BC but he comes at the end of process of expansionary attempts by various rulers ("The Warring States", etc). This is the era of Maya pre-classic (in southern Guatemala) and Olmecs (on the Gulf coast of southern Mexico), which represent first urban-like communities and kingdoms in Mesoamerica. In South America this period sees the arrival of farming on the shore of Lake Titicaca (which was to become a focus of intensive farming and urbanism of Tiwanaku about 1000 years ago), and first big ceremonial centres, foci of dispersed but farming growing populations, at sites like Chavin du Huantar. This period sees the founding of sites that were to development into cities in the Niger river in west Africa, the earliest phases at place like Jenne-Jeno and Dia. In short, all over the work human population densities increase, proportions of the populations not engaged in their own subsistence increase (but are still a miniscule minority bu modern western standards) and technologies requiring heavy wood fuel use increase in scale and global frequency. 

Time for Big Archaeology

When I was asked by the journalist from New Scientist where I put the start of the "Anthropocene" I suggested 5000 BP. By 3000 BP there is certainly no doubt (the date chose by the headlines in other coverage). Erle I know does not want to commit to any one date for this transition, and I think we would both emphasize that there have been several step changes, often different in timing in different regions, in the relationship between human population and landuse and land transformation. These changes and landuse relationships need to be better-studied and better quantified. Archaeology, which I represent among the contributors on the PNAS paper, has a lot to contribute here. Archaeologists in a sense have been gathering such data without realizing its relevance to issues of long-term global change, and archaeologists are generally very region and period focused-- archaeologists, we might say, have their heads down holes-- with less awareness of the macro-scale and really long-term comparisons. I think that it is time for that to change, and I hope that more archaeologists will start see how their evidence can contribute to better models of long-term landuse and ecosystem management. It is time for archaeologists to become a bigger part of these discussions. 

We need to get some BIG ARCHAEOLOGY going. Then we can return to the issue of when the Anthropocene began.

Thursday, 21 February 2013

Earlier sorghum in Sudan

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

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

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

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

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

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

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

Wednesday, 20 February 2013

Unravelling agricultural packages

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

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

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

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

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

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