the trouble with two-row barley

I still seem to be playing blog catch-up, but I had to record something from a few months ago, which should be forcing us to think about the prehistory of barley in a whole new way. .. Palmer et al. of the Warwick molecular archaeobotany lab group of Robin Allaby published a major paper on plant ancient DNA in PLoSone this summer, "Archaeogenetic Evidence of Ancient Nubian Barley Evolution from Six to Two-Row Indicates Local Adaptation." On the one hand it has some nice clear ancient DNA results from the Nubian site of Qasr Ibrim, which allows these samples to be placed phylogenetically in relation to the gene the control whether barley is two-row or six-row. They have found what at first seems counter intuitive-- that all the barley samples have the six-row mutation, despite the fact that Nubian barley is usually regarded archaeologically as two-row, based on its symmetrical grains.

Cereal in Libya earlier than Egypt? New data from Huah Fteah

The spread of agriculture to Egypt presents a number of contrasts from that in Europe of east of the Fertile Crescent. For one thing it seems to be long delayed, with our conventional dates for the earliest cereal agriculture in Egypt, such as in the Fayum at 5000-4500 BC-- by contrast cereal agriculture is established in Greece and Pakistan by 7000 BC. What is more Near Eastern animal domesticates (sheep and goat) had reached Egypt at least 1000-1500 years earlier and spread rapidly through the Sahara. New data from Libya, rather than the Nile, suggests a new wrinkle in this story: cereal agriculture did spread earlier (by 6000 BC?), and probably was established in part of the Nile Delta, but made little headway up the Nile. How have I come to this conclusion?  [ed. June 2010: but see my own comment on the radiocarbon dates that have now overturned this]

In the latest issue of the journal Libyan Studies (vol. 40, 2009), there is a long preliminary report on the new Society for Libyan Studies/ Cambridge project at the famous Haua Fteah rock shelter, and thereabouts, the "The Cyrenaican Prehistory Projecy 2009" As part of this renewed work systematic archaeobotany is being carried out both at Haua and at nearby Hagfet al-Gama. Results from the macro-botanical work by Jacob Morales (normally based on the island of Gran Canaria) are presented over a few pages in Libyan Studies (pp. 83-88), and seem to be highly significant, if understated. Seeds are generally few and not surprisingly most are wild species. But of note is the the occurrence of barley grains and free-threshing tetraploid wheat (T. durum) rachis from the 2008 samples of Hagfet al-Gama. These are yet to be directly dated, but the cultural association is with the socalled Lybico-Capsian period, characterized by being non-ceramic and conventionally termed "Mesolithic". The Neolithic, in which older work identified domesticated sheep and goats along with ceramics, dates from ca. 5500 cal.BC-- based on the the latest radiocarbon dates. These finds from the Lybico-Capsian then suggest that domesticated cereals, deriving from the Near East, were already present somewhat earlier. Of course we must await more data, and direct dates; as well as results from new faunal analyses to see if any domestic fauna occurred alongside this pre-ceramic Libyan cereals... at present, however, we have tantalizing prospect of an earlier, hitherto undetected diffusion of cereals to northern (Mediterranean) Libyan, presumably over land via the Nile Delta-- where equivalent evidence is likely buried under meters of alluvium. Such a scenario makes the delayed diffusion of cereals into Middle or Upper Egypt and the Nile Valley all the more striking. In this region the 'Primary Pastoral Community' (sensu Wengrow) seems indeed to have been rather averse to cereal farming.

rice genetics watch: structure in Chinese rices but not domestication genes?

• In the Oct. 2009 issue of Theoretical and Applied Genetics, a large Chinese research group (Zhang et al.) looked Genetics structure among Chinese rice landraces, with over 3000 Chinese rice populations. They find clear population structure, not just between indica and japonica as expected, but also within each of these. Interesting they report that the structure in indica seems to relate to flowering time (early, middle or late flowering varieties), which suggests that early differentiation after indica originated may be focused on seasonality (and constraints of seasonal land and water availability). In the case of japonica (primarily temperate japonica one presumes), seasonality is pretty much always restricted to the warm wet summer, as China has dry, cool winters that are not conducive to rice. Instead structure seems to divide Chinese japonica landraces on the ground of soil and water adaptations, and whether they are best grown ion paddies or on upland rainfall. Indeed, as predicted from the archaeology the earliest ecological efforts in rice domestication in China are likely to have focused on water manipulation (see Fuller & Qin in World Archaeology), while early dispersal must have also seen diversification in rainfed and less labour intensive systems of cultivation. On the whole an interesting approach that one would like see extended beyond China.
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• Another paper also with Zhang et al. authorship (but a different Zhang), that came out at the end of the summer in New Phytologist looked in more detail at the phylogeny of sh4 and qsh1 non-shattering (domestication) genes, and provides a coallescent model of their origin in terms of fixation time. Their estimate this trait should have been fixed in ~100 years seems a throwback to the kind results that models produced a decade ago, now at odds with the archaeobotanical evidence on domestication rates. The authors are at odds to explain this by positing thhat the now universal(?) sh4 domestication gene evolved after initial domestication and then diffused throughout rice (and replaced some earlier domestication genes). Not a particular elegant, nor historically/archaeologically compelling model. I am forced to assume that something is amiss in the math or the assumptions of the model. Can an apparent rapid bottleneck be artefact of another process in the way the apparent monophyly can (as per Allaby et al 2008). I also note that the phylogeny that relate domesticated sh4 to wild populations the same or a close gene, on the surface suggests an origin of sh4 from a Lao rufipogon or an Indian nivara-- but surely these wild taxa, and the indica and japonica types deriving from them should not group together in a population phylogeny when they have different chloroplast genomes (with a common ancestor in excess of 70,000 years ago!). Of course a Neighbourjoining tree, however much bolster by bootstraps and Montecarlo methods is still just a cluster analysis that is not a particularly logical or robust way to look for phylogenetic relationships within a species that hybridizes. Thus the method employed here denies the reticulate evolution which is so clearly a part of evolutionary story of rice, as so elegantly argued in earlier papers by Sang & Ge or more robustly in the recent papers of Kovach et al or McNally et al. I am therefore provisionally not at all sure what this sh4 data is actually telling us.

Rice genetics watch: many sweet-smelling genes

Although it is now a couple of months old, the paper by Kovach et al. (2009) in PNAS in August on the "Origin and Evolution of Fragrance in Rice" is an important contribution on the cultural history of rice. It is a clear example of selection by cultural preferences for rice that cooks a certain way, in this case with sweet or 'jasmine' aroma. Clearly many people from many cultural traditions have preferred their aromatic rices, whether Indian Basmati or Thai Jasmine rice, and this trait has been selected just as surely as ecological or domestication traits . But equally some people prefer otherwise, for their rice to smell of rice, which is true through Central China and much of east Asia.

While the responsible gene, BADH2, has been known for a while what is of interest here is that mutations in the sequence that produce fragrant rice have been distinguished and these have been tested over a very large diverse geographical sample. A single mutation is most widespread throughout regions with fragrant rice. It is clear that this originally from an early japonica lineage, presumably East Asian. And my inclination would be to see this evolving en route as Neolithic rice dispersed from S. China to SE Asia, (although it could be a later wave). But there are 9 additional more minor alternative mutations to the same gene to the same effect. They show clear geographical patterning, and the implication of that is this geographically separate groups have recurrently developed a preference for and selected for aromatic rices. It remains to be determined. Whether some of these were developed truly independently, with local fragrant mutations being kept or pushed to low frequency as the dominant BADH2 came in, or else these local aromatic variants were selected to mimick a preference developed after fragrant rice arrives. Of course the story may be different in different cases...

Au Revoir Levi-Strauss

This blog returns, with a start, at the news that Claude Levi-Strauss died today. Startling because I hadn't even realized he was still alive! Although he probably hasn't influenced too many archaeobotanists, he certainly changed the way we think anthropologically about food, what is classed as edible, defined as cooked or rotten and how we refract much of what we mean to be cultural through a lens of cooking. In a general way, his brand linking cooking traditions to cultural cosmologies does run through the recently published (preliminary) study I wrote with Mike Rowlands on a "Macrogeography of Substances: Food & Sacrifice Traditions in East, West and South Asia" [pdf]. Levi-Strauss also plays the role of one of the characters (alongside the late Mary Douglas who lived and wrote to the ripe age of 86, less than Levi-Strauss' 100) interpreting archaeological feasts and human food sociality in Martin Jones' book Feast. As my tribute to Levi-Strauss I can think only to quote from one the myths he recounts on the origins of agriculture according to the Brazilian Munduruku:

In former times, game and cultivated plants were unknown to the Mundurucu.

They fed on wild tubers and tree fungi.

It was then that Karuebak, the mother of manoic, arrived and taught men the art of preparing it.

One day, she ordered her nephew to clear an area of forest, and she announced that soon bananas,

cotton, caras (Dioscorea), maize, the three varieties of manioc, watermelons, tobacco and cane

sugar would grow there. She ordered a ditch to be dug in the newly cleared area,

and asked to be buried in it. Care should be taken not to walk over her.

A few days later, Karuebak's nephew found that the plants listed by his aunt were growing on

the place where she lay; however, he inadvertantly walked on the hallowed ground, and

the plants at once stopped growing. This determined the size to which they have grown ever since.

A sorcerer, displeased at not having been informed of the miracle, caused the old woman to perish

in the hole where she lay. Since she was no longer there to advise them, the Indians

ate manikuera [manoic] raw, not knowing that this particular variety of manioc is poisonous

and emetic in that form. They all died, and next morning went up into the sky where they

became stars. Other Indians, who had eaten manikuera first raw and then cooked,

were transformed to honey flies. And those who licked the remains of the cooked manikuera

became the kind of bees which produce bitter, emetic honey..."

-- From Honey to Ashes, p. 56 (Levi-Strauss 1966)

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.