DNA barcoding and phylogenetic relationships of Ardeidae (Aves: Ciconiiformes).

The avian family Ardeidae comprises long-legged freshwater and coastal birds. There has been considerable disagreement concerning the intrafamilial relationships of Ardeidae. Mitochondrial cytochrome c oxidase subunit I (COI) was used as a marker for the identification and phylogenetic analysis of avian species. In the present study, we analyzed the COI barcodes of 32 species from 17 genera belonging to the family Ardeidae. Each bird species possessed a barcode distinct from that of other bird species except for Egretta thula and E. garzetta, which shared one barcoding sequence. Kimura two-parameter distances were calculated between barcodes. The average genetic distance between species was 34-fold higher than the average genetic distance within species. Neighbor-joining and maximum likelihood methods were used to construct phylogenetic trees. Most species could be discriminated by their distinct clades in the phylogenetic tree. Both methods of phylogenetic reconstruction suggested that Zebrilus, Tigrisoma, and Cochlearius were an offshoot of the primitive herons. COI gene analysis suggested that the other herons could be divided into two clades: Botaurinae and Ardeinae. Our results support the Great Egret and Intermediate Egret being in separate genera, Casmerodius and Mesophoyx, respectively.

Mitogenome of Fejervarya multistriata: a novel gene arrangement and its evolutionary implications.

In this study, we determined the complete nucleotide sequence of the mitochondrial (mt) DNA of the paddy frog Fejervarya multistriata. mtDNA is 17,750-bp long and contains 13 protein-coding regions, 2 ribosomal RNA, non-coding genes, and 23 tRNA because of the presence of an extra copy of tRNA-Met. The gene arrangements among two related species of Fejervarya were compared, and the combined mtDNA data were subjected to a phylogenetic analysis. Interestingly, we observed a unique translocation of the tRNA-Leu gene, similar to that reported in previous studies on two Fejervarya species. Phylogenetic analyses supported the classification into two evolutionary clades, Ranidae and Dicroglossidae, as well as placement of Hylarana guentheri in the genus Babina. Our results suggested that Fejervarya limnocharis and Fejervarya multistriata may be conspecific, because of its low pairwise genetic distance. However, these results must be further validated with additional analyses.

Characterization and evolution of the mitochondrial DNA control region in Ranidae and their phylogenetic relationship.

The control region is considered to be one of the most variable parts of animal mitochondrial DNA (mtDNA). We compared the mtDNA control region from 37 species representing 14 genera and 4 subfamilies of Ranidae, to analyze the evolution of the control region and to determine their phylogenetic relationship. All the Ranidae species had a single control region, except four species that had two repeat regions. The control region spanned the region between the Cyt b and tRNAleu genes in most of the Ranidae species. The length of the control region sequences ranged from 1186 bp (Limnonectes bannaensis) to 6746 bp (Rana kunyuensis). The average genetic distances among the species varied from 1.94% (between R. chosenica and R. plancyi) to 113.25% (between Amolops ricketti and Euphlyctis hexadactylus). The alignment of three conserved sequence blocks was identified. However, conserved sequence boxes F to A were not found in Ranidae. A maximum likelihood method was used to reconstruct the phylogenetic relationship based on a general time reversible + gamma distribution model. The amount of A+T was higher than G+C across the whole control region. The phylogenetic tree grouped members of the respective subfamilies into separate clades, with the exception of Raninae. Our analysis supported that some genera, including Rana and Amolops, may be polyphyletic. Control region sequence is an effective molecular mark for Ranidae phylogenetic inference.

Predictive potential role of glutathione S-transferase polymorphisms in the prognosis of breast cancer.

The current study aimed at evaluating the associa-tion between GSTM1 null/present, GSTT1 null/present, and GSTP1 IIe105Val polymorphisms and clinical response to chemotherapy and treatment outcome of breast cancers patients. Genotyping of GSTP1 rs1695, GSTT1 deletion, and GSTM1 deletion was performed by Polymerase Chain Reaction Restriction Fragment Length Polymor-phism (PCR-RFLP) assay. We found that patients with GG genotype of GSTP1 IIe105Val and null genotype of GSTM1 were more likely to have a poorer response to chemotherapy than homozygotes of the most frequent genotype; the ORs(95%CI) were 0.37(0.18-0.74) and 0.59(0.36-0.97), respectively. By the Cox proportional hazards model, patients with the GG genotype of GSTP1 IIe105Val and null genotype of GSTM1 were found to be correlated with shorter overall survival of breast cancer; the adjusted HR (95%CI) were 2.51(1.17-5.32) and 2.00(1.15-3.48), respectively. Thus, our findings provided statistical evidence that the variants of GSTP1 and GSTM1 polymorphisms could influence the response to chemotherapy and overall survival in breast cancer patients treated with chemotherapy.

Screening and identification of microsatellite markers associated with cold tolerance in Nile tilapia Oreochromis niloticus.

Tilapia is an important fish cultured in tropical and subtropical areas. Cold sensitivity limits the expansion of tilapia culture into colder regions of the world, and mass mortalities of cultured tilapia have been reported due to severe cold currents in winter. Since the late 1990s, several strains of Nile tilapia have been domesticated to improve the ability to adapt to low temperatures. Previous studies revealed that these varieties were more cold-tolerant than the founder population and overwintered naturally well in ponds in the west-south area of Guangdong Province. In this study, to develop tilapia strains with improved cold tolerance for breeding programs through marker-assisted selection, two microsatellite markers, UNH916 and UNH999, showed complete co-segregation with cold tolerance among the polymorphic microsatellite primers. Our results provide a foundation for identifying resistant gene(s) linked with these markers, as well as identifying simple sequence repeat markers associated with cold tolerance that can be used for maker-assisted selection programs in tilapia breeding to increase the growing range and productivity of tilapia aquaculture.

DNA barcoding and phylogenetic relationships in Timaliidae.

The Timaliidae, a diverse family of oscine passerine birds, has long been a subject of debate regarding its phylogeny. The mitochondrial cytochrome c oxidase subunit I (COI) gene has been used as a powerful marker for identification and phylogenetic studies of animal species. In the present study, we analyzed the COI barcodes of 71 species from 21 genera belonging to the family Timaliidae. Every bird species possessed a barcode distinct from that of other bird species. Kimura two-parameter (K2P) distances were calculated between barcodes. The average genetic distance between species was 18 times higher than the average genetic distance within species. The neighbor-joining method was used to construct a phylogenetic tree and all the species could be discriminated by their distinct clades within the phylogenetic tree. The results indicate that some currently recognized babbler genera might not be monophyletic, with the COI gene data supporting the hypothesis of polyphyly for Garrulax, Alcippe, and Minla. Thus, DNA barcoding is an effective molecular tool for Timaliidae species identification and phylogenetic inference.

DNA barcoding and phylogenetic relationships of genera Picoides and Dendrocopos (Aves: Picidae).

Picoides and Dendrocopos are two closely related genera of woodpeckers (family Picidae), and members of these genera have long been the subjects of phylogenetic debate. Mitochondrial cytochrome c oxidase subunit I (COI) is a powerful marker for the identification and phylogenetic study of animal species. In the present study, we analyzed the COI barcodes of 21 species from the two genera, and 222 variable sites were identified. Kimura two-parameter distances were calculated between barcodes. The average interspecific genetic distance was more than 20 times higher than the average intraspecific genetic distance. The neighbor-joining method was used to construct a phylogenetic tree, and all of the species could be discriminated by their distinct clades. Picoides arcticus was the first to split from the lineage, and the other species were grouped into two divergent clades. The results of this study indicated that the COI genetic data did not support the monophyly of Picoides and Dendrocopos.

DNA barcoding and evolutionary relationships of the Phasianidae family in China.

A DNA barcode is a short sequence of standardized genomic region that is specific to a species. According to studies of bird species, the 694-bp sequence of the mitochondrial gene encoding cytochrome c oxidase 1 (COI) is extremely useful for species identification and phylogeny. In the present study, we analyzed the COI barcodes of 31 species from 18 genera belonging to the Phasianidae family in China. Kimura two-parameter (K2P) distances were calculated between barcodes. We found that the average genetic distance between congeneric species was 24 times higher compared to the average genetic distance within species. Each bird species had a barcode that was distinct to all other bird species. The neighbor-joining method was used to construct a phylogenetic tree, which grouped all of the genera into 2 divergent clades. In conclusion, DNA barcoding is an effective molecular tool for Phasianidae species identification and phylogenetic inference.