Transgenic biotechnology and its products provide important solutions for the great challenge of global food security. Biosafety assessment of genetically modified organisms (GMOs) including their food and environmental safety is a prerequisite for the commercialization and safe application of transgenic biotechnology products. However, existing methodologies cannot meet the urgent requirements for rapid biosafety assessment of the increasing number of new and sophisticated GMOs. Therefore, a new, more efficient and objective biosafety assessment methodology is needed. The decision tree, a widely used methodology for data mining and analysis, has a particular function in solving complicated problems. This article introduces the concepts, characteristics, and categorization of a decision tree, as well as methods for decision tree construction. Our objective is to explore the potential of establishing a diagnostic platform for biosafety assessment of GMOs in an efficient and accurate way. This biosafety assessment platform should also be useful for predicting the safety of the new generation of GMOs, and for educating the public on environmental biosafety, thereby providing a solid base for further development of transgenic technology and safe application of transgenic products.

Intra- and inter-population methylation diversity at CCGG sites were surveyed in the genomes of Oryza nivaraandO. rufipogonusing a modified MSAP (methylation-sensitive amplification polymorphism) technique. These two wild species were closely related to cultivated rice in that they share the common A genome. Results revealed that methylated bands were uniform among different individuals of the same IRGC (International Rice Germplasm Center) accession, but polymorphic among different populations within the IRGC. Methylated bands could be divided into two categories, i.e., the conserved group (Class I), and the polymorphic group (Class II). Comparing the gene sequences of the two classes to the homologous sequences of japonica and indica varieties, Class I was conservative, but Class II was variable and evolutionarily active. DNA methylation diversity was an informative indicator of genetic diversity in Oryza. However, further studies of population differentiation and species evolution are needed.

Betula luminifera, a precious timber species in southern mountain areas of China, can be found only in natural reserves because of over harvesting. We examined the genetic diversity and genetic structure of six natural populations of B. luminifera distributed in Zhejiang, Fujian, Jiangxi, Guangxi, and Guizhou using AFLP markers. A total of 323 polymorphic loci were amplified and 355 alleles were detected using nine pairs of primers. Percentage of polymorphism loci (PPL) ranged 93.20-98.60% and Nei’s gene diversity (h_j) ranged 0.3143-0.3645, suggesting a high genetic diversity in natural populations of B. luminifera. At the species level, the total genetic diversity (H_t) was 0.3616. High gene flow (N_m = 3.5962) was detected among populations, and the genetic differentiation coefficient was 0.0650. AMOVA analysis showed that genetic variation among the populations accounted for 11.49% of the total. Genetic distance was the largest (0.0665) between Zhejiang (LA) and Guizhou (XW) populations and the smallest (0.0173) between Jiangxi (LN) and Guangxi (LS) populations, indicating that LN and LS populations may originate from the same ancestor. Mantel test revealed that genetic distance was not significantly related to geographical distance (r = 0.423,P = 0.113) but was significantly relative to average temperature difference of each location (r = 0.449, P = 0.017). In combination with on-site investigation, we conclude that the present status of genetic diversity and genetic structure of natural populations of B. luminifera was strongly affected by harvesting and habitat fragmentation. We propose some suggestions on its conservation.

In this study, rDNA ITS sequences were analyzed to compare the genetic diversity of Brachionus calyciflorus from the coal ash contaminated (Lake Hui) and two uncontaminated lakes (Lake Tingtang and Lake Fengming). The results showed that two sibling species in Brachionus calyciflorus species complex were defined in both Lake Tingtang and Lake Fengming, but only one sibling species was found in Lake Hui. The coal ash pollution decreased the number of sibling species. Based on the sequences of sibling species I coexisting in all the three lakes, the haplotype diversity of the rotifer population from Lake Hui was the lowest (h=0.9516), and the nucleotide diversity of the rotifer population from Lake Hui (π=0.0066) was lower than that from Lake Tingtang (π=0.0073) but higher than that from Lake Fengming (π=0.0052). The lowest nucleotide diversity of the rotifer population from Lake Fengming might be attributed to the combined effects of the pollution from surrounding agricultural fields and higher predation pressure from Asplanchna and copepod. Among the three lakes, a lower N_m (1.95) but a higher F_st (0.11358) were found between rotifer populations from Lake Tingtang and Lake Fengming, but higherN_m values (>4) were confirmed between the rotifer populations from Lake Hui and Lake Tingtang as well as Lake Hui and Lake Fengming, with the lowerF_st values of 0.03535 and 0.00276, respectively. AMOVA indicated that a higher percentage of variation (12.87%) was found between the populations from Lake Tingtang and Lake Fengming, but lower percentages (3.78% and 2.78%) were evaluated between the populations from Lake Hui and Lake Tingtang as well as Lake Hui and Lake Fengming. There was a moderate level of gene exchange, but no obvious differentiation between the populations from coal ash polluted and unpolluted lakes.

To assess the genetic diversity, population structure and demographic history of Neosalanx jordani, we sequenced complete mitochondrial DNA (1,141 bp) from the cytochrome b (cyt b) gene for 129 individuals from five populations in the Yangtze River and the Huaihe River basins. We identified18 haplotypes, and haplotype diversity was high (h=0.590±0.047). Nucleotide diversity was relatively low (π = 0.00088±0.00011) among all haplotypes. Phylogenetic analysis failed to detect significant geographic structure. Analysis of molecular variance (AMOVA) revealed significant genetic subdivision among individuals within populations and among populations within basins but not between basins, indicating distribution of genetic diversity was inconsistent with contemporary hydrological structure. We suggest that the present complex genetic pattern ofN. jordani resulted from multiple unrelated founding dispersal events (long-distance colonization), contiguous population expansion, and restricted gene flow. Demographic analysis revealed that this species may have experienced a relatively recent population expansion, and the majority of mutations occurred 18.97 kyr ago. This timing is consistent with the estimated time of sea level rise and the formation of large-scale appropriate habitats during the last glacial maximum (LGM). Thus, we suggest that all populations, especially those with high genetic diversity, should be separately managed and conserved.

Based on the differences in caudal peduncle, snout length, predorsal profile and the lateral color pattern, Ng & Kottelat ( 2007) supposed that the currently recognized Pseudobagrus fulvidraco represent at least two distinct species, P. sinensis from northern China and P. fulvidraco from southern China. We examined the forenamed morphologic characters and sequenced the cytochrome bgene segments of 70 specimens to test the validity of P. sinensis. We found the differences in predorsal profile and the lateral color pattern do not occur together with the differences in caudal peduncle and snout length. Results of molecular phylogenetic and population genetic analyses were: (1) the most common haplotype detected was shared by P. sinensis and P. fulvidraco; (2) the reciprocal monophyly of both species was not confirmed whereas all samples of the two species were grouped in a monophyletic cluster with 100% bootstrap support; (3) gene flow is ongoing between populations of P. sinensis and P. fulvidraco (Nm = 4.7); and (4) the haplotype network did not detect any disjoint groups corresponding to the two species. We thus speculate that P. sinensis is not valid species but probably a synonym of P. fulvidraco. Low genetic divergence was detected among P. fulvidraco populations of China’s main river drainages, which was supposed to be resulted from a recent population expansion that occurred about 101,000-141,000 years ago. No significant geological architecture was detected from Chinese populations ofP. fulvidraco and the historical river connection might have promoted the gene exchange among different geological populations.

Morphological taxonomy in the fish sub-family Cynoglossinae is complicated and contentious. To clarify these ambiguities, the molecular phylogenic relationships among 14 Cynoglossinae species were studied by analyzing partial 16S rRNA and Cyt b mitochondrial gene sequences. Similar phylogentic topology inferred from both gene fragments demonstrated that Cynoglossinae is a monophyletic group. However, the phylogenetic relationships revealed by the mitochondrial DNA sequence analyses were not consistent with those inferred from morphological classification. In contrast with morphological classification, reciprocal monophyly was not detected between Paraplagusis japonica and the species in the genus Cynoglossus. Neighbor-Joining (NJ) and Maximum Parsimony (MP) trees showed that those species in the three sub-genera Cynoglossus, Cynoglossoides and Areliscus clustered on an independent branch. Also, synonymic phenomena possibly existed in the following three groups of species: C. lighti andC. joyner, C. abbreviatus and C. purpureomaculatus, as well as in C. semilaevis, C. gracilis and C. trigrammus. Our results highlight the open questions surrounding the morphological classification of Cynoglossinae species. Information on molecular phylogenic relationships will likely be of help in revising the morphological classification of Cynoglossinae species.

Scale is a critical factor in species ecology, and multi-scale approaches can potentially better depict the relationship of the bird species and environment. Yellow River Delta Nature Reserve(YRDNR)is a important site for red-crowned crane during migration and wintering. By using habitat suitability models and varying the spatial scale from 10 to 1,500 ha, we developed univariate models to analyze contributions of each environmental factor at each spatial scale to red-crowned crane occurrence. Moreover, multivariate models at single and multi-scales were built to seek optimum habitat suitability model. The results showed that univariate models varied among the environmental factors and with spatial scales. Within multivariate models, the single-scale model at the 50 ha scale performed best. The multi-scale model, in which each environmental variable was entered at the scale at which it had performed best in the univariate model, was superior to all single-scale models. Moreover, the results showed that the suitable habitat area of red-crowned crane in the southern part of YRDNR is far more than in the north. For effective protection of red-crowned crane habitat in YRDNR, we suggest that monitoring, assessment, reassignment of wetland should be strengthened and human disturbance should be under surveillance.

Acer barbinerve(Aceraceae) is one of several understory tree species which occur in temperate forests in the Changbai Mountain region in Northeast China. We studied sex ratios and the spatial distributions of A. barbinerve and their relationships with environmental factors. In 2009, we mapped and sexed all reproductive A. barbinervetrees within a 5.2-ha (260 m×200 m) middle-aged experimental field plot and a 1.0-ha (100 m × 100 m) old-growth plot. In both plots, the sex ratio of reproductive trees was significantly male-biased. A further analysis revealed that the sex ratio was male-biased in small trees (DBH < 2 cm), and turned to a balanced ratio in larger individuals (DBH ≥ 2 cm), suggesting that males may reach maturity at smaller size than females. A univariate O-ring statistical analysis showed that under the complete spatial randomness (CSR) null model, males and females in the middle-aged plot occurred as clumped distributions at 0-88 m scales and 1-13 m scales, respectively. And both genders were distributed randomly in the old-growth plot. Under the heterogeneous Poisson null model, males and females were distributed randomly at 0-100 m scales in the middle-aged plot. The bivariate O-ring statistics indicated that under the random labeling null model, males and females showed spatial repulsion at 1-4 m scales, and then occurred as spatial independence at 4-100 m scales in the middle-aged plot, and both genders showed spatial independence at 0-50 m scales in the old-growth plot. Apparently, both males and females were influenced more by environmental heterogeneity in the middle-aged plot than in the old-growth one. Stand density were found to have a negative relationship with the distribution of females in the middle-aged plot, but it only explained 3.73% of the total variation, and showed litter effect on males. Environmental factors explained even less in the old-growth plot.

Based on the ongoing Sino-German grazing experiment, which was designed to test how grazing intensity and management regimes (traditional system vs. mixed system) would affect the aboveground net primary productivity (ANPP) and compensatory growth of a typical steppe ecosystem in Inner Mongolia dominated by Leymus chinensis and Stipa grandis. Our experimental treatments included two management systems (e.g., a traditional versus a mixed system) and seven levels of stocking (i.e., 0, 1.5, 3.0, 4.5, 6.0, 7.5, and 9.0 sheep/ha). The traditional system was managed with grazing and haymaking on two different areas. The mixed system was managed with a yearly shift between grazing and haymaking on the same area. The results showed that, with increasing stocking rate, aboveground net primary productivity (ANPP) declined in both traditional and mixed grazing plots. At high stocking rates, ANPP in mixed grazing plots was significantly higher than that in the traditional grazing plots. Our results were partially in agreement with the grazing optimization hypothesis. Under the two management regimes, and using different methods for estimating the annual ANPP, we observed overcompensation, equal-compensation, and under-compensation in plant growth along a gradient of stocking rates. Equal-compensation was generally observed in the low stocking rate plots, while under-compensation was found in the high stocking rate plots. For most systems, compensatory growth could be simulated with linear or quadratic models when the percent biomass eaten by sheep was used as an index for estimating the relative stocking rate. Our study suggests that stocking rate, grazing regime, topographic position, and methods for estimating the net aboveground productivity were all important factors determining the magnitude and directions of estimated ANPP responses to grazing.

Spatial patterns of species richness and range size along environmental gradients have long been central issues to biogeography and biodiversity. Because of their unique isolation effects on species distributions, much emphasis has been put on insular environments in developing and testing biogeography theories. Rapoport’s rule suggested an increasing trend of species range width along with increasing altitude. Taiwan, the largest island in China, is characterized by a significant altitudinal gradient, subtropical monsoon climate, as well as a rich and unique flora. Here, we offer the first report on the altitudinal patterns of species richness and species range size of Taiwan’s vascular plants, and analyze the relationship between altitudinal range size and range midpoint to test Rapoport’s rule. We established a database of 4,751 plant species (including subspecies levels), belonging to 241 families and 1,466 genera. Among these, 3,330 species have altitudinal range records and were analyzed. Taxonomic richness at the family, genus and species levels decreased with increasing elevation in terms of all plants and invasive species, and a hump-shaped altitudinal pattern of species richness was found for endemic plants. With regard to taxonomic groups, pteridophytes and gymnosperms richness exhibited hump-shaped patterns, while decreasing richness with increasing altitude was found for three subgroups in angiosperm (i.e. herbs, evergreen and deciduous woody plants). Relationships between species range size and midpoint elevation varied among assemblages as well as among methods applied to the same assemblage. The distribution of invasive plants supported Rapoport’s rule, while that of endemic species and overall species did not. The distribution of pteridophytes supported Rapoport’s rule, while gymnosperms did not. For angiosperms, no consistent patterns were found when different methods were applied. By comparing Taiwan and adjacent large insular and continental mountains, we suggest that the altitudinal patterns of precipitation might contribute to that of species richness. Our test of Rapoport’s rule suggested that, even on the same mountain, altitudinal variation of distributional patterns among different assemblages can result from different mechanisms.