Phylogeography of Oryza rufipogon: History, Demography and Climate Change

Date of Award

Spring 5-15-2013

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Evolution, Ecology & Population Biology)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



Asian wild rice (Oryza rufipogon) is a plant species widely distributed across the eastern and southern parts of Asia. A member of the Poaceae, Oryza rufipogon is commonly recognized as the direct ancestor of cultivated Asian rice (O. sativa). Due to its great economic, cultural and evolutionary significance, many studies have sought to resolve the patterns of genetic variation in this pair of species. The main focus of this thesis work is to elucidate the phylogeography of O. rufipogon by determining the patterns of genetic variation across geographical space. Further, I seek to determine the historic, evolutionary and environmental factors that created such patterns.

By examining a set of genome-wide, sequence based markers in a collection of samples that covers the whole distribution range of O. rufipogon, two genetic groups (Ruf-I and Ruf-II) were detected. Geographically, the two groups form an east-west cline. Cluster analysis and PCA indicate that the eastern group (Ruf-I) is similar to O. sativa indica, while the western group (Ruf-II) is not similar to either of the cultivated varieties. This pattern is congruent with a hypothesis that O. sativa was domesticated in China. Further analysis based on coalescent simulation and diffusion approximation approaches suggest that there is an asymmetrical pattern of historical gene flow between O. sativa and O. rufipogon, mainly from cultivated rice into its wild relative. This introgression is also one possible cause for genetic differentiation between Ruf-I and Ruf-II. Similar approaches were also used to determine the timing and strength of the domestication bottleneck, and population size fluctuations in O. rufipogon. To further explore the factors responsible for differentiation between Ruf-I and Ruf-II, a species distribution modeling approach was applied to a much larger sample of O. rufipogon. The result of this analysis suggests that, during the last glacial period, there was a climatic vicariance in the O. rufipogon species range. A xeric region formed during the last glaciation in the Indochinese Peninsula which isolated O. rufipogon into disjunct eastern and western populations. Today the climate is warmer and wetter, and the distribution of O. rufipogon is continuous. This xeric region roughly corresponds to the geographic transition area of Ruf-I and Ruf-II today. These results suggest historical vicariance as another factor that contributes to the phylogeographic pattern in O. rufipogon. Finally, the species distribution models predict that O. rufipogon is less vulnerable to future climate change. Therefore, asymmetric gene flow from cultivated rice is considered to be a greater threat than climate change to the conservation of the species.


English (en)

Chair and Committee

Barbara A. Schaal

Committee Members

Kenneth M. Olsen, Justin C. Fay, Alan R. Templeton, Elizabeth A. Kellogg, Peter Richardson


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