Abstract
BackgroundThe rice genus (Oryza) contains many wild genetic resources that are vital to the well-being of humans. However, little is known about the process by which the genus diversified or the factors that drove its speciation. Here, we integrated the phylogenetic, molecular dating and biogeographic methods to investigate the spatial-temporal patterns of Oryza diversification, and used a series of model tests to examine whether intercontinental migrations and/or key innovations were associated with significant changes in diversification rates in the genus.ResultsOryza became differentiated in tropical Asia in the Miocene. There were two migrations from the ancestral area into Africa and Australia during the Miocene. We inferred at least 10 migration events out of tropical Asia since the Pleistocene, mainly involving the species adapting open habitat. A rapid increase in diversification rates of the whole Oryza occurred during the Pleistocene. Intercontinental migrations from tropical Asia to other tropical regions were positively correlated with shift in habitat, but not with changes in life history. A habitat preference shift from shade tolerant to open habitat predated the burst in diversification rates.ConclusionsRice species may have been pre-adapted to invade open habitat. Significant increase in diversification rates occurred during the Pleistocene and is associated with range expansion and habitat shift, but not with life history. The rice genus provides an excellent case supporting the idea that range expansion and invasion of novel habitats can drive the diversification of a group.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0459-1) contains supplementary material, which is available to authorized users.
Highlights
The rice genus (Oryza) contains many wild genetic resources that are vital to the well-being of humans
Phylogeny and divergence time estimates Two phylogenetic analyses (BI and maximum likelihood (ML)) of the combined dataset with 20 plastid DNA regions generated a wellsupported framework (Additional file 2: Figure S1) that was highly congruent with that produced by BEAST through co-estimation of phylogeny (Fig. 2a)
Our analyses show that Oryza became differentiated in tropical Asia in the Miocene, but increased diversification did not occurred until the Pleistocene
Summary
The rice genus (Oryza) contains many wild genetic resources that are vital to the well-being of humans. Understanding the diversification patterns and potential driving factors of a group with important wild genetic resources is vital for the well-being of humans and has far-reaching implications for the work of policy-makers and conservation biologists. The rice genus (Oryza) is of economic importance due to Asian cultivated rice (Oryza sativa L.), which provides food for more than half of the world’s population. It was domesticated from wild relatives [4] that provide important. Divergence time estimates have suggested several rapid diversification events in Oryza across different genome lineages and temporal scales.
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