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MBE Advance Access published online on December 20, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl204
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Multilocus Analysis of Nucleotide Variation and Speciation in Oryza officinalis and its Close Relatives

Lin-Bin Zhang* and Song Ge*,{dagger}

* State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing 100093, China
{dagger} The Graduate School, Chinese Academy of Sciences, Beijing 100039, China

Corresponding author: Song Ge, State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China, E-mail: gesong{at}ibcas.ac.cn, Tel: +86-10-62836097, Fax: +86-10-62590843

Accepted for publication December 18, 2006.

Nucleotide variation in 10 unlinked nuclear genes was investigated in species-wide samples of Oryza officinalis and its close relatives (O. eichingeri and O. rhizomatis). Average estimates of nucleotide diversity were the lowest in O. rhizomatis ({theta}sil = 0.0038) and the highest in O. eichingeri ({theta}sil = 0.0057) that is disjunctly distributed in Africa and Sri Lanka. These wild rice species appeared to harbor relatively low levels of nucleotide variation relative to other plant species because the diversity level of O. eichingeri is only 23% to 46% of those in Zea species and 35% of that in Arabidopsis thaliana. The lower nucleotide diversity in these Oryza species could be best explained by their smaller historic effective population sizes. The speciation model test indicated that O. officinalis and its close relatives might have undergone a process of population contraction since divergence from their ancestor. Incongruent topologies among 10 gene trees, particularly regarding the positions of O. eichingeri and O. rhizomatis accessions might be attributed to lineage sorting arising from ancient polymorphism and hybridization/introgression between the Sri Lankan O. eichingeri and O. rhizomatis. However, the null hypothesis of the isolation model was not rejected for any contrast between taxa, which suggested that no subsequent gene flow shaped the present patterns of nucleotide variation since their divergence and that introgression was not pervasive in this group of species. Our molecular dating provides an approximate divergence time of 0.37 Myr between two geographical races of O. eichingeri, much more recent compared to the times of other speciation events in this group (0.63 to 0.68 Myr). A long-distance dispersal from West Africa to Sri Lanka was more likely to play a role in the disjunct distribution of O. eichingeri.

Key Words: nucleotide variation • divergence • speciation • Oryza officinalis


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