Illustration of the major results in HUANG et al., pp. 641–651 in this issue. Oryza rufipogon (left) and O. nivara (right) are two closely related species that have sympatric distribution in south and southeastern Asia. They are distinct both morphologically and ecologically, thus providing a good model to study speciation. Using population genetics analysis, the authors investigated the molecular adaptation of Pss, a seed storage protein gene that might involve ecological divergence for the two species. They demonstrated that the origin of O. nivara was associated with the adaptive divergence on the coding region of Pss. Phylogenetic analysis indicates that the sequences from the Pss coding region form two reciprocal monophylies corresponding two species (tree in left), while the sequences from the combined neutral loci give rise to a tree on which individuals from the same locality cluster together (tree in right). Similarly, principle component analysis shows that individuals from the same species are more closely related than those from different species (plot in left), contrary to the analysis on the combined neutral loci, where individuals from the same locality would be more closely related irrelevant to the species identity (plot in right). Art plate was prepared by the authors.vergence for the two species. They demonstrated that the origin of O. nivara was associated with the adaptive divergence on the coding region of Pss. Phylogenetic analysis indicates that the sequences from the Pss coding region form two reciprocal monophylies corresponding two species (tree in left), while the sequences from the combined neutral loci give rise to a tree on which individuals from the same locality cluster together (tree in right). Similarly, principle component analysis shows that individuals from the same species are more closely related than those from different species (plot in left), contrary to the analysis on the combined neutral loci, where individuals from the same locality would be more closely related irrelevant to the species identity (plot in right). Art plate was prepared by the authors. [Detail] ...