Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon
Article first published online: 1 AUG 2013
© 2013 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Ecology and Evolution
Volume 3, Issue 9, pages 3047–3062, September 2013
How to Cite
Ecology and Evolution 2013; 3(9): 3047–3062
- Issue published online: 8 SEP 2013
- Article first published online: 1 AUG 2013
- Manuscript Accepted: 23 JUN 2013
- Manuscript Revised: 17 JUN 2013
- Manuscript Received: 20 FEB 2013
- T.T. Chang Genetic Resources Center (TTC-GRC)
- International Rice Research Institute
- Biosystematics Group of Wageningen University
- Species divergence;
- SSR diversity;
- sympatric populations;
- wild Oryza
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 Oryza series Sativae species in Asia Pacific: Oryza 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 Bayesian clustering and neighbor-joining analyses. At the regional scale, the two species seem more differentiated in South Asia than in Southeast Asia as revealed by FST 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). Oryza nivara (HE = 0.67) exhibits slightly lower diversity and greater population differentiation than O. rufipogon (HE = 0.70). Bayesian inference identified four, and at a finer structural level eight, genetically distinct population groups that correspond to geographic populations within the three taxa. Oryza meridionalis and the Nepalese O. nivara seemed diverged from all the population groups of the series, whereas the Australasian O. rufipogon appeared distinct from the rest of the species.