The drug before the calorie? Some hazy thinking on Cannabis domestication

Many have been excited this week about headlines claiming marijuana (Cannabis) was domestication in China 12,000 years (making it the first crop in East Asia). As the reputable journal Nature put it "pot farming first blossomed" in China 12,000 years ago. But was it so? How clear or otherwise in the evidence? Is it really farming? The study by Ren et al in Science Advances paper is important-- it represents the largest collection of Cannabis genomes sequences, it provides some important information on subpopulations and genes that have been selected for differently in fibre hemp from drug strains. However, I finds is dicussion and conclusions riddles with both imprecision (about chronology, geography and cultures) and inaccuracies. So what should be questioned?.

A major source of inaccuracy lurks in sampling and geographical representation. This is compounded by the fact that in many countries growing or collection or transporting of Cannabis is illegal (although legalization is on the rise). Thus traditional drug varieties have not been sampled across most of Central Asian countries, Afghanistan, Russia, Iran. It should go without saying that sampling in the modern time plane will miss past diversity that has been lost to ha bitat destruction and environmental change; such a problem, for example, has plagued some genetic studies of rice-- as wild population no longer exist in the regions were it was first cultivated (such that a modern genome map is not a map of origins). But even so the limited sampling across free-growing (feral/ wild) outside of South Asia and China) is notable. Compare the map of Ren et al (above) with that from the Cannabis book by Clarke and Merlin (2013), which highlight how much more wild/feral diversity there is out there across Asia and eastern most Europe, including 'wild' populations south of ot eh Caspian sea in Iran and along the Volga River in Russia. Even the map from Clarke and Merlin is incomplete with regards to Afghanistan where Vavilov collected apparently wild drug types of Cannabis (C. indiva var. afghanica) in the 1920s.

Given how few wild/feral samples that they have can they really rule out multiple domestications. Genetic analyses often err on the side of single origins. Simulation work (Allaby et al 2008 PNAS) have shown that this will be true even for crops with multiple origins, because gene flow among crops of different origins and pruning of lost branches (not sampled or not surviving to present). Their analytical methods are more modern and more sophisticated but I am not sure they can rule out multiple origins, and they certainly can’t rule out origins from regions not sampled or where wild populations are extirpated (e.g. Japan). Also wild populations (lets assume there are some in central Asia) can be heavily inundated with gene flow from crops over time make their original dinstictiveness hard to find in modern genomes.

A major issue is imprecision in dating. Genomic dervied estimates will never rival radiocarbon dating on archaeobotanical remains. Their proposed date of origins (is this domeatication?) has 6000 year error margins. And it not clear what they date! Was a divergence  between two wild population separated due to climatic vicariance at the end of the Pleistiocene or start of the Holocene, or is it meant to be the domestication bottleneck? The equivalent genomic dates for Asian rice domestication are ca. 18,000 BP and something close to 10,000 for African rice. Both of which are way off. African rice is domestication at more like 3000 BP and Asian rice at more like 8000 BP (of course it matters whether one is talking about the beginning or end of a process, as domestication takes 3000-4000 years in terms of morphological evolution/ genetic fixation.

By contrast archaeological dates are much more precise, at worst with 100-200 year error margins, but Ren at all quote these very imprecisely. It is as if they wish archaeology was less precise, but even then it would not approach the dating imprecission attached the the genomic dates. The say "~3000 BP" for the appearance of Cannabis in India, but if we are rounding off it is closer to 4000, as it occurs in the Late Harappan horizen (3900-3500 BC). Although Indian epics are not well dated some parts of them are from oral traditions that probably also date around then and make reference to Cannabis- I think Ren et al refer to this as ~2000 BP. Cannabis comes to India in my view as part of “Chinese horizon”, which is really just piece meal adoption of various things coming in via central Asia including crops and technologoies (harvest knives) from China, peaches, apricots, millets, japoonica rice. For discussions of this see, for example Fuller & Boivin (2009); Stevens et al (2016). Whether or not it arrived in South Asia earlier, or was already utilized from wild populations in the Himalayas, does not really make much differece to the whether or not cultivation began at the start of the Holocene in China. The imprecision in genetic dating, however, makes it about as likely that domestication took place around the start of the Yangshao period (~5000 BC), the period when we generally see the ending of the millennia long domestication process for the native China millets (

They are also quite imprecise about geography: are they suggesting a NW China (Xinjiang) or NE (Chifeng) source? And if either of these then discussion of early cord-marked pottery in South China (mostly south the Yangtze) is really not relevant, and yet they discuss this as though it indicates the use of hemp cords-- for which there is simply no evidence. 

Cannabis is undoubtedly an important crop brought into cultivation early in east Asia, esepcially for its medicinal and/or social uses, but becoming important for larger oily seeds and fibres over time. But in my view its development as a crop either parallels or is even inspired by the increasing importance of cultivation of other taxa, like the China millets. And this process could easily have played out multiple times-- perhaps in very different contexts in parts of central Asia or Jomon Japan, even amongst non-farming cultures. While genomic data will contribute to this, modelling such data really requires some calibration points in time and space, which will ultimately come from archaeobotany.

Chicken origins: closing in with new genomic evidence

wild Gallus gallus spadiceus

The past week saw the publication of a landmark genomic study on chickens (Wang et al 2020, Cell Research), which clarifies much about origins, and focuses some questions for further research. For a news summary see Lawler's Science piece.

It is transformative because it includes a substantial sample of genomes from across all of the wild subspecies of Red Jungle Fowl (142 wild red jungle fowls) and other wild Gallus species. The first thing to note is that is does support the reality of these different wild taxa. They aren’t merely geographical feral populations derived from escaped chickens, but they are differentiated from each other, making it reasonable to ask which population(s) are ancestral to domesticated chickens. In addition there has, of course, been gene flow via introgressions with domesticated chickens, but this has been on a more limited scale. So the answer to big question (of origins) appears to be Gallus gallus spadiceus. G. g. spadiceus is geographically focused on Burma, Yunnan, Guangxi, northern Thailand and bits of Laos. This struck me as the most surprising—this geographical derivation. If one favours a Chinese origins then you would look to G. g. jaboulliei (of the Guangdong and Fujian and perhaps further north in the past); if one favours an Indus domestication then one looks to G. g. murghii. Previously I have accepted the likelihood of an Indus Chicken domestication and a spread through India in post-Harappan times (e.g. Fuller 2006). This now appears unlikely. Instead it probably means that wild jungle fowls attracted attention in the Harappan period as pretty birds that were captured sometimes, traded, etc.,but not really domesticated subsistence species. Presumably the first Bronze Age Mesopotamian and Ramesside Egyptian “chickens” were actually pet wild jungle fowl-- fancy exotic birds-- and not connected to chickens as we understand them now. The "multi-colored birds of Meluhha" that were imported to Mesopotamia at the end of the Third Millennium BC from the Indus region, are plausible painted ivory statuettes of murghii jungle fowl (see, e.g. During-Caspers 1990).

These new genetic data also make it clear that as chickens spread out of their northern SE Asian homeland they did pickup some genetic material through introgression with local wild jungle fowl (such as G. g. murghii in northern India) and even grey jungle fowl in South India (the source of yellow legs: G. sonneratii). This process can be called “introgressive capture” and it is widespread in most livestock and many crops. This process has sometimes confused genetic studies into inferring multiple domestications, but with more genomic data it can now be disentangled (see Larson and Fuller 2014). 

It is also quite exciting that they have some genetic loci that might be under positive selection as part of the domestication process. One of the real mysteries with animal domestication is what constitutes domestication in a genetic sense in terms of adaptations. In plant it is well known that certain genes for seed dispersal, growth habit, dormancy, grain size, etc. were selected. We can find this evidence genetically and tie it to morphological changes in the archaeobotanical record. There is so far nothing equivalent in animals that links genetic loci to the morphological adaptations we see with animal domestication. So on a more theoretical level this may be the first step to actually starting to unravel the genetics of animal domestication.

These raises fascinating questions then about the contexts in which G. g spadiceus was domesticated—what kinds of human societies and agricultural economies did it interact with in its wild form and how did it get incorporated into ecology of human settlements. Equally at what period and in what contexts did these early chickens then spread. Their phylogenetic results suggest the first wave of chickens spread through SE Asia and SW China only.  Sadly we know little about the Neolithic in Myanmar, or Guangxi or Southern Yunnan; we do have some data from northern Yunnan where Chinese millet and rice agriculture (with pigs) arrives from the North around 2600 BC. One presumes there was some further Southern diffusion towards the China/Burma borderlands. And perhaps it was in these borderland zones where early sedentary rice/millet farmers began to isolate some G. g. spadiceus populations that came feed within the human settlement niche. As hypothesized in Larson and Fuller (2014), chickens likely followed a commensal pathway to domestication. But we now need to refine the map (right). And work out when this happened.

There estimate of the age of the last common ancestor of domesticated chickens and G. g. spadiceus 9500 BP (+/- 3000). But I would regard domestication any time between 10000 BC and 4500 BC as highly unlikely. As the authors themselves not in the first paragraph of their discussion such genetic estimates of domestication age tend to be over estimates (by upto 15,000 years!), so these are not exactly reliable.  In fact I would regard the tendency genetic coallesence ages as to tell us anyting about the timing of domestication to be a highly  misleading tradition that is entrenched in genetics but has little to back it up. Take the example of rice (Oryza sativa), where the genetic estimate of last common ancestor of cultivated rice and modern wild population is ca. 18,000 (Choi et al 2017). But archaeologically even the more generous estimates are ~10,000 (and more like 7,000-6500 by more cautious approaches). I suspect a more general problem is that what is being picked up the last major cladogenetic event that structured wild populations and not domestication itself. Often this can be expected to be something climatic, so 9500 BP is telling us something about how Early Holocene climatic changes—which restructured vegetation in big ways—restructured wild jungle fowl. Then it was one of these localized population that millennia later got domesticated. In all likelihood that localized population that was actually domesticated won’t exist anymore. It is also worth noting that the reality of domestication bottlenecks is itself somewhat dubious and is in the past year or two come to be questioned. Where ancient DNA is available (e.g. maize, sorghum, barley) it is demonstrable that no such bottleneck occurred and age estimates (see Allaby, Ware and Kistler 2019) that conceive some sort of a bottleneck may not be really telling up about domestication. 

Given what we know of the archaeology of SE Asia, one would tend think the initial  domestication and spread of chicken is unlikely earlier than the grain-based Neolithic that starts around 2500 BC (in southern bits of China) and reaches southern Thailand at 2000 BC. However, as far as I know there are no archaeological chicken finds at early sites. So I wonder whether the first spread of domesticated chicken might represent a secondary later spread perhaps closer to 1000 BC (the period when Bronze working spread southwards from China); this might also be the period when new crops spread like sticky rice. It may be that at that time chickens also spread rapidly via trade routes to India. I have long argued (e.g. Fuller 2007) that in South India the Dravidian linguistics suggest arrival of chickens after the South, South-Central and Central languages had fully diverged (which is something like 3000 years ago). Not long after this there are good chicken terminologies in Sanskrits and Prakrits from the 1^st Millennium BC, so it makes sense that chickens really only became established as livestock in India at around that time, and of course it is the later Iron Age when they first turn up in the west , such as the Hellenistic era evidence from the Levant (Perry-Gal et al 2015), or as an exotic animal in western Europe (Sykes 2012).

Structured diversity in tea does not mean multiple domestications

Genetic population structure of tea.

When and where were tea domesticated? And how many times? This is a question I get asked sometimes, and a paper published a few years ago was just brought to my attention that claims to have genetic evidence for three separate domestications, by Meegahakumbura et al. (2016) in PLOSone. I disagree. The paper convinced me of quite the opposite. It remains entirely likely that tea was domesticated only once in ancient times, even if there were widespread use of wild tea leaves across their wild range by people who encountered them-- but a key problem remains determining what that wild range was. The Meegahakumbara paper is an interesting one in terms of raising the question as to how much underlying geographical structure there is in the genetic diversity of tea, and how this relates to different cultural traditions of use, and which (if any) can be regarded to evolving into domesticated forms. But in the end there are severe limitations to their study. Despite some sampling from "wild" populations in India and China, as well as cultivars, there is a lack of samples from in between (northern Vietnam, Myanmar and presumably Laos, which are all presumably within the range of wild teas. What is really at issue is whether or not the large tree forms of tea are primarily wild (and recently managed or cultivated) or represents a distinct domesticated form, and this in turn raises the issues of what is "domestication" in tea. Domestication implies morphological adaptations, underpinned by genetics, which have been favoured through the propagation over generations by people. We know full well what this entails in cereals and seed crops (see, e.g. this Annals of Botany article); we can propose what is involved in tree fruits (which are harvested for fruits and presumably early on cultivated from seed: see "long and attenuated"); and we can also propose what is common about domestication in tubers and other vegecultural crops (see this recent Annals of botany article). But what about tea? Since tea can be propagated by seed or by cuttings it might share some similarities with either tree fruit or vegecultural domestications, but its use for leaf harvesting makes it quite different. Characteristics that might fit in the vegecultural domestication syndrome, include increased proportion of edible (leaf) to inedible (trunk) parts, and more asynchronous production of those. In developmental terms there appear to be selection for dwarfism-- smaller leaves, smaller stature, and more compact growth, which together with human management give teas their very trimmed hedge look (below).

Tea (C. sinensis sinensis) cultivation in Zhejiang
(Photo: DQ Fuller, 2004)

So what did Meegahakumbara et al. find? They demonstrated 3 distinct populations, and a 4th (lasiocalyx) that looks admixed between the Indian and Chinese tree teas (Figure at top). Truly domesticated tea (C. sinensis sinesis) looks to a be a strong clade. That is (in my view) the only really domesticated form. It has distinctive morphology (dwarfism).  It could already be distinct by the Han period, or at least under selection, since small, immature leaves are among the grave goods in the Yangling tomb of a Han Dynasty queen in Shaanxi, indicating trade from distance Yunnan already by 2200 years ago (see this Scientific Report). While it could be that tea was still a wild utilized plant, it might make sense that by this period experiments with cultivation had begun with an ancestral form of C. sinensis sinensis. It is also plausible that some cultivation developed in parallel with the distinct species C. taliensis, but its cultivation never spread beyond the Myanmar-Yunnan border regions (see, this paper on taliensis tea), so it is less relevant to the main domestication story of tea.

But is there any reason to assume that the distinct populations of large tea forms of tea, which they refer to as Assam tea (C. sinensis assamica). They divide this tall tree tea (see left) into two geographical groups (Indian assamica and Yunnan assamica, which leads to the somewhat oxymoronic terminology of "Chinese assam tea"). I do not see any reason in these data, or rationale provided, to not assume that Chinese tea is a domestication bottleneck from the Yunnan tree tea (assamica sensu  lato). The Assam and Yunnan populations of tree teas are distinct as one would expect of any geographically distant populations of a wild species. Trees of this assamica tea are also wild through large parts of northern Vietnam (see Zhao et al. 2017), and I would expect them also in Laos and parts of Myanmar.  In India these tree teas were used from the wild by a few local minority tribes prior to the British introduction of tea drinking and Chinese domesticated tea to India. But these were presumably only ever gathered wild. These Assam tree teas only came into cultivation (equivalent to pre-domestication cultivation) in the colonial era.  though they have now been cultivated by ~200 years, there seems no basis to assign them to domesticated status.

The Yunnan tree teas (What they call Chinese Assam tea) are presumably also native to the forests of parts of Yunnan, where they were also used by indigenous people. In this region their cultivation and management has continued while perhaps unmanaged populations went extinct in the wild. They could still be also the source of domesticated C. sinensis Chinese tea, or related to that source.

Tree (assamica) tea, leaves and fruits
(after a photo in the Hangzhou Tea museum)

The Cambod teas (C. lasiocalyx) look to me like part of the structured variation of a wild species that included geographical populations: i.e that the tea trees of Yunnan, India and adjacent Northern SE Asia (Vietnam, etc) borderlands should probably all be C. assamica (or  C., sinensis assamica, as taxonmically described by Zhao et al. 2017).  In their K=3 structure analysis these are grouped with Indian Assam wild tea trees, so it may be that lasiocalyx is just a northerly somewhat smaller variant of wild tea trees. It is plausible that domesticated Chinese tea came from this Cambod end of the wild range, i.e. further east, like SE Yunnan and is more distance from the Assam end of the geographical variation. It is a pity their is no geographical information on the assamica and lasiocalyx populations-- in terms of where and what habitats they come from. Although with a species like this it is not really surprising if wild populations have been completely lost. One is hard pressed to identify truly wild populations of some of the world's more popular nuts, whether chestnuts or walnuts, as these trees have been so heavily anthropogenically influenced in terms of where they grow.

So the origins of tea cultivation: southwest China, some place and time still to be determined. But the use of wild tea leaves by local peoples, widespread from Northeast India through Vietnam.

On the history of tea, see especially this magnum opus by Van Driem, reviewed here.

Panicum domestication and early sedentism in Northeast China

For the past decade the Xinglongwa culture of eastern Inner Mongolia (Liao River valley) has been regarded as a likely cultural context for the domestication of common millet (Panicum miliaceum), on the basis of significant quantities of Panicum grains associated with some of the many houses excavated at the site of Xinglonggou (see, e.g. Zhao 2011). Recently, new excavations by a Chinese-Israeli collaborative team (with some London archaeobotanists) explored parts of two new small settlement sites of this period, Jiajiagou (5950-5700 BC) and Tachiyingzi (5550-5450 BC), including intensive flotation, have been published this week in PLOSone. At both sites a single dwelling was excavated and sampled, and the archaeobotanical data indicate a predominance of wild plant foods, including walnuts, apricot endocarps, hawthorns, Phellodendron, but Panicum miliaceum is also present is small quantities-- 16 in total at both sites, with more and higher ubiquity at the later site. Most of these Panicum grains are more elongate then plump, with size and L/W ratios that correspond better to Panicum miliaeceum subsp. ruderale, known today as a weedy species but probably descended from, or at least comparable to the origins wild progenitors. We take this to suggest that grain size/shape was still under going evolution over the course of the 6th millennium BC, and thus it may not have been finished evolving into its domesticated form. This fits the now recurrent pattern of protracted domestication processes in cereals (explored previously when "de-centering the fertile crescent", and demonstrated more statistically in Allaby et al "Geographic mosaics and changing rates of cereal domestication").

These data, along with those from Xinglonggou indicate that while Neolithic sedentism had been established in Northeast China by the early 6th Millennium BC, the evolution of domesticated Panicum miliaceum and the establishment of agricultural economies still took rather longer. Another conclusion of the paper is that sedentism and this domestication process took place during stable and quite conducive climatic conditions. This argues against the hypothesis that domestication in this case was driven by climatic stress, or that it should be linked to major climatic fluctuations that characterize the start of the Holocene (a hypothesis promoted by Bar-Yosef 2011, amongst others)

It is worth noting that the later site (Tachiyingzi) also has the presence of a few Setaria italica and S. viridis, and a couple more plump grains (pictured above). While none of these grains was directly dated there is some possibility that more fully domesticated grains will prove to be intrusive. Amongst the direct AMS dates, on wild foods, four proved to be 6th Millennium BC, but one date on fragments from lotus seeds turned out to be intrusive and late Bronze Age. This highlights the need for more direct dating of crop remains, a point highlighted by recent debates over the arrival of wheat in Late Longshan China, for which numerous false alarms have been dismissed via direct radiocarbon dating (see "Assessing the occurrence and status of wheat in late Neolithic central China: the importance of direct AMS radiocarbon dates from Xiazhai").      

So the case for a millet domestication in Northeast China in strengthened. This does not rule out other dometciation centres-- which there must have been for Setaria italica at least, and perhaps Panicum milieceum. Domestication can be regarded as taking place alongside and after the emergence of sedentism, but further data are needed to better document this, and to assess the extent to which initial cultivation  of wild millet was linked to the shift to sedentism or not. 

In Memoriam Alison Weisskopf (1960-2018)

Alison and Oryza nivara in
Orissa, Sept. 2010

Alison Weisskopf (1960-2018), passed away peacefully in hospice in the presence of her immediate family on 11 January 2018. She was a beloved colleagues at the Institute of Archaeology, a fixture in the archaeobotany laboratory for many years and a leading figure in archaeological phytolith research, respected globally. Her research legacy is substantial as her work takes a distinctively ecological assemblage approach to reconstructing rice cultivation ecology as well as crop processing. This has proved innovative and has proved fruitful, and can be expected to continue to inspire further research and agricultural ecology approaches to phytoliths around the world. Despite first being diagnosed with late stage cancer in 2010, she soldiered on was at her most productive as a researcher over the past half dozen years, which is readily evident from her publications list. 

Bangladesh, Nov. 2013: ethnobotany

She has made lasting empirical contributions on archaeological research in China, Southeast Asia (Vietnam, Thailand, Cambodia), and South Asia (Bangladesh, Sri Lanka, India). Through ethnobotanical fieldwork (in India, Thailand, Laos) and archaeological projects (in China, Bangladesh, Fiji), many further collaborations she was a key colleague in many international networks and she leaves behind many friends around the world.

Alison joined UCL as a BSc Archaeology student in 2000/01, essentially a career reboot as a mid-life adult. She demonstrated a strong affinity for environmental archaeology and archaeobotany from the beginnings of her studies. She took my “Plants and Archaeology” in 2001/02, and a new course on “Origins of Agriculture” the following year. Her BSc dissertation on phytoliths (“A study of the phytoliths from the late Bronze Age site of Krasnoe Smarskoe, Samara Valley, Russia, and the information they provide on agro pastoral economies and environments”) supervised by Dr. Arlene Rosen was passed with distinction in 2003. In receipt of a AHRC scholarship, she continued her studies in the MSc Palaeoecology of Human societies, with a dissertation on “An investigation of the Neolithic ash mound and settlement at Sanganakallu in the south Deccan, India, using phytoliths and macro-archaeobotanical material”, combined analyses of plant macro-remains and phytoliths and received a distinction in 2005.

Liu River, near Huizui, Henan, China, 2006

She began her PhD in 2005, again funded through an AHRC studentship. She submitted her PhD thesis, Vegetation, agriculture and social change in Neolithic north central China, a phytolith study, in 2009 and was awarded her doctorate in 2010. Her doctoral research took her on field to China several times, such as to the sites of Huizui and Xipo, where she worked alongside colleagues including Arlene Rosen (now University of Texas at Austin), Gyoung-Ah Lee (University of Oregon) and Liu Li (Stanford University). Her PhD represents years of dedicated laboratory work. She later published a revised version of her PhD as a monograph in 2014.

Sept 2010: Sampling Oryza rufipogin in Orissa, with
Rabi Mohanty and Mukund Kajale

In 2009 she took up a post-doctoral research associate position funded as part of a NERC project  'The Identification of Rice in Prehistory' (2009-2012), which came to be dubbed the Early Rice Project, and spawned follow on research projects, including 'The Impact of Evolving of Rice Systems from China to Southeast Asia' (2013-2016), and 'The impact of intensification and de-intensification of Asian rice production: transitions between wet and dry ecologies' (2016-2019). During a intermission between the first and second NERC projects she secured funding through a British Academy small grant to explore comparisons between phytoliths and diatoms in rice paddy soils, and she received a travel grant from the Thai Ambassador to the UK for ethnobotanical fieldwork on non-rice plant use in Thailand. Her research, and her development of phytolith approaches to rice cultivation ecology was central to these projects and their success. This sent Alison into the field to study modern rice ecologies, both cultivated and wild, in far flung parts of Asia, from central China to Laos and the highlands of northern Thailand, through Bangladesh and Assam, remote parts of Odisha state in India, and the Western Ghats mountains along western coast of India. Her unique experience and expertise has meant that she attracted archaeological collaborations and samples for analysis from an even wider range of countries. She authored 29 academic papers or book chapters, in addition to 1 monograph, with many more still in the pipeline. For a list her published academic papers and chapters: see here.

While many have approached phytoliths typologically and metrically to attempt to look at morphological differentiation between domesticated and wild rice (e.g. bulliforms or double-peaks), Alison’s innovation was to focus on the plant communities that occurred with rice and were sampled in harvests, sub-sampled in crop-processing and ended up to systematically recorded, quantified and discriminated in the micro samples from archaeological sediments. In her fieldwork and analyses, her focus on plant communities and how human communities intersected these is evident. It offers a legacy for phytolith archaeology.

Ethnobotanical fieldwork in Thailand,
Nov. 2012: with Katie Manning.

Alison, herself was a key node in our community. Having worked in the archaeobotany lab as a post-graduate student and post-doctoral staff member for some 15 years, she was often the focus of discussions, both of science and of social life. She has also trained and supported numerous students, offered countless cups of tea, words of encouragement, and a warm sense of humour. She is warmly remembered.

I invite comments to be posted to this blog by those who knew and miss here. And I append below various photos of Alison in action.

Gyoung-Ah Lee and Alison on the Liu river, Henan, China (2006)

Alison collecting rice weeds in Bangladesh, Nov. 2013.

Nov 2011: Northern Thailand: Cristina Castillo (Left) and ALISON (right) with Karen rice farmers in Northern Thailand

Ellie Kingwell-Banham and ALISON WEISSKOPF in Maharashtra, India (Sept. 2010)

14 July 2004, IoA foyer on lab botanical shirt day: Phil Austin, Emma Harvey, Meriel McClatchie, Jon Digby, ALISON WEISSKOPF, Emma Jenkins. Alison was an MSc student at the time, and was apparnelty the original source of the idea for this day.  Below a full photos of the whole lab group.

Dorian, ALISON, and Deepika Tripathi at the IWGP in Thessaloniki (2014)

Indo-Pacific Prehistory Association conference, Siem Reap, Jan. 2014. Participants in session on "Foraging and Farming". Alison fifth from Left.

Early Rice and Its Weed Flora, Symposium at Peking University May 2011

Buckwheat origins remain elusive

Harriet Hunt and colleagues have provided a new critical assessment of data and potential data on origins of the buckwheats (Fagopyrum esculentum and F. tartaricum) in a Vegetation History and Archaeobotany article. Buckwheat is an important carbohydrate crop at high elevations in Asia, as well as parts of Japan and Europe, but it has remained quite elusive archaeobotanically.

It is absent from the many large charred seed assemblages in central China, or the charred and Fagopyrum identifications as distinct from many other Polygonaceae. Even if we accept all identifications of Fagopyrum, there are several wild taxa in this genus that will have nothing to do with the cultivtion of the crop. They consider how reliable stratigraphic dating controls are for many of pollen sequences, but even so, pollen never allows for the direct dating nor direct association with human activities that archaeobotany does.
waterlogged assemblages of the Lower Yangtze. In the Indian Himalayas where it is traditionally an important crop, finds have been few, restricted to later First Millennium BC and medieval finds in Nepal. The new review by Hunt et al has compiled evidence from archaeobotanical macro-remains, a few reported based on apparent archaeological starch remains, and the many more reports from pollen diagrams. They take a threshold of fairly high quantities in pollen diagrams, but less clear is whether one can always rely on

Distribution of wild Fagopyrum species (Campbell 1997, IPGRI)

One of their key conclusions is that the past distribution of wild Fagopyrum species, including the wild progenitor of F. esculentum, was more widespread. Extending further north, even to the north of Sichuan. This certainly seems plausible and could support a domestication in Sichuan north of where modern wild populations (in NW Yunnan) have tended to suggest domestication. They point to a few pollen cores from Shaanxi and Gansu apparently 5000 years old or more, as perhaps relating to early cultivation-- although the absence of grain finds in these regions which have had considerable archaeobotanical sampling in recent years surely calls into question the paper's tentative conclusion that cultivation had begun before 5000 BP.  Another problem with many of these pollen cores is the reliability of dating. For example, the pollen sequence at Xishanping, which was collected through an archaeological sequence, has a number of inverted radiocarbon dates, suggesting reworked residual materials, but the short (and old) chronology followed by Hunt et al. removes the out of sequence dates-- which would make sense if this were a lake core with constant sedimentation, rather than a sequence 5 varied archaeological layers. A safer, and archaeologically logical reading of the original stratigraphy (see raw data in Li et al 2007) date makes the buckwheat pollen occurrence only slightly older than 3000 BP. (The short chronology also implies that wheat was present at this Gansu site before 2600 BC, which does not fit with the accumulated evidence on wheat's arrival in Gansu (as noted already in a previous blog), especially AMS dates (see Stevens et al 2006).

A more critical reading of the dates in the sequence of the earlier pollen cores find little support for any substantial quantities of Fagopyrum pollen before around 4000 years ago, so I stand by previous inferences of domestication taking place around this period. Nevertheless from the Second Millennium BC onwards, some archaeological seeds of Fagopyrum, possible supported by starch finds points to cultivation of this crop, with a focus on west Central China and southwest China, consistent with early dispersal around the eastern front of the Tibetan plateau. Nevertheless with central and eastern China, the lower reaches of the Yellow and Yangtze basins buckwheat appears to have been absent, from macro-remains (and supported by early Chinese written sources). In this regard some of the apparent pollen reports from natural cores in the Lower Yangtze seem unlikely to represent cultivation. Despite being clearly present among the crops known in early Tibetan languages (and many related Burmic languages), and having likely been loaned from a Tibetan language into Chinese since the Han dynasty period (see Bradley 2011), buckwheat remains elusive in Asian archaeology.

This new paper by Hunt et al. provides a solid starting point for new research on buckwheat origins, with a thorough compilation of pollen and archaeobotanical evidence (in China)long with some critical thinking on the rather limited genetic data.

Early Rice Project symposium last week

Last week we hosted in London a symposium for the Early Rice Project, 

Investigating the evolution and impact of rice cultivation through the later prehistory of monsoon Asia. We brought in colleagues and collaborators on the archaeology of India, Southeast Asia and China, from countries across several continents, and had a success full exchange, not just on the archaeobotany of the region and new data (much of it generated at UCL through our NERC and ERC projects), but also on the stories of domesaticated fauna, our current understanding of Neolithic spread processes, Mesolithic persistence, demographic growth and the emergence of complex societies and irrigation. What is clear is that there is much new to say about rice, when it first arrived in several regions of monsoon Asia, and as it was transformed into the cornerstone species in the subsistence base of large complex societies. Nevertheless the meeting highlighted also the major gaps in empirical evidence, both geographically and chronologically. We hope to be able to pull this together for publication to further broaden out our dialogue on what we know and what we need to know. There has certainly been a rapid increase in data as the chart (below) of published, or recently counted archaeological spikelet bases indicates (from my introduction presentation)..

Some recent outputs from the Early Rice Project include publication of ancient DNA from charred rice grains from sites in Thailand and India (Castillo, Tanaka et al.), which add some flesh on the skeleton of the Proto-indica hypothesis; and publication of the first of a new generation spatial modelling of the early geography of rice, this one aimed at deducing the most like region (or regions) from which rice originated and spread, in particular the originals of early japonica rice that was so important to the Neolithic developments in China and throughout Southeast Asia (Silva et al. in PLOSone).  See also, the paper on phytoliths as a reflection of weed flora (Weisskopf et al 2014), the first of several in the pipeline that will illustrate new and more robust approaches to determining past rice ecology.

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.

Unravelling agricultural packages

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

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

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

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

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

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

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

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

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

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

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

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

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