Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon

Abstract Genetic variation patterns within and between species may change along geographic gradients and at different spatial scales. This was revealed by microsatellite data at 29 loci obtained from 119 accessions of three O ryza series Sativae species in A sia P acific: O ryza nivara Sharma and Shastry , O . rufipogon Griff., and O . meridionalis Ng. Genetic similarities between O . nivara and O . rufipogon across their distribution are evident in the clustering and ordination results and in the large proportion of shared alleles between these taxa. However, local‐level species separation is recognized by B ayesian clustering and neighbor‐joining analyses. At the regional scale, the two species seem more differentiated in South A sia than in Southeast A sia as revealed by F ST analysis. The presence of strong gene flow barriers in smaller spatial units is also suggested in the analysis of molecular variance ( AMOVA ) results where 64% of the genetic variation is contained among populations (as compared to 26% within populations and 10% among species). O ryza nivara ( H E = 0.67) exhibits slightly lower diversity and greater population differentiation than O . rufipogon ( H E = 0.70). B ayesian inference identified four, and at a finer structural level eight, genetically distinct population groups that correspond to geographic populations within the three taxa. O ryza meridionalis and the N epalese O . nivara seemed diverged from all the population groups of the series, whereas the A ustralasian O . rufipogon appeared distinct from the rest of the species.