Abstract
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.
Abstract from the paper’s OpenAlex record, shown for indexing and research. Copyright remains with the authors or the publisher. Read at the source ↗
The text the model read, with the source record’s inline markup (italics, sub- and superscripts) rendered and its character entities decoded; quote offsets refer to the raw text.
Claims 13
Claim · model-written summary
Two genetic groups, Ruf-I and Ruf-II, were detected in Oryza rufipogon.
- Taxon
- Oryza rufipogon
Oryza rufipogont0 - Outcome
- two genetic groups (Ruf-I and Ruf-II)e0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“two genetic groups (Ruf-I and Ruf-II) were detected”
t0“Phylogeography of Oryza rufipogon”
Claim · model-written summary
The two wild rice groups form an east-west cline.
- Taxon
- Oryza rufipogonOryza rufipogont0
- Outcome
- east-west clinee0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the two groups form an east-west cline”
t0“Phylogeography of Oryza rufipogon”
Claim · model-written summary
Eastern Ruf-I was similar to cultivated O. sativa indica.
- Taxon
- Oryza rufipogonOryza rufipogont0
- Material
- Ruf-Ie0
- Outcome
- similar to O. sativa indicae0
- Comparator
- O. sativa indicae0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the eastern group (Ruf-I) is similar to O. sativa indica”
t0“Phylogeography of Oryza rufipogon”
Claim · model-written summary
Western Ruf-II was not similar to either cultivated variety.
- Taxon
- Oryza rufipogonOryza rufipogont0
- Material
- Ruf-IIe0
- Outcome
- not similar to either of the cultivated varietiese0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the western group (Ruf-II) is not similar to either of the cultivated varieties”
t0“Phylogeography of Oryza rufipogon”
Claim · model-written summary
Coalescent and diffusion analyses suggested asymmetric historical gene flow from cultivated rice into O. rufipogon.
- Taxon
- O. rufipogonOryza rufipogone0
- Outcome
- historical gene flowe0
- Qualifier
- mainly from cultivated rice into its wild relativee0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“an asymmetrical pattern of historical gene flow between O. sativa and O. rufipogon, mainly from cultivated rice into its wild relative”
Claim · model-written summary
Introgression from cultivated rice was proposed as a cause of Ruf-I and Ruf-II differentiation.
- Taxon
- O. rufipogonOryza rufipogone1
- Outcome
- genetic differentiation between Ruf-I and Ruf-IIe0
- Qualifier
- This introgressione0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“This introgression is also one possible cause for genetic differentiation between Ruf-I and Ruf-II”
e1“the distribution of O. rufipogon is continuous”
Claim · model-written summary
Distribution modeling suggested glacial climatic vicariance in the O. rufipogon range.
- Taxon
- O. rufipogonOryza rufipogone0
- Outcome
- climatic vicariancee0
- Qualifier
- during the last glacial periode0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“during the last glacial period, there was a climatic vicariance in the O. rufipogon species range”
Claim · model-written summary
A glacial xeric region in the Indochinese Peninsula isolated eastern and western O. rufipogon populations.
- Taxon
- O. rufipogonOryza rufipogone0
- Outcome
- disjunct eastern and western populationse0
- Qualifier
- A xeric region formed during the last glaciation in the Indochinese Peninsulae0
- Setting
- Indochinese Peninsulae0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“A xeric region formed during the last glaciation in the Indochinese Peninsula which isolated O. rufipogon into disjunct eastern and western populations”
Claim · model-written summary
O. rufipogon now has a continuous distribution under warmer, wetter climate.
- Taxon
- O. rufipogonOryza rufipogone0
- Outcome
- distribution of O. rufipogon is continuouse0
- Qualifier
- Today the climate is warmer and wettere0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Today the climate is warmer and wetter, and the distribution of O. rufipogon is continuous”
Claim · model-written summary
The former xeric region roughly matches today’s transition between Ruf-I and Ruf-II.
- Taxon
- O. rufipogonOryza rufipogone1
- Outcome
- geographic transition area of Ruf-I and Ruf-IIe0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“This xeric region roughly corresponds to the geographic transition area of Ruf-I and Ruf-II today”
e1“the distribution of O. rufipogon is continuous”
Claim · model-written summary
Historical vicariance was suggested as a contributor to O. rufipogon phylogeography.
- Taxon
- O. rufipogonOryza rufipogone0
- Outcome
- phylogeographic patterne0
- Qualifier
- historical vicariancee0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“historical vicariance as another factor that contributes to the phylogeographic pattern in O. rufipogon”
Claim · model-written summary
Species distribution models predicted lower vulnerability of O. rufipogon to future climate change.
- Taxon
- O. rufipogonOryza rufipogone0
- Outcome
- vulnerable to future climate changee0
- Direction
- lesse0
- Qualifier
- future climate changee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“species distribution models predict that O. rufipogon is less vulnerable to future climate change”
Claim · model-written summary
The authors considered gene flow from cultivated rice a greater conservation threat than climate change.
- Taxon
- O. rufipogonOryza rufipogone1
- Outcome
- threat than climate change to the conservation of the speciese0
- Direction
- greatere0
- Comparator
- climate changee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“asymmetric gene flow from cultivated rice is considered to be a greater threat than climate change to the conservation of the species”
e1“the distribution of O. rufipogon is continuous”