Tuesday, 25 August 2009

Millets and Mistakes

In Last week's Science the journalist Andrew Lawler, published an extended series of News Focus articles on Chinese civilization. The central piece focuses on the origins of civilization, highlighting for example the impressive urban settlement of Liangzhu (a kind of walled Neolithic Venice, many centuries before the Shang Dynasty) which ought to be better known to world archaeology than it is. (I had my own tour of some of the mutliple sites that compose it, and its multimedia museum, with site director Liu Bin in July). Also of note is his one page sidebar entitled "Go East, Young Archaeologist" on the specialists trained outside China, which features Jimmy Zhao, who has been instrumental in getting serious archaeobotany established in the minds and manners of Chinese archaeologists, and has been promoting flotation in China for the past decade.

What I would like to pursue here, however, are some observations on archaeobotany, and pick out some mistakes or misleading statements, with reference to the origins of millet agriculture which features in another sidebar, "Millets on the Move." Lawler begins which a point that seems to look increasingly true, that millet(s) were cultivated and presumably domesticated before rice, and were the staple foods of the northern China region where the classic Chinese civilization later emerged (focused on Erlitou rather than Liangzhu). He makes reference to the recent early dates (ca. 8000 BC) associated with Panicum miliaceum husk (lemma/palea) phytoliths reported from storage pits at Cishan (blogged previously). However, I must disagree the there is any hard evidence that the Panicum miliaceum at Cishan was morpholoigcally domesticated (i.e. non-shattering, with marked increased grain size, etc.), nor is there even clear evidence for cultivation, unless one assumes that large stores could only be ontained from cultivation, which in turn implies that we know the Early Holocene wild ecology of this species (which we don't) and that it did not form extensive collectible stands, as wild wheat, barley or rice or teosinte do (see discussion on my earlier Dadiwan blog and comment from L. Barton). I also must reiterate that there is much about the archaeology of the Cishan find (stratigraphiy, cultural context, and dating that require further work.

A lack of scientific clarity in Lawler's piece, however, is indicated in that millet is always used in the singular and the species (there are two major domesticates in ancient China) is never specified. And things get worse... as Lawler explored the hypothesis (favoured by Martin Jones and Cambridge millet group) that Panicum miliaceum (but NOT Setaria italica) spread before 5000 BC acroos temperate Eurasia from China to India. This hypothesis is plausible, but there is not yet any good clear data for this, only hints that it might yet emerge from ongoing and unpublished genetic work. Lawler acknowledges an alternative, which I would favour, that Panicum may have had a seperate domestication in the west somewhere near the Caspian and Black Seas. Well-dated, clearly-identified and numerically large assemblages of Panicum miliaceum outside China are mostly millenia later. To illustrate his case, Lawler produces a map which shows a major lapse in scientific clarity:

This map, although redrawn from that in Hunt et al (2008), is extremely mis-leading, especially when coupled with the text that hook-line-and-sinker swallows the notion that "millet" spread in the early Neolithic to Europe, without apparently realzing what "millet" is (or millets are). Millet is more than one species anyways despite the English misnomer-- in modern India one can find 12 domesticated species of "millet" in cultivation, with several more restrcted to Africa). The early dispersal of "millet" that Martin Jones favours, applies to broomcorn millet (Panicum miliaceum), as does the recent early find at Cishan, although Neolithic North China also boasts foxtail millet (Setaria italica), by about 6000 BC or so. For the map of Lawler, however, the "millet" in the caption actually means the genus Panicum or the genus Setaria, and does not require that these be cultivated or domesticated finds. What is most grevious in this map are the dots in Western Asia and Egypt. This map in its original, illustrated all reports identified to genus level of Setaria or Panicum-- both of which are major genera of grasses with multiple wild species-- in which the error margins of calibrated radiocarbon dates may place them as early as 5000 cal.BC (although often the dates are likely to be later). The dots in Western Asia, include sites such as Abu Hureyra in Syria, which is a well-known site to students of early wheat and barley agriculture. At this site it is argued (by Hillman et al. 2001) that wild rye and perhaps two-grained einkorn were brought into cultivation in the Late Pleistocene during the Younger Dryas, while later PPNB levels have evidence for domesticated wheats, barley and other Near Eastern crops. "Millet" is represented at this site by small number of wild Setaria, of either S. pumila or S. verticillata, and certainly not Setaria italica nor Panicum miliaceum. Other dots in Syria and Cyprus include Tell Mureybit, El Kowm, Bouqras, and Khirokhitia, which Lawler has now awarded domesticated Chinese millet in the Pre-Pottery Neolithic. Meanwhile, three dots occur in Egypt, representing Early Holocene "Neolithic" sites like Nabta Playa. These sites are Neolithic in the sense of having pottery but not in having agriculture. Archaeobotanical evidence from these sites shows wild savannah grass gathering, including wild sorghum and a range of other species, including wild Panicum sp. and wild Setaria sp., but there is certainly no suggestion that these were cultivars or related to S. italica or P. miliaceum. While Hunt et al (2008: S6) were explicit in trying avoid the pitfall of "over representing.... securely identified domesticated finds", Lawler appears to have jumped headfirst into this pit!

The dot in Iran (representing Daulatabad R37) is also problematic as early millet finds there are more likely local wild species, while evidence for domesticated Panicum miliaceum is probably later form the latter Third Millennium BC at Tepe Yahya (a time period which fits with the reports of broomcorn millet appearing in Yemen before 2000 BC-- see the recent Boivin/Fuller review dealing with the prehistory of Arabia). A more detailed and critical look at the sites in Europe would show that these also include numerous Setaria sp. and some Panicum sp. reports that are of local wild species. In addition, quantities of reported Panicum miliaceum are extremely low and it remains entirely plausible that these represent wild, weedy Panicum miliaceum subsp. ruderale as a weed rather than domesticated broomcorn as a crop-- a point admitted in the Hunt, Jones, et al. paper from which the map derives (see page S14). Of course there is a bias towards focuing of wheats and barley in European archaeobotany, and careful documentation of the early Panicum has been less thorough. More archaeobotanical efforts are needed in this direction, like that being pursued by the Cambridge millet group, but dumbing-down for, and misleading, the educated readers of Science is not.

Rice genetics watch: another grain size and yield gene

Shan et al. (2009) in Theoretical & Applied genetics report mapping of the gene spd6 which in wild O. rufipogon appeasr to reduced panicle size, grain number and grain size. This is likely to be yet another important gene that selection of early farming acted upon to increase yields (and grain sizes), along side genes such as qsw5, sw5, and gs3 that have been reported in recent years to affect grain size, and ghd7 and gn1a which affect p0anicle size and grain number. The new spd6 has been identified by a cross of a Hainan wild rice and the Chinese indica type, Teqing; it is not yet possible to draw any conclusions about the phylogenetic or geographical distributions of variants at this locus.

Friday, 21 August 2009

Tuareg Trade & Archaeobotany

A new article in the latest Azania (in its new format), reports on the excavations at Tadmakka, in northeast Mali, carried out by Sam Nixon in recent years. These excavations of about 5 meters of stratigraphy produced a wide range of evidence for trans-Saharan trade between ca. 750 and 1400 AD, with a very significant cultural change, interpreted as 'Tuaregization' (a more Nomadic turn) from about 1300 AD. This article focuses on the material culture, the sequence, but includes summary comments on the animals and plant remains. Full details of the archaeobotany (carried out at UCL) are forthcoming.

This site provides the earliest significant evidence of trans-Saharan trade, including specifically gold trade and local gold coin production. Plant evidence also suggests a mixture of local crop-procduction, wild plant gathering and possible trade in grains; of particular interest is the evidence for free-threshing wheats-- but more on that when the archaeobotany is published. Some more information on the project is already available on-line here.

Thursday, 13 August 2009

Locating American bean domestications

A couple of recent papers of the UC Davis crops sciences group, continue the research tradition of Paul Gepts in providing further refinements in out undrerstanding of Phaeseolus vulgaris domestications, especially in terms of locating these two domestications and identifying closed related wild popualations.

Kwak and Gepts published in Theoretical & Applied Genetics 118 [March 2009] an open access paper on a phylogenetic and population structure analysis on wild and domesticated beans, reinforcing earlier inferences of separate Mesoamerica and SOuth American origins.

Further details on the Mesomaerican wild populations, their relationships and distributions, can be found in another paper by Kwak, Kami and Gepts (2009) The Putative Mesoamerican Domestication Center of Phaseolus vulgaris Is Located in the Lerma-Santiago Basin of Mexico, Crop Science 49: 554-563. This study concludes that Mexican beans did not originate in the Rio Balsas valley favoured for maize origins--and supported by recent archaeobotany work, but elsewhere in Southwest Mexico. This was on the News feeds of the Crop Society of America last week.

Review on lentil domestication

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

Thursday, 6 August 2009

Rice genetics watch: SNPs confirm widespread hybridization events

Published in PNAS last week was another major genetic study rice genetic diveristy, phylogenetics and genome structure. The study lead of Ken McNally at IRRI, entitled "Genomewide SNP variation reveals relationships among landraces and modern varieties of rice" once again confirmed the wide divergence between indica and japonica, as well as the rather distinct and intermediate position of the aus group of rices, adpated to dry cultivation Bangaldesh and thereabouts. Their summary phylogeny illustrated this clearly:

The dataset set size, in terms of numbers of accessions is quite small (20 selected varieties), but that it made of for this is the large coverage of the genome and the detail of genome structure revealed by its focus on single point mutations (Single Neuclotide Polymorphisms or SNPs). They covered 3.6 million base-pairs of sequence and discovered nearly 160,000 SNPs! In all of this the deep divergence of indica and japonica, which must precede the beginnings of cultivation was indicated. Even if morphological domestication traits are shared (such as the reduced shattereing of the sh4 mutation, or the Prog1 gene for erect growth) this must be attributed to much more recent hybridization probable since the start of management/cultivation. I favour a hypothesis of the introduction of introduce domesticated japonica to the Ganges or Indus where hybridization took place with unimproved proto-indica cultivars. (A key distinction here is between cultivation and domestication). Such a hypothesis, which can explain the genetics of domesticated rices is at odds with claims for an early Holocene rice domestication in the Ganges, e.g. at Lahuradewa, which does not fit with the genetic make-up of modern indica. But such early and important hybridization events were probably not the last.

The key conclusion of this study is that this is evidence for a large degree of hybridization between the different domestic rice clades, i.e, between indica and japonica, and between these and aus. This is an important conclusion, as it means we can not consider the long-term history of these rice lineages as separate but rather we must see them as entangled. With these lineages crossed (intentionally or unintentionally) over the millennia of cultivation to produce a greater range of varieties and adaptations. This may seem obvious but many (most?) prehistories of rice paint extremely simplistic (and unrealistic) pictures, whether one takes common archaeological accounts such as single origins linked to Austronesian or Austroasiatic expansions, or one takes some recent geneticist just-so stories of decreasing 'primitiveness' of rice varieties as one move north or west from Island SE Asia as indicative of an early (and stealth) origin somewhere in the Islands from which Chinese rice derived (e.g. as postulated in the recent Izawa et al. paper).

We can look forward to some future unravelling of the complex, entangled history of rice spreads and hybridizations.

This study got some on-line publicity, e.g. on ScienceDaily, but which seems to have missed the key point about how major hybridization has been in the evolutionary history of rice!

Wednesday, 5 August 2009

Where from the earliest Old World cotton?

I have received a recent query about early cotton in Nubia and South Asia, vis-a-vis the early occurrence of apparent cotton fibres in plaster from Dhuweila in Jordan (published by Betts et al 1994, J. Archaeological Science). This came in response to discussion of the find in the recent review I co-wrote with Nicole Boivin on the Holocene prehistory of Arabia (including several discussions of crops). I reproduce here my emailed reply as to why I have not committed on the possibility suggested by Betts (et al.) of a Nubia OR South Asian source. I have added links to references cited.

The Nubian source is based on reported cotton from Chalcolithic (A-Group) Nubia, first reported by Chowdhury & Buth in 1970 in Nature. The Indian Expedition to Nubia has preliminary reports on the archaeology in Indian Archaeology: A Review 1961-62 (which can be downloaded), and more extensively in Fouilles en Nubie (1961-1963). The A-Group Nubian cotton is problematic, with criticism published previously be me and by Zohary & Hopf. First it comes from goat dung, which does not necessarily indicate textile processing (admitted in the original Chowdhury publication). Second it comes from an undated excavation where it is alleged to be associated with A-Group ceramics (i.e. 3300-3100 BC-- mid-Third M. BC as cited by Betts [1994] is simply a mis-dating by the Indian archaeologists of 1962 who never got to grips with the Nubian sequence-- the dating of which was sorted out later, e.g. Trigger 1965; but especially Nordstrom 1972, Williams 1986; the region is largely depopulated at 2600 BC except for the Old Kingdom outpost at Buhen), but I am very worried that goat dung containing cotton seeds in Lower Nubia is more likely intrusive from later (Late Meroitic/Post-Meroitic) when cotton was known to be widely cultivated in the region. Stratigraphy in Nubia is always problematic. (I speak from experience in the 4th cataract), due to heavy deflation and reburial with windblown sand. For a published case-in-point consider Wadi Kubbaniya: Late Palaeolithic with charred wild plant remains AMS-dated to 16,000 bp and un-carbonized barley AMS'd at 500 bp [although not from the same excavation season] ! Things get mixed and the depth of deposit at Afyeh where it was found (the Indian Expedition to Nubia) was not very far beneath the surface. If it were from Nubia, how come there are no further cotton finds for 3000 years in the region? (Nevertheless, it would be nice to have more details about the Afyeh excavations, which remain largely unpublished and somewhere in the ASI archives in Delhi). I would note that Chowdhury also identified the Afyeh cotton as G. herbaceum based on a cross section of the seed coat. Perhaps this method works, but I have been unable to replicate it on the SEM (in modern material), which is a pity as it would be great to be able to track the two cotton species from archaeobotanical finds.

In addition, Naive African cotton, Gossypium herbaceum, is reported wild only much further south in Africa. It is of course possible it has gone extinct in Nubia, but if it were in 4th M. BC Nubia then it should on biogeographic grounds have been in Egypt too-- there is nothing in the Lower Nubian flora which is not in Egypt. (Is it likely the Egyptians would have overlooked using a species like this?). But, if one does postulate extinct wild Gossypium herbaceum as far north as Nubia then why not in mid-Holocene (wetter) Arabia as well?

Mehrgarh Period II has cotton seeds and fibres preserved in the earliest copper beads (Moulherat et al. 2004). On present evidence it seems the best, and only reasonable candidate. There can be presumed (but not proven) to come from Gossypium arboreum.

I must admit to remaining perplexed about the Dhuweila find. If textiles were traded long-distance one would not expect them to be valued, not used in tempering plaster. But perhaps this was not a common temper but a rare inclusion where someone tore a frayed tunic or something; the Dhuweila team got lucky-- one would need some systematic and quantitive approach to plaster temper to establish this.

My (obscure) article on Indian cotton and flax archaeology may be of some interest, as it reviews the archaeobotanical finds of these two species in India and Pakistan, with some notes on elsewhere [pdf]. For an updated review of cotton in Nubia see the chapter by Clapham and Rowley-Conwy in the recently published Hillman Feitschrit.

Monday, 3 August 2009

Gordon Hillman honoured with Feitschrift

Yesterday, Gordon Hillman had some surprise visitors, Andy Fairbairn and Ehud Wiess (and I tagged along), who presented him with a feitschrift in his honour, published last week by Oxbow Books, Several years in writing, editing, and production the volume came as pleasant surprise to Gordon.

Gordon is pcitured here with the Feitschrift in his honour and the two editors, his former students Andy Fairbairn (University of Queensland) and Ehud Weiss (of Bar-Ilan University & the Weizmann Institute of Science). This book reflects the wide impact of Gordon's research, teaching and ideas both amongst colleagues (inlcuding junior colleagues like myself), but especially amongst his students, drawn from all over the world).

In typical fashion, Gordon offered us tea but suggested that first we ought to get out and collect some Deschampsia (D. caespitosa, the tufted hair-grass), as it was at the end of its ripening window (of less than 2 weeks or so). With his characteristic enthusiasm and eneregy we headed to Pevensey Marsh with baskets and seed beaters to have a short session at paddling up some spikelets from the extensive stand that grows in an under-grazed area of the marsh. (It has small red grains, not dissimilar from the Ethiopian crop tef in terms of size).
There was more time spent sitting and eating some fruit (foraged by Andy & Ehud from a supermarket) than actually collecting, with conversation taking up issues of harvesting windows for wild grasses, acorn gathering, processing and tree ownership, seaweed collection and Australian Auracaria pinecones. Having caught up we headed back to Gordon's kitchen to dehusk and grind some Deschampsia and Festuca he had gathered earler in the week and dried. And some simple wild grass biscuits were griddle cooked to accompany our cup of tea.

It is inspiring to see Gordon still add it, regularly out in field and forest, gathering, experimenting with processing and eating. And, he is still working on a book that gathers all of this knowledge and experience on wild food plants together.

The feitschrift contents have been presented previously on this blog. The book can be ordered from Oxbow Books. A full tally of Gordon's published works (so far) can be found here.

Saturday, 1 August 2009

Parallel origins: true modern human lithics in India (as true for agriculture)

The latest publication from the Petraglia & Korisettar palaeolithic research team, working in South India, was published last week in PNAS—Population increase and environmental deterioration correspond with microlithic innovations in South Asia ca. 35,000 years ago. This study dovetails nicely with recent simulation modelling effort of some UCL colleagues (Adam Powell, Mark Thomas, and Stephen Shennan, director of the Institute of Archaeology), published in Science last month. (The appearance of these two papers close together is entirely coincidental). This simulations suggest that behavioural innovations, such as modern human behaviour, should be expected to emerge when circumstances are right (especially due to demographic factors of higher interactoing populations), and to be maintained only if demographic circumstances permit (and therefore disappear if populations decline).

These two studies together represent importance counters of an orthodoxy that sees ‘modern’ behaviour as emerging once, and therefore being a great invention when hard cognitive architecture came into place, perhaps even driven by a key genetic mutation for intelligence. Such is the orthodoxy implied by classic textbooks on human evolution, such as by Richard Klein (at least as was used when I was a student) or the recent reviews by Paul Mellars (e.g. his Science paper of 2006). In this view modern humans, heir cognitive abilities and the behavioural application of those abilities emerged once (in Africa) and spread out of Africa (once) to bring intelligent modern everywhere else (perhaps at sometime between 60,000 and 40,000—depending on whether one prefers to emphasize the earliest possible dates for Australia or the Upper Palaeolithic transition in Europe). The evidence from South Asia shows clearly that toolkits were middle Palaeolithic (and in this sense not ‘modern’) from >75,000 to 35,000 years ago, and yet genetics suggests that these would have been anatomically modern humans (and they must have moved through South Asia earlier than their arrival in Australia sometime between 60,000 and 50,000). The bottom line is there is a good evidential case to be made, congruent with the modelling of Powell et al., that the cognitive architecture for modern behaviour was around but the innovations that we regard as ‘modern’ emerged when social and environmental circumstances demanded.

There is a parallel here to where thinking on agricultural origins is moving. There has long been an orthodoxy that agriculture was a great and rare invention, and that agriculture came to most regions by the migration of farmers from a few centres of the influence of a good idea. In the more extreme cases, only 3 centres of origin (Mexico, Near East and China) are accepted. But the evidence of archaeobotany—where it is available—combined with the biography of wild progenitors, and where avail able the genetics of crops/livestock, suggest that there was many more centres in which societies converged on agriculture—the behavioural changes towards manipulation of the environment in favour of the reproduction of a few food species (domestication, the genetic sense, was an unintended consequence of these behavioural shifts, when the genetics of the species allowed). In my most recent attempt to sift through the combined data, I concluded that there is strong case for 24 separate instances of agricultural origins globally—although as many of these are poorly documented and geographically close together one might reduce this to 13, as per the map below from Purugganan & Fuller:

The point is that agriculture, like modern human behaviour, was not a one time great invention, but the product of social and environmental circumstances to which human groups with the same cognitive potential responded in parallel ways. The question in both cases is: what were the common denominators of those circumstances?