Parallel Speciation of Wild Rice Associated with Habitat Shifts.

The occurrence of parallel speciation strongly implies the action of natural selection. However, it is unclear how general a phenomena parallel speciation is since it was only shown in a small number of animal species. In particular, the adaptive process and mechanisms underlying the process of parallel speciation remain elusive. Here, we used an integrative approach incorporating population genomics, common garden, and crossing experiments to investigate parallel speciation of the wild rice species Oryza nivara from O. rufipogon. We demonstrated that O. nivara originated multiple times from different O. rufipogon populations and revealed that different O. nivara populations have evolved similar phenotypes under divergent selection, a reflection of recurrent local adaptation of ancient O. rufipogon populations to dry habitats. Almost completed premating isolation was detected between O. nivara and O. rufipogon in the absence of any postmating barriers between and within these species. These results suggest that flowering time is a "magic" trait that contributes to both local adaptation and reproductive isolation in the origin of wild rice species. Our study thus demonstrates a convincing case of parallel ecological speciation as a consequence of adaptation to new environments.

Population genetic structure of Oryza rufipogon and Oryza nivara: implications for the origin of O. nivara.

Ecological speciation plays a primary role in driving species divergence and adaptation. Oryza rufipogon and Oryza nivara are two incipient species at the early stage of speciation with distinct differences in morphology, life history traits and habitat preference, and therefore provide a unique model for the study of ecological speciation. However, the population genetic structure of the ancestral O. rufipogon has been controversial despite substantial study, and the origin of the derivative O. nivara remains unclear. Here, based on sequences of 10 nuclear and two chloroplast loci from 26 wild populations across the entire geographic ranges of the two species, we conducted comprehensive analyses using population genetics, phylogeography and species distribution modelling (SDM) approaches. In addition to supporting the two previously reported major subdivisions, we detected four genetically distinct groups within O. rufipogon and found no correlation between the genetic groups and either species identity or geographical regions. The SDM clearly showed substantial change in the distribution range of O. rufipogon in history, demonstrating that the repeated extinction and colonization of local populations due to multiple glacial-interglacial cycles during the Quaternary was most likely the main factor shaping the confounding population genetic structure of O. rufipogon. Moreover, we found significant differences between the two species in climate preferences, suggestive of an important role for climatic factors in the adaptation, persistence and expansion of O. nivara. Finally, based on the genetic pattern and dynamics of the O. nivara populations, we hypothesize that O. nivara might have independently originated multiple times from different O. rufipogon populations.

Prediction of pathological activity in Crohn's disease based on dual-energy CT enterography.

PURPOSE: To explore the feasibility of predicting the pathological activity of Crohn's disease (CD) based on dual-energy CT enterography (DECTE). METHODS: The clinical, endoscopic, imaging and pathological data of 55 patients with CD scanned by DECTE were retrospectively analyzed; the pathological results were used as a reference standard to classify the diseased bowel segments into active and inactive phases. The normalized iodine concentration (NIC), energy-spectrum curve slope K, dual energy index (DEI), fat fraction (FF) of the arterial phases and venous phases were compared. To assess the parameters' predictive ability, receiver-operating characteristic curves were used. The Delong test was used to compare the differences between the diagnostic efficiency of each parameter. RESULTS: A total of 84 intestinal segments were included in the study, including 54 active intestinal segments and 30 inactive intestinal segments. The NIC, energy-spectrum curve slope K and DEI were significantly different between active and inactive bowel segments in the arterial and venous phases (P < 0.05), while FF were not significantly different (P > 0.05). The largest area under the curve (AUC) of NIC, energy-spectrum curve slope K and DEI were higher in arterial phase than in venous phase. For identifying the intestinal activity of CD, the maximum AUC of NIC in arterial phase was 0.908, with a sensitivity of 0.833 and a specificity of 0.800, and the DEI in arterial phase had the highest sensitivity (0.944). CONCLUSION: The NIC, energy-spectrum curve slope K and DEI can effectively distinguish the active and inactive phases of the intestinal segments of CD patients and provide good assistance for determining further treatment.

Development of microsatellite markers for Miscanthus sinensis (Poaceae) and cross-amplification in other related species.

PREMISE OF THE STUDY: We developed microsatellite loci for the biomass crop Miscanthus sinensis to investigate genetic diversity and population structure of M. sinensis and its closely related species. METHODS AND RESULTS: Fourteen microsatellite loci were identified from an enriched genomic library of M. sinensis and tested in one M. sinensis population. The number of alleles per locus ranged from 1 to 15, with a mean of 7.0. The observed and expected heterozygosities varied from 0.318 to 0.864 and from 0.424 to 0.901, respectively. Of them, 12 primers could be applied to three other species in Miscanthus (M. sacchariflorus, M. floridulus, and M. lutarioriparius). CONCLUSIONS: These markers will be important for further analyzing population genetics and evolutionary history, as well as facilitating molecular breeding of Miscanthus sinensis and its related species.

Predictive Value of Early Response to Chemoradiotherapy in Advanced Esophageal Squamous Cell Carcinoma by Diffusion-Weighted MR Imaging.

OBJECTIVE: To explore the value of diffusion-weighted imaging for early response detection of locally advanced esophageal squamous cell carcinoma with concurrent chemoradiotherapy. METHODS: Fifty-five (42 males, 13 females) patients with locally advanced esophageal cancer who were undergoing chemoradiotherapy were recruited for this study. Diffusion-weighted imaging was performed in all patients before therapy, at the first weekend, the second weekend, and the end of chemoradiotherapy. The rate of change in apparent diffusion coefficient value and the maximum diameter between pretherapy and posttherapy were calculated. RESULTS: Fifty-five patients with locally advanced esophageal squamous cell carcinoma were classified as responders (40 cases) and nonresponders (15 cases). Before chemoradiotherapy, the responders group had a significantly lower apparent diffusion coefficient values than the nonresponders group (t = -4.815, P = .000). At the 3 time points after chemoradiotherapy (first weekend, second weekend, and the end of chemoradiotherapy), there was no statistically significant difference in apparent diffusion coefficient values between responders and nonresponders (P > .05). The responders group had a significantly higher rate of change in apparent diffusion coefficient value than the nonresponders group at each time point (P < .05). At the first weekend of chemoradiotherapy, the rate of change in the maximum diameter was not significantly different in the 2 groups (t = 0.928, P = .357). There was a negative correlation between the tumor apparent diffusion coefficient value of pretherapy and the reduction ratio of tumor maximum diameter at the end of chemoradiotherapy (r = -0.592, P = .000). CONCLUSIONS: The change rate of apparent diffusion coefficient value by the end of the first week after beginning chemoradiotherapy may be a sensitive indicator to detect the early response to locally advanced esophageal squamous cell carcinoma.

Isolation and characterization of microsatellite loci for a bioenergy grass, Miscanthus sacchariflorus (Poaceae).

PREMISE OF THE STUDY: Microsatellite loci were developed for the biomass C4 grass, Miscanthus sacchariflorus, and proved to be suitable markers for population genetic studies and germplasm management of this species. • METHODS AND RESULTS: Twenty-three polymorphic microsatellite loci were identified from an enriched genomic library of M. sacchariflorus. The polymorphism was assessed in 50 individuals from two populations in China. The number of alleles per locus varied from two to 18, with a mean of 8.13. The observed and expected heterozygosities ranged from 0.2 to 1.0 and from 0.198 to 0.898, respectively. • CONCLUSIONS: These new markers will be useful for further investigation of genetic diversity and population genetic structure as well as molecular breeding of Miscanthus species.

Contrasting population genetic structure and gene flow between Oryza rufipogon and Oryza nivara.

The cross compatible wild relatives of crops have furnished valuable genes for crop improvement. Understanding the genetics of these wild species may enhance their further use in breeding. In this study, sequence variation of the nuclear Lhs1 gene was used to investigate the population genetic structure and gene flow of Oryza rufipogon and O. nivara, two wild species most closely related to O. sativa. The two species diverge markedly in life history and mating system, with O. rufipogon being perennial and outcrossing and O. nivara being annual and predominantly inbreeding. Based on sequence data from 105 plants representing 11 wild populations covering the entire geographic range of these wild species, we detected significantly higher nucleotide variation in O. rufipogon than in O. nivara at both the population and species levels. At the population level the diversity in O. rufipogon (Hd = 0.712; theta (sil) = 0.0017) is 2-3 folds higher than that in O. nivara (Hd = 0.306; theta (sil) = 0.0005). AMOVA partitioning indicated that genetic differentiation among O. nivara populations (78.2%) was much higher than that among O. rufipogon populations (52.3%). The different level of genetic diversity and contrasting population genetic structure between O. rufipogon and O. nivara might be explained by their distinct life histories and mating systems. Our simulation using IM models demonstrated significant gene flow from O. nivara to O. rufipogon, indicating a directional introgression from the annual and selfing species into the perennial and outcrossing species. The ongoing introgression has played an important role in shaping current patterns of genetic diversity of these two wild species.

Microsatellite analysis of genetic diversity and population genetic structure of a wild rice (Oryza rufipogon Griff.) in China.

Genetic diversity and population genetic structure of natural Oryza rufipogon populations in China were studied based on ten microsatellite loci. For a total of 237 individuals of 12 populations collected from four regions, a moderate to high level of genetic diversity was observed at population levels with the number of alleles per locus ( A) ranging from 2 to 18 (average 10.6), and polymorphic loci ( P) from 40.0% to 100% (average 83.3%). The observed heterozygosity ( H(O)) varied from 0.163 to 0.550 with the mean of 0.332, and the expected heterozygosity ( H(E)) from 0.164 to 0.648 with the mean of 0.413. The level of genetic diversity for Guangxi was the highest. These results are in good agreement with previous allozyme and RAPD studies. However, it was unexpected that high genetic differentiation among populations was found ( R(ST) = 0.5199, theta = 0.491), suggesting that about one-half of the genetic variation existed between the populations. Differentiation (pairwise theta) was positively correlated with geographical distance ( r = 0.464), as expected under the isolation by distance model. The habitat destruction and degradation throughout the geographic range of O. rufipogon may be the main factor attributed to high genetic differentiation among populations of O. rufipogon in China.