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.