2012 Vol. 33, No. E3-4
Masu salmon, Oncorhynchus masou masou, is one of the most valuable fishery species that has been introduced to China, though to date no studies on the genetic diversity and genetic relationship among hatchery populations has been performed with molecular markers. We undertook such a study and sampled 120 individuals from three hatchery stocks and analyzed 20 microsatellite loci. All loci were polymorphic and a total of 91 alleles were detected. A relatively low level of genetic diversity was revealed with effective number of allele of 3.1094, 3.3299 and 3.1894 and expected heterozygosity of 0.6600, 0.6648 and 0.6638 in the three stocks, respectively. Deviations from Hardy-Weinberg equilibrium were found due to heterozygote deficit. Accordingly, evidence of genetic bottlenecks were found in the three stocks. An individual assignment test demonstrated that 85% of individuals were correctly assigned into their original stocks. Pairwise Fst revealed that significant differentiation occurred between these three stocks. The results of the study indicated that disequilibrium of genetic structure and differentiation has occurred in all three stocks. This information collectively provides a basis for measures to avoid of loss of genetic diversity and introgression in Chinese aquaculture.
2012, 33(E3-4): 40-46. doi: 10.3724/SP.J.1141.2012.E03-04E40
The FTZ-F1 genes encode orphan receptors of the nuclear receptor superfamily and in mammals have been found to play important roles in the proper development of the adrenal-gonadal axis and sex-determination. We isolated the homologue of FTZ-F1 in genetically improved farmed tilapia (gfFTZ-F1). The full-length cDNA was isolated from the ovary, which included an open reading frame encoding a predicted protein of 486 amino acids. Sequence, tissue distribution and phylogenic analysis of the FTZ-F1 showed that the gfFTZ-F1 belonged to SF-1/Ad4BP group and that gfFTZ-F1 transcripts were only expressed in the gonads and kidney but not in other tissues. Likewise our data suggests that the gfFTZ-F1 gene may share similar functions with other fish and mammalian counterparts, though further study is needed to make any definitive conclusions.
2012, 33(E3-4): 47-56. doi: 10.3724/SP.J.1141.2012.E03-04E47
Since the birth of molecular evolutionary analysis, primates have been a central focus of study and mitochondrial DNA is well suited to these endeavors because of its unique features. Surprisingly, to date no comprehensive evaluation of the nucleotide substitution patterns has been conducted on the mitochondrial genome of primates. Here, we analyzed the evolutionary patterns and evaluated selection and recombination in the mitochondrial genomes of 44 Primates species downloaded from GenBank. The results revealed that a strong rate heterogeneity occurred among sites and genes in all comparisons. Likewise, an obvious decline in primate nucleotide diversity was noted in the subunit rRNAs and tRNAs as compared to the protein-coding genes. Within 13 protein-coding genes, the pattern of nonsynonymous divergence was similar to that of overall nucleotide divergence, while synonymous changes differed only for individual genes, indicating that the rate heterogeneity may result from the rate of change at nonsynonymous sites. Codon usage analysis revealed that there was intermediate codon usage bias in primate protein-coding genes, and supported the idea that GC mutation pressure might determine codon usage and that positive selection is not the driving force for the codon usage bias. Neutrality tests using site-specific positive selection from a Bayesian framework indicated no sites were under positive selection for any gene, consistent with near neutrality. Recombination tests based on the pairwise homoplasy test statistic supported complete linkage even for much older divergent primate species. Thus, with the exception of rate heterogeneity among mitochondrial genes, evaluating the validity assumed complete linkage and selective neutrality in primates prior to phylogenetic or phylogeographic analysis seems unnecessary.
2012, 33(E3-4): 33-59.
2012, 33(E3-4): 57-59. doi: 10.3724/SP.J.1141.2012.E03-04E57
A new record species Heterodera ripae was found in the rhizosphere soil of nettle (Urtica sp.) on the bank of the Mangniu River in Shenyang City, Liaoning Province, China. The new record species can be characterized by vulval cone bifenestrate with circular or subcircular semifenestrae, vulval slit length averaging 34.2 µm, vulval bridge mostly broad, underbridge weak, bullae absent；the second-stage larvae stylet knobs rather wide and slightly projecting anteriorly，tail length averaging 43.7 µm and hyaline region length averaging 22.3 µm