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.
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China. linli09@ibcas.ac.cn.|University of Chinese Academy of Sciences, 52 Sanheli Road, Beijing, 100049, China. linli09@ibcas.ac.cn.
Li
L
Lin
College of Horticulture and Landscape Architecture, Southwest University, 2 Tianhe Road, Beipei Distinct, Chongqing, 400715, China. ecologytang@aliyun.com.
Liang
L
Tang
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China. baiyj@ibcas.ac.cn.|University of Chinese Academy of Sciences, 52 Sanheli Road, Beijing, 100049, China. baiyj@ibcas.ac.cn.
Yun-Jun
YJ
Bai
Department of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes, Peking University, 5 Yiheyuan Road, Haidian Distinct, Beijing, 100871, China. zytang@urban.pku.edu.cn.
Zhi-Yao
ZY
Tang
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China. wangwei1127@ibcas.ac.cn.
Wei
W
Wang
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China. zhiduan@ibcas.ac.cn.
Zhi-Duan
ZD
Chen
D005075:Biological Evolution; D017753:Ecosystem; D012275:Oryza / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D018087:Plastids / Q000235:genetics