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).

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, 'Leo' Aoi Hosoya (1967-2019)

It is with sadness that I report the passing of an archaeobotanical colleague and friend, Leo Aoi Hosoya, who passed on 10 July 2019. Our condolences go first to her family, her husband and daughter. Many archaeobotanists at the IWGP held in Lecce in June 2019 will recall her paper presented in absentia, that began with an amusing video message from Leo. Sadly her health did not improve. "Leo" was actually her adopted English name, based on her zodiac sign, as she had thought that her Japanese name, Aoi, might be difficult to manage for the English. So as Leo she became known to many of us and she played a role in international research not just through her own work (on archaeobotany in Japan and China) but through her place in international networks and networking, facilitated by good humour, friendliness and lack of negativity; she was always contagiously optimistic.

IWGP 1995, Innsbruck: left to right:
Gardar Guðmundsson, Mary Anne Murray,
Lydia Zapata, Leonor Pena-Chocarro,
Ann Butler and Leo Hosoya
 [Photo courtesy M.A. Murray]

Aoi was born 14 August 1967. Her global journey could be said to have begun with her post-graduate degrees at Cambridge (from 1992), including her MPhil and PhD. I met her when I started my Master's there in 1995 and we were lab-mates once I started my PhD in 1996. Together with Marco Madella and Victor Paz we formed a group of young researchers interested in various parts of Asia, concerned with rice, millets, etc. and how research approaches that were well-established in Europe, such as analysis of arable weed floras and crop-processing could be translated into new approaches to understanding the Asian past. Leo's work towards her PhD, focused on the Yayoi period in Japan, was very much pioneering, addressing the patterns of crop processing in rice and millets for the first time. She was among the very first archaeobotanist to pull rice spikelet bases out of flotation samples, which we later realized would be essential for studying rice domestication. But her knowledge of Japanese ethnohistorical and archaeobotanical sources also opened my mind to the rich traditions of use and processing of acorns, which very much went on to influence my thinking about nut use in the Neolithic. Her Phd was completed in 2002, but published in a revised monograph-like article in Senri Ethnologica in 2009 [PDF], its title's phrase"Sacred Commonness" reflects her strong interest in relating the mundane of crop processing and agriculture to greater symbolic and social patterns that run through past societies. Her interest in theorizing the social while working through empirical science remains inspiring. Her time as a PhD student in Cambridge brought her to her first International Work Groups for Palaeoethnobotany in 1995 and 1998. (See also the in memoriam of Prof. Martin Jones here).

Leo Hosoya, Dorian Fuller, field trip
during the IWGP 1998, Toulouse, France

For several years, Leo was a post-doctoral research associate at the Research Institute for Humanity and Nature (Chikyukan) in Kyoto. There she was part of the team of a project "Agriculture and Environment Interactions in Eurasia- A 10,000 year history" directed by Prof. Yo-Ichiro Sato, where I was lucky enough to be an invited researcher in 2007 and 2009. She was also part Junzo Uchiyama's Project "NEOMAP", which was looking comparatively on the Neolithic traditions throughout northeastern Asia. Those were optimistic times for international collaborations, new empirical archaeobotanical research and integration across various datasets. For me, Leo was ever a guide to parts of Japan and Japanese archaeology, that I would have otherwise missed. From visits to sites in Hokkaido or Aomori (such as Komakino, below left, or Kiusu, shown at the top), to a memorable trip over the mountains from Kyoto to visit the Torihama shell midden museum to chase down measurable bottlegourds (in 2009; sadly I could find no photos of anything but gourds and woodend tools from that trip- although it resulted in one joint publication on East Asian gourds). It was also a time of many food-centered parties held at the guest house of RIHN.

Leo Hosoya at back left. 

It was at this time that both Leo and I came independently to collaborations with the Zhejiang Institute on the archaeobotany of Tianluoshan, an exciting Neolithic discovery in the Lower Yangtze region made in 2004. Over the years of 2006 and 2007 we made a few tips each to the site to work on sieving and sorting soil samples for plant remains to document the extensive wild food use at the site and the many rice spikelet bases, which lead to recognition of an assemblage in which rice was still undergoing evolution of domestication (another joint publication in Science). This work built on Leo's early efforts both of pulling rice spikelet bases from flotation samples that started in her PhD and of understanding acorn use, which she usefully summarized in this 2011 article.

from Left: Xugao Chen, Ying Zhang, Yunfei Zheng, Dorian Fuller
Ling Qin, Leo Aoi Hosoya, Guoping Sun

While in Kyoto, Leo took a lead roll in organizing some targeted archaeobotanical meetings, bringing together archaeobotanists, geneticists and ethnographic perspectives, first on rice (held in Kyoto in 2009), and later on millets held in Tokyo in 2012. Both lead to special journal issues edited by Leo, on rice, and millets. Subsequent meetings on rice that were held in Beijing and London very much grew out of that first Kyoto meeting. In 2009 she also came to London on a British Academy Darwin researcher's award, and conducted some preliminary work on the processing and detoxification of peach and apricot seeds, plausibly used as nuts or famine foods in Neolithic China (article pdf here).

In subsequent years she became involved in ethnoarchaeological work on rice storage in Bali (2016), which contributed to her ongoing wholistic approach to understanding rice, not just as an agricultural product but as part of social and culinary reorientation of society, as part of what she referred as the "routine-scape" (2014).  Most recently she has been one of the sub-project leaders of a major Japanese-lead international project on "Integrated Studies on Rice-based civilization" for which she has taken a multi-proxy approach to understanding of cooking pots have been used and how this changes over the course of the intensification of rice use in the Lower Yangtze Neolithic an the Yayoi in Japan. She presents some of this work in a chapter published in honour of Martin Jones' retirement, and at the symposium held in Cambridge in Nov. 2018; her chapter "Rice and the Formation of Complex Society in East Asia: Reconstruction of Cooking Through Pot Soot- and Carbon-deposit Pattern Analysis" can be downloaded as part of the book Far from the Hearth (2019). Her in absentia presentation for 2019 IWGP was on the same project, and its holistic approach to an archaeology of cooking is an inspiration for the rest of us to keep working and to enjoy a good meal and a shojiu in Leo's memory.

Please add you own thoughts and recollections using the comment function.

 I can add photos that are  emailed to me.

Rice archaeology symposium, Kyoto, 2009

Leo Hosoya chairing presentations at Rice Symposium

Leo Hosoya (centre) during discussions on the Rice symposium, Kyoto 2009. Prof. Sato (speaking)

Early rice symposium, Peking University, May 2011. Leo Hosoya in front row (second from right)

Early  Rice symposium dinner, from Left: Alison Weisskopf, Heejin Lee, Yuchao Jiang, Michele Wollstonecroft, LEO HOSOYA, Peter Bellwood, Mrs. Bellwood, Mukund Kajale 

The exCambridge Contingent at the International Millets symposium, Tokyo Museum, 2012.
From Left: Victor Paz, Marco Madella, Leo Hosoya, Dorian Fuller, Martin Jones, Xinyi Liu

More photos from the Tokyo meeting (courtesy of Tania Valamoti)

June 2008: Junzo Uchiyama, Leo Hosoya, Oki Makamura (of NEOMAP project)

Pitt-Rivers lab Christmas lunch (1998?), from L: Lila Janik, ?, Martin Jones, Chris Stevems, LEO HOSOYA, Marco Madella,, Hanna Zawadzka, Victor Paz, Dorian Fuller

Pitt RIver laboratory photos ca 1998. Leo Hosoya, seated at right

(Photo courtesy of Tania Valamoti: see appended comment below)

xx

South Indian aridification press release

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

Does starch evidence push back foxtail millet domestication?

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

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

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

Millet ethusiasts and gerbil enthusiats

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

Bay of Bengal ardification data and South Indian agricultural adaptation

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

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

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

Another IWGP theme:Food Globalization in Prehistory Across Eurasia

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

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

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

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

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

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

Pearl millet demographic modelling: 3rd millennium BC and importance of flowering time

A new article in Molecular Biology and Evolution by Clotault et al "Evolutionary History of Pearl Millet (Pennisetum glaucum [L.] R. Br.) and Selection on Flowering Genes since Its Domestication" has some exciting and intriguing results. They have done demographic modelling, using a number of different scenarios of gene flow, based on 20 random genes, and they have also looked for selective sweeps, finding evidence for strong selection on flowering-time related genes. Although they have only modelled single domestication scenarios (which is by no means a done deal in Pearl millet), they have nevertheless taken into explicit account the notion of protracted domestication process (sensu Allaby et al 2008 or Allaby 2010), with gradual fixation of domestication traits, with exponential rather than instantaneous population growth after the bottleneck. 

They find a bottleneck strength and reduction of genetic diversity that fall amongst those estimated for other crops. Their estimated time for domestication returned an intriguingly plausible 4800 years ago, just a few centuries before the earliest archaeological evidence for domestication pearl millet in the Tilemsi valley (see Manning et al, blogged previously). The evidence they have found for selection on flowering related genes makes a whole lot of sense, because the dispersal of pearl millet from a Sahelian zone southwards crossed many different ecological zones, for which adjustments in seasonality would indeed have been important.

Millet starches: towards a systematic and quantitative approach

Yang Xiaoyan et al. have published their latest key to millet starch identification (for China) in J. of Archaeological Science "From the modern to the archaeological: starch grains frommillets and their wild relatives in China". This is an important development, partly because it is the largest comparative study yet from that part of the world (although arguably still not large enough in terms of taxa and populations!), but mainly because it provides some highly plausible and well-quantified guidelines on millet starch identification. It shows quite clearly that there is quite a lot of variation within a grain, a species and genus, the Paniceae, but also degrees of underlying similarity. The take home message is that every individual starch  is unlikely to be identifiable to the same level, to species or genus, but that some may be highly suggestive (the especially large and wrinkled examples are more common in Setaria italica than in wild Setaria or Panicum), and if on an assemblage level morphometric can be used to assess the probability of certain taxa. In other words it is the first step in building a probabilistic, rather than some qualitatively absolute, determination that the Chinese millets or there wild relative were present. Interestingly it indicates that Setaria italica is in principle far more recognizable than Panicum miliaceum, which has more 'generic' millet-grass starch. This means that rather than trying to take a small sample of few starch grains and pronounce a species presence that may not be believable, a more stasticial approach can be taken to determine a degree of likelihood. Such a quantitative apporach also open the possibility of tracking assemblages changes, which in turn might be connected to other lines of evidence for agriculture change or even plausibly put together in models about population change such as domestication processes, since Setaria viridis and Setaria italica differ in their starch grain assemblages. It also raises another potential area of investigation, which require further work, environmental conditions, since there does appear to latitude-related variation amongst  Setaria italica populations studies-- so further work is needed. The this is the best step in the right direction we have seen increasingly popular Chinese starch research world.

From Burma to Japan: more on rice and linguistics

Two additional paper on rice/cereal agriculture spread and historical linguistics have been published on-line. I recall both from their presentations at Cornell in September as being inciteful and informative: one by David Bradley collects the vocabularies of various cereal crops, always including rice, but also millets and buckwheat in various Tibeto-Burman languages. He concludes that for Tibeto-Burman languages it is the Chinese millets (Setaria and Panicum) that can be most readily reconstructed back, with rice somewhat later. Of interest is that buckwheat appaears later in in common to Eastern Tibeto-Burman languages, who also share barley terms, the latter possibly borrowed from Indian languages. This may be evidence truly independent origin of high mountain agriculture in the eastern Himalayas or Tibetan plateau (buckhwheat), with agriculture in such regions instead being "additive" in the sense that local species were domesticated by farmers who moved in from elsewhere (the lowlands) with other crops (millet).

The other by John Whitman provide a synthesis of linguistic and archaeological evidence for the spread of agriculture in Korea and Japan. The image (left) is from Whitman, and summarizes the archaeological picture. He makes a good case that this fits with known linguistic and epigraphic evidence.

Previous papers in this series blogged here (more linguistics) and here (more archaeological).

African Archaeobotany 2011

I am still trying to see through my Holiday period intention of flagging some of the archaeobotanical highlights of 2011. Africa, as a continent, remains one of the archaeobotanically least known and so it worth noting a number of contributions over the past year.

One of the best itegrated studies (from anywhere, not just Africa) of wood charcoal alongside seeds, pollen and other lines of evidence for the study of changing cultivation practices, including shifting cultivation in Burkino Faso by Hohn and Neumann, which is in press but on-line.

A important book released in 2011 was Marijke van der Veen's monograph in the Journal of African Archaeology series on Consumption, Trade and Innovation, which reports the archaeobotanical evidence from the Red Sea trade port of Quesir, an site with both Roman and Islamic era evidence as a port site [table of contents PDF]. It has excellent illustrations and straight forward quantitative analyses that highlight the different food traditions of the Roman and Islamic periods, highlights trade in foods (fruits, nuts, spices), and the much more 'globalized' of pan-Indian Ocean in character, with lemons, eggplants and watermelons consumed for their seeds. I am particularly taken by the evidence for two-way flow. This is not just about importing spices and bananas from the East, but I am struck by how many European imports, like hazelnuts, were also consumed in the Egyptian desert. The evidence for imported spices in Roman and Medieval western Europe, reviewed by Livarda 2011, is remarkably Asian-centric (black pepper, cardamon, a single medieval nutmeg) but some African Melgueta pepper has been reported from European Medieval contexts.

Some small contributions from the lab here in London came out, too:

Manning et al. reported the earliest archaeological Pearl Millet, with direct dates between 2500 and 2000 BC from the Tilemsi valley in NE Mali, and evidence from chaff impressions for non-shatteing domestication traits. The discussion (and supplement) include a database summarizing the whole archaeological record of pearl millet.

Giblin and Fuller reported the first archaeobotanical results from the first flotation in Rwanda, dating from ca. 400 AD to 1200 AD, with sorghum, pearl millet and cowpea from the earliest samples. Of note is the recurrence of finger millet, and this article includes a discussion and supplementary database of the whole archaeological record of finger millet.

Nixon, Murray and Fuller published the archaeobotany from Tadmekka/ Essouk in NE mali the trans-Sahaan trade route. It was Islamic era trade city, with excavated material between 700 and 1400 AD. Amongst the staples were pearl millet and wild grains (Echnichloa, Brachiaria), but there is also evidence for wheat (imported or locally irrigated) and cotton processing (imported or locally irrigated), and several fruits. It includes an effort to tabulate the sum of archaeobotanical evidence for medieval west Africa.

Ruas and Tengberg (from the Paris archaeobotany lab) published an archaeobotanical study from Igiliz in southern Morocco, the first ever from the region, which included a detailed consideration of Argan oil production (blogged previously).

Although not strictly Africa, another study from the Paris lab, Bouchard, Tengberg and Pra report evidence from Mada'in Salih in Saudi Arabia, which expands our archaeological evidence for cotton cultivation, and is discussed alongside that from Bahrain, in relation to the role of arid Arabia in producing cotton as part of date palm oasis cultivation systems in Antiquity.

The last article taken with Sarah Walshaw's article on Swahili era Pemba from the previous year (World Archaeology 2010: "converting to rice"), frames the northern and southern limits of early Old World cotton production.

One looks forward to the new contributions at this years African Archaeobotany Workshop. For my part, we are making some progress on flots from SE Kenya, SW Ethiopia, and some from Mali from Kevin MacDonald's Sorotomo project.

Obscure crops of 2011 and an obscure book

I am ever the fan of the obscure crop, the "lost crop", or the highly local. I have drawn attention previously to the forgotten oil-millet of Taiwan, and tef-- which is obscure to those less familiar with Ethiopian agriculture-- a couple of years ago. I thought it might be interesting as part of a end of 2011 review, to compile some of the more obscure crops that got archaeobotanical attention in publications this past year.

1. Abutilon theophrasti,  socalled "China jute" or velvetleaf, was reported in quantity from a Hungarian Late Neolithic site in a storage jar (5th millenium BC) by Medovic and Hovrath. This is the only archaeological evidence for its cultivation that I know of, and it highlights the mystery surrounding where this crop comes from. This species can grown for bast fibre, similar to jute, but fruits and seeds are also edible. This find tend to lend support to the hypothesis of an eastern Mediterranean origin rather than an in China with early dispersal to Europe before 4000 BC.

2. Argan (Argania spinosa)-- the argan oil tree (or "goat-turd oil" as I have often heard it called), has its first(?) archaeological record from Southern Morocco, published by Marie-Pierre Ruas Margareta Tengberg & al. in Vegetation History and Archaeobotany. They also provide an excellent ethnographical description (and photos) of the gathering and processing: fruit eaten by goats; stones cleaned out of goat droppings, and pressed for oil... one of the priciest oils out there (if not the most pricey). Hunting for unadulterated bottles of the stuff was a recurrent theme in the markets of Fez or Meknes when I was on excavation in Morocco some years ago.  Even small 50mL bottles, when you can find them, in London can set you back nearly 10 pounds. But its is a wonderfully distictive oil for salad dressing for, better, bread-dipping...

But for those into obscure and lost crops, a nice obscure book is Threatened Crop Sepcies Diversity by Korous Khoshbakht and Karl Hammer (a prolific researcher on crop diversity!). Actually published in 2010, in Tehran by Shahid  Behesti University Press, it is unlikely to turn up in your local book store (but there is a PDF to be found from an Iranian site). I was lucky enough to find one with a Christmas card from Prof. Hammer in my post a few weeks ago, a real holiday treat. What a gem, with short account on obscure wheats, from Triticum karamyschevii, to forgotten millets such as Digitaria sanguinalis, to farmer preserved plants such as the banana relative Musella lasiocarpa, which is apparently now extinct in the wild, but it remains in cultivation as a raw fibre material and pig fodder by ethnic minorities like the Yi. Moringa hildbrantii, an endemic of Madagascar, appear to survive only in hedges and planted fences as an ornamental and medicinal. It includes nice summaries of the extinct Silphium of ancient Libya, or the more recent extirpated domesticated forms of German Pellitory (Anacyclus officinarum) grown in parts of Europe, such as Germany, as a medicinal up to the 19th century, but apparently now extinct in its domesticated form, but survived by it likely wild progenitor A. pyrethrum. 

Nevertheless, other obscure and endangered crops are missing (such as  the oil-millet of Taiwan  or Khasi hills millet, Digitaria cruciata, or South Indian browntop millet, Brachiaria ramosa). Also missing are some of the archaeobotanically well-known lost crops, the striate emmeroid wheat of prehistoric Europe, first published by Jones et al 2000, for example, or the Bronze Age Greek oilseed forms of Lallementia (Jones and Valamoti 2005), or the domesticated sumpweed of North America, Iva annua var. macrocarpa, extinct from the native cultivars of the midwest by the time serious European records became available, but clearly recognized archaeologically (e.g. Yarnell 1972).

Loss of diversity of cultivars is undoubtedly a tragedy of our time, but it also is not entirely new; diversity of cultivars has been being gained and lost since agriculture began.

More on rice and millet in South China and Southeast Asia

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

Recognizing immature millets

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

Gansu Province survey archaeobotany

A recent issue of the Chinese Science Bulletin contains an archaeobotanical paper from what appears to be a new archaeobotanical research group. An ChengBang et al. report evidence from survey archaeobotany in Qinan and Li counties, and as such follows in the path laid by flotation as part of field surveys published previously from the Yiluo Survey (Lee et al 2007) and the Ying Survey (Fuller and Zhang 2007; see also our GIS study in Journal of Archaeological Science). This new study is based on 96 samples, from something like about 40 sites (although this is not entirely clear). Unfortunately the full dataset is not published, and we are given a glimpse of it through summary data presented as bar chart of absolute counts of Panicum and Setaria grains. Not the most informative means of comparing across sites and periods with very different sample sizes. The presence of rice (7 grains in the Late Yangshao) and wheat and barley (from the Western Zhou period) are only referred to in the text description. No reference is made to any other species, whether pulses, fruits or weeds. One novel addition to the study was a stable carbon isotope study of the millet grains, which shows that Setaria tends to have a somewhat higher value than Panicum, as expected since although both are C4 plants they have different forms of the C4 mechanism. A novel technique but the results are still close enough that this is unlikely to replace morphological identification! While it is nice to see more archaeobotanical research being carried out in China, the attention to only cereals, the lack of discussion of archaeological context (it is even unclear which sites numbers are which period), a less helpful method of quantification, and the lack of full details makes this study a rather frustrating addition.

The arrival of wheat in China

The extensive set of direct dates, on the largest early assemblage of wheat and barley in China, provides important new evidence on the arrival of West Asian crops, and western stimulus, into China. Rowan Flad, Li Suicheng, Wu Xiaohung and Jimmy Zhao, have recently reported new archaeobotanical evidence and AMS dates from the Gansu corridor site of Donhuishan in short article in The Holocene, "Early wheat in China: Results from new studies at Donghuishan in the Hexi Corridor." Importantly, the evidence includes the first large assemblage of wheat rachis remains. These provide the first clear confirmation of what has long been taken for granted, that the early wheat in China is only hexaploid bread wheat, leaving the eastern margins of tetraploid naked wheats (durum) somewhere in central Asia and to the south in India. This article also provides an updated review of all the early wheat finds that have been published from China.

In my version of their map (left), I have colour-coded wheat reports by broad period. First of all, it can be seen that finds line up along the eastern line of the classical silk road, running through the Gansu corridor and along the Lower Yellow river basin. It should noted that while the earliest finds are all attributed to 2500-2000 BC, or even more than 2500 BC in the case of Xishanping, none of these earliest finds is directly AMS dated. The case on Donghuishan reported by Flad et al., provides a warning call against putting too much faith in single or few or associated dates, as the earlier evidence from Donghuishan has suggested the wheat could be closer to 2500 BC rather than the 1600-1500 BC age indicated by numerous dates, including 4 directly on barley (but not wheat). Nevertheless it still seems plausible that wheat and barley entered China by ca. 2500 BC, even if the wheat crop did not take off until closer to 2000 BC. This period of arrival ion China is paralleled by the adoption from the west also of sheep, cattle and probably copper metallurgy (with a possible parallel spread to Southeast Asia-- as argued recently by Whyte and Hamilton). The counter current was provided by Chinese millets, as both Panicum miliaceum and probably Setaria italica arrive in northwestern India around this period, and Panicum is also reported in Yemen (ca. 2200 BC) and in Sudan by ca. 1700 BC. On the dispersal of westwards and southwards through the Indus to Arabia and Nubia, see discussion the paper "Cattle, Crops and Commensals" that I recently published with Nicole Boivin in the French periodical Etudes Ocean Indien [pdf]. I have also argued that japonica rice followed this route west from the Yellow river and in India (see discussion in my article in the recent rice issue of Archaeological and Anthropoloigical Sciences)

Interestingly the barley from Donghuishan, like that from Xishanping, is notable since most sites in China that have yielded wheat have lacked barley. This indicates that the adoption of wheat went through a strong cultural filter in which is was only wheat rather than wheat and barley that was adopted in much of central China. This provides a curious contrast from other regions of Asia, whether west Asia, central Asia of South Asia where wheat and barley are almost always found together archaeologically. In India these two winter cereals are also often found with evidence for pulses crops like lentils, peas or chickpeas. None of these Southwest Asia crops appears to have made it into prehistoric China. Thus the diffusion of crops into (and out of) China was selective process of cultural choice.