Tuesday, 22 December 2009
Friday, 18 December 2009
Wednesday, 4 November 2009
- 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.
- 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.
Tuesday, 3 November 2009
Tuesday, 25 August 2009
Friday, 21 August 2009
Thursday, 13 August 2009
Thursday, 6 August 2009
Wednesday, 5 August 2009
Monday, 3 August 2009
Saturday, 1 August 2009
The latest publication from the Petraglia & Korisettar palaeolithic research team, working in
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
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 (
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?
Friday, 31 July 2009
Tuesday, 30 June 2009
3. The recent genetics paper I have seen that I am most impressed with is the study by Yamane et al (2009, in Rice) of the phylogenegentics of Hd6, one of the genes involved in regulating heading (flowering), and linked to response to photoperiod (daylength). It is clear that non-responsive plants have one of two alternate forms of the responsive (short-day) type, corresponding to two indica vs. japonica domestication pathways. It also suggests that a non-reponsive type found mainly in temperate japonica rices also derives from the wild and is found in some South Chinese wild rices. This story is entirely reminiscent of the case in barley recently brought to light by Huw Jones and colleagues.
Monday, 29 June 2009
For more on the history & archaeology of Nubia, try this site from the expert Dr. David Edwards.
For a googlemap of many sites in Nubia, including Kerma (which you can see if you zoom in), try here.
Thursday, 25 June 2009
They report three new radiocarbon dates on bulk charcoal samples, which calibrate to between 8000 and 9000 BC. This means that the 50cm or so of cultural stratigraphy now has to account for 5000 years, or more, of human occupation. One has to conclude that this occupation was unlikely to have been permanent and sedentary. Importantly, they also recovered more plant remains, including more rice from the lower levels (Period 1A). Details of numbers, densities and samples from flotation are not reported. New finds also include a large ceramic fragment tempered with rice husk, and apparently some rice grains, as well as carbonized grains and spikelets. They suggest that these are domesticated on the basis of three criteria, grain size and grain ratios (using what might be termed the ‘Vishnu-Mittre index’), husk patterns, and the alleged presence of non-shattering rachises (i.e. spikelet bases).
Spikelet bases. Lets start with the last observation first.
Clear criteria for distinguishing three categories of spikelet bases, one of which is definitely of domesticated type, have been recently published (Fuller et al. Science 2009; Fuller & Qin 2008), although these publications probably post-date when this report went to press. Nevertheless, earlier work by Gill Thompson (1996; 1997) provided clear illustration of the differences between typical wild and typical domesticated spikelet bases. There are four spikelet bases shown in their Figure 16, one which is shown in close-up (Fig 16.3: above) as an example of the non-shattering type. Its long rachilla is still attached, which is a trait occassionally (but rarely!) encountered in domesticated rice, and when it does occur it usual in East Asia rices that possess multiple non-shattering alleles and it seems most common in modern varieties adapted to machine harvesting. Rather the attached rachilla is typical of rice harvested immature and green. As noted in the
It should be noted that both of these represent spikelets that do not appear to have broken during dehusking, and that appear thin and deformed, and are likely immature (green spikelets), which did not contain fully-formed grains. These therefore look more like green-harvested, wild rice spikelets than the threshed remains of a domestic rice harvest! But these are illustrated as the best candidates of Lahuadewa "domesticates". What is more they both have preserved awn bases. While the loss of awns is not a definitive trait of domesticated rice (many varieties, especially of tropical japonica) are awned, the presence of awns is typical of wild rices. The pictures therefore do not agree with what is stated in the text, but quite the opposite.
What about husk patterns? The basis of using husk patterns to distinguish definitively between O. nivara, O. rufipogon and O. sativa has never been clearly demonstrated or published. Quite the contrary this seems to be a non-replicable, subjective judgement. The idea is that domesticated rice is nicely ordered with square cells, and wild rice is wild and disordered. There is perhaps more of the magic of metaphors than a real method here I suspect—in any case I have never been able to see this, and one can find exceptions to this in evefy box of wild or domesticated reference material. The original inspiration of this came from the work of T. T. Chang (and was then developed by Vishnu-Mittre and his students in
I suspect that there may be some tendencies of difference between wild and domesticated spikelets husks on a popualtional level, akin to the weak tendencies in husk phytolith form, all of which are probably linked to selection for larger, fatter grains. The husk patterns therefore should show trends of gradual change overtime as grains do, but until methods of measuring and quantifying this over time are developed, this is a non-method, and seems a leap of faith too far.
Grains. This report provides a table of grain measurements, on 26 grains (although judging by the photos I wonder if some of this included attached husk, which would elevate some measures and create greater variance). It should be noted that these are all Period 1A grains with no comparison provided to later periods. Thus there is no possibility of looking for the temporal trends that one expects with domestication. In any case it is clear from examining these measurements that they break into two size groups, one is small and the other larger. This is easily illustrated in the following chart.
The smaller-grained group is comparable to non-sativa small-grained rices (e.g. O. officinalis), while the other falls into a size range that could be domesticated rice. However, when length and width measurements are taken as a scatter plot, all of these grains fall within the range defined by modern O. rufipogon and (especially) O. nivara. None of them fall into the range of domesticated rice. In order words none of them is bigger than a baseline that might be defined on the basis of modern measurements. Both the large and small groups contain ‘Vishnu-Mittre indices’ that are >2 and ~1.7, which are alleged to distinguish domesticated and wild rices. Internally this data deconstructs the usefulness of this index as a marker of domestication. Modern measurements on populations of wild domesticated rice grains certainly do not bear these indices out!
The two populations are illustrated also by scatter plot, below, where the Lahuradeva specimens (light green) are plotted over the scatter of modern populations that were plotted in Fuller et al (2007, Antiqiuty; measurements by Emma Harvey). To compare the modern and ancient grains I have added a +10% increase to the archaeological specimens as a reasonable standard correction for charring. It can be seen that the Lahuradewa grains plots nicely with Oryza nivara, while the shorter grains plot with O. granulata and O. officinalis.
Because comparison with modern rice grains may be complicated by the charring factor, I have taken two archaeological populations from
Interestingly, if these grains are compared to those from the later Neolithic in the
This evidence is probably to be expected, given that genetic evidence indicates that several key mutations had to be introduced to proto-indica via hybridization from domesticated japonica, including sh4, for non-shattering, prog1 for erect growth habit, as well as rc for white pericarp. The real leap forward for indica rice was perhaps closer to 2000-1800 BC. Nevertheless the roots of rice cultivation were laid down earlier, but it remains unclear if this was as early of the eariest dates at Lahuradewa or whether these were periodic seasonal rice gatherers.
Diatoms. It is also suggested that the diatom assemblage from the lake sediments indicates rice growing fields. Are they suggesting, implausibly, paddy fields at this date? There is simply too little background work on the ecology of diatoms in natural wetlands where Oryza nivara, O. officinalis, etc, grow to be able to justify this statement. The diatom species that now inhabit rice fields existed before there were rice fields, and they had to come from somewhere. The habitat of wild rices seems the obvious place.
(Appendix) Some general notes on the plant assemblage. Plant taxa reported from Period 1A are: rice (reported as wild and domesticated, but see below), wild Setaria (referred to yellow foxtail millet, S. pumila), Chenopodium (referred to C. album), Coix lachryma-jobi, Artemisia sp., Silene conoidea. The Silene appear to have intact light-coloured hila (Fig. 6.8), which makes one a little concerned that they may be uncharred and intrusive, but maybe not. The rice grains as illustrated are for the most part plump and appear mature, but they are relatively short (more a feature of O. nivara than typical modrn indica), except for a few elongate, thinner grains (Fig. 6.5), at least one of which is poorly formed, which are referred to O. rufipogon; indeed they are quite plausibly rufipogon, but may also include immature grains.
Period 1B (probably 2500-2000 BC, although one wood charcoal date goes back to ca. 2800/2900 BC): apart from rice, finds include free-threshing wheat, barley, lentil, Cyperus, Coix lachryma-jobi, Artemisia, Setaria cf. pumila [Saraswat persists in the use of S. glauca, a taxonomically illegitimate name—Linnaeus’ type specimen was pearl millet not yellow foxtail!-- but lets not squabble], kodo millet (Paspalum scrobiculatum)—these are in the husk and look more likely to be wild/weedy specimens rather then the crop. The rice includes many grains referred to Oryza sativa (reasonable), some O. rufipogon (which again look like they may include immature grains: Fig. 8.8), and some O. officinalis (very short and wide), with length of ~3mm or less (Fig. 8.9). It’s a pity that these and the sativa type grains were not measured for comparison to the Period 1A material. Impressively there is some husk material of O. officinalis. This adds another site to evidence for the exploitation (or at least harvesting) of more than one rice species in the