Tuesday, 20 July 2010

Divergence and gene-flow between the wild rices

A important study has recently come out in the journal Molecular Ecology, on  "Ecological divergence in the  face of gene flow in two closely related Oryza species (Oryza rufipogon and O. nivara" by Zheng and Ge. In it they have sequenced a few chloroplast and nuclear DNA loci (7 in total) across 26 populations of these two wild rices. Nivara and rufipogon represent two ends of a adaptive spectrum in the wild genepool of Asian domesticated rice, with O. nivara being an annual adapted to seasonal water from the monsoon and lacking daylength seaonsality controls (so its life cycle is driven by water availability), while O. rufupogon sensu stricto is a perennial occurring in perennial wetlands, and is often highly structured in terms of the seasonality of seed set (especially important in its northern range in China). As I have discussed previously in a 2009 World Archaeology paper, these differing ecologies had important consequences for how these plants would have been utilized by hunter-gatherers, with the perennial rufipogon requiring more environmental manipulation to force it to produce more grain.

In this study Zheng and Ge show that these two wild rice ecotypes are well diverged overall, and they estimate a last common ancestor about 160,000 years ago, but they also show evidence for recurrent gene flow. This strongly suggests that these have diverged as ecological adaptations despite being in continued genetic contact, providing a nice case of the strength of natural selection in pushing divergence even when species ranges overlap (i.e. a case of sympatric speciation). It is interesting to note that the divergence time they have calculated is very similar that those calculated for the last common ancestor of indica and japonica domesticated rices, which have ranged in various studies between 86,000 and ~400,000 years ago, but most focus on 100,000-200,000, much like nivara and rufipogon. As many have argued (see for example the recent "Rice consilience" review article), indica and japonica appear to have different origins in cultivation from different maternal ancestors, one from a nivara-like annual and the other from Chinese rufipogon perennials-- although they also have undergone recurrent geneflow (see  McNally et al 2009 on SNPs and hybridization), which has introduced selected domestication traits amongst others. Thus the process of differentiation in cultural ecologies in the rice crop, despite continued geneflow, continues that ecological and genetics dynamics of the wild progenitors.

5 comments:

P Priyadarshi said...

The date of divergence between ancestors of Indica and Japonica rice at about 150,000 years back noted above by Fuller, carries much meaning and significance. If we change our mindset of considering all our pre-Neolithic ancestors as mere animals, then we can think that most probably it was man which carried wild rice seeds from India to Southeast Asia and from there to South China. Rice could not have been carried by air, or by birds. Humans whether gatherer-forager or modern, always carry some food with them, even if that food has been just gathered from the wild growth.

Finding of Hathnora skull (300,000 years old) and Laterite baby (60,000 years old), both within the range of ancestral or Archaic Homo sapiens, makes an early migration of Humans to Southeast Asia, who may have been the ancestors of Lake Mungo 3 man, which belonged to a Homo sapiens sapiens lineage older than the famous African Eve's.

Mishra et al note intense interaction between India and Java during this period and argue "The archaeological, paleontological and hominin records of India and Java are compared. It is argued that during the Lower and Middle Pleistocene, the palaeolithic technology in both the regions was Large Flake Acheulian (LFA) which is attested to by numerous sites in Peninsular India, some finds from Pinjor exposures in NW India and the site of Ngebung in the Sangiran dome area of Java. We argue that the non-Acheulian assemblages attributed to this period actually come from later contexts. During the Lower and Middle Pleistocene, fauna in Java associated with Homo erectus was related to the Indian Pinjor fauna. Although hominin fossils have not been found in India for this time period, it is likely that Homo erectus was the maker of the LFA tools in India, given the presence of LFA in Java in strata with a Pinjor related fauna and Homo erectus." (India and Java: Contrasting records, intimate connections, Quaternary International, 2009, 223-24:265-270.)

P Priyadarshi said...
This comment has been removed by the author.
P Priyadarshi said...

Some more statements by Fuller require comment.

"with O. nivara being an annual adapted to seasonal water from the monsoon and lacking daylength seaonsality controls (so its life cycle is driven by water availability), while O. rufupogon sensu stricto is a perennial occurring in perennial wetlands, and is often highly structured in terms of the seasonality of seed set "

We can discuss point wise:

1. Wild perennial Rufipogon of Southeast Asia (and south China) is more appropriate for gatherer-forager subsistence, because the plants do not need to be sown annually, they are perennial. Only the spikelets of paddy need to be harvested whenever they re-grow from axillry buds-- the plants were left rooted at harvesting. This further supports the conclusion that the southern Chinese, who may have had hardly rufipogon paddy plants from Southeast Asia, were foragers and not true farmers during early Neolithic of south China. Threshing was also difficult with that breed of paddy (discussed elsewhere in another comment). Hence harvesting the spikelets was the only way to get food while preserving the plant for next year. Conversion from perennial to annual life was not easy for rufipogon, and that is why Chinese Neolithic had to wait until Indian seeds of annual O. sativa indica probably arrived in China from India, and cross pollinated the Chinese variety.

2. Perennial varieties grow only in those areas which are water logged for the whole of the year. Hence water management is not needed. It is the annual variety which needs intense water management. The seeds are first groen as saplings, 3 to 4 inches long. Then they are uprooted and then sown in rows in a field where much has been created with the help of buffalo or ox. It is exactly when saplings are ready, mud must also be raedy. Thus both the two actions requre water at a fixed gap of about a month. This necessarily requires water management.

3. Bellwood and many others have claimed that rice cultivation at early stage was entirely dependant on buffalo (for mud creation in rice fields). [Fuller, Dorian, “Non-human genetics, agricultural origins and historical linguistics in South Asia”, in Petraglia, M. D. and Allchin, B. (Eds.), The Evolution and History of Human Populations in South Asia, Springer, 2007, p. 399. Also see: Groves, C. P., “Domesticated and Commensal Mammals of Austronesia and Their Histories”, in Bellwood, P., Fox, J. and Tryon, D., The Austronesians: Historical and Comparative Perspectives, 1995. And, Bellwood, The First Farmers, 2005, p. 84.] Groves demonstrates that buffalos were domesticated in India from where they were carried to the Southeast Asia. Later DNA studies of buffalo confirmed that domesticated buffalo originated in India and was taken to Southeast Asia and China after domestication.[Kumar, Satish et al, Phylogenography and domestication of Indian river buffalo, BMC Evolutionary Biology 2007, 7:186,]

4. Bandicoot-rat, Bandicota bengalensis, a noted rice-field pest in Indonesia originated in Mahanadi delta in association with buffalo. It migrated to Southeast Asia with rice and buffalo migration from India. [Groves, C. P., Of mice and men and pigs in the Indo-Australian archipelago, Canberra Anthropology 1984, 7:1-19.] DNA study of rats and mice have also proved this fact of migration from India.

5. Chen (1993) found that ‘deletion type Cp DNA’ is found in ‘annual’ varieties of Oryza rufipogon, which is Indian in geographic distribution, and ‘non-deletion type CpDNA’ is found in ‘perennial rufipogon’ found in Southeast Asia in the wild. This DNA is essential for cultivation.

Ignoring such basic facts, which of course are disturbing to the archaeobotanist Sino-centric authors, is no good for unearthing the true history of rice or anything.

P Priyadarshi said...
This comment has been removed by the author.
P Priyadarshi said...
This comment has been removed by the author.