Range expansion and habitat shift triggered elevated diversification of the rice genus (Oryza, Poaceae) during the Pleistocene.

BACKGROUND: The 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. RESULTS: Oryza 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. CONCLUSIONS: Rice 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.

Reconstructing atmospheric CO2 during the Plio-Pleistocene transition by fossil Typha.

The Earth has undergone a significant climate switch from greenhouse to icehouse during the Plio-Pleistocene transition (PPT) around 2.7-2.4 million years ago (Ma), marked by the intensification of the Northern Hemisphere glaciation (NHG) ~2.7 Ma. Evidence based on oceanic CO2 [(CO2)aq], supposed to be in close equilibrium with the atmospheric CO2 [(CO2)atm], suggests that the CO2 decline might drive such climate cooling. However, the rarity of direct evidence from [CO2]atm during the interval prevents determination of the atmospheric CO2 level and further assessment on the impact of its fluctuation. Here, we reconstruct the [CO2]atm level during 2.77-2.52 Ma based on a new developed proxy of stomatal index on Typha orientalis leaves from Shanxi, North China, and depict the first [CO2]atm curve over the past 5 Ma by using stomata-based [CO2]atm data. Comparisons of the terrestrial-based [CO2]atm and the existed marine-based [CO2]aq curves show a similar general trend but with different intensity of fluctuations. Our data reveal that the high peak of [CO2]atm occurred at 2.77-2.52 Ma with a lower [CO2]aq background. The subsequent sharp fall in [CO2]atm level might be responsible for the intensification of the NHG based on their general temporal synchronism. These findings shed a significant light for our understanding toward the [CO2]atm changes and its ecological impact since 5 Ma.

Molecular Structure and Phylogenetic Analyses of the Complete Chloroplast Genomes of Three Medicinal Plants Conioselinum vaginatum, Ligusticum sinense, and Ligusticum jeholense.

Most plants of Ligusticum have an important medicinal and economic value with a long history, Ligusticum sinense and L. jeholense ("Gaoben") has long been used in traditional Chinese medicine for the treatment of carminative, dispelling cold, dehumidification, and analgesia. While in the market Conioselinum vaginatum (Xinjiang Gaoben) is substitution for Gaoben, and occupies a higher market share. These three Gaoben-related medicinal materials are similar in morphology, and are difficult to distinguish from each other by the commonly used DNA barcodes. The chloroplast genome has been widely used for molecular markers, evolutionary biology, and barcoding identification. In this study, the complete chloroplast genome sequences of C. vaginatum, L. sinense, and L. jeholense were reported. The results showed that the complete chloroplast genomes of these three species have typical quadripartite structures, which were comprised of 148,664, 148,539, and 148,497 bp. A total of 114 genes were identified, including 81 protein-coding genes (PCGs), 29 tRNA genes, and four rRNA genes. Our study indicated that highly variable region ycf2-trnL and accD-ycf4 that can be used as specific DNA barcodes to distinguish and identify C. vaginatum, L. sinense, and L. jeholense. In addition, phylogenetic study showed that C. vaginatum nested in Ligusticum and as a sister group of L. sinense and L. jeholense, which suggested these two genera are both in need of revision. This study offer valuable information for future research in the identification of Gaoben-related medicinal materials and will benefit for further phylogenetic study of Apiaceae.