Population status, threats and conservation of the Yangtze finless porpoise

The Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis) is currently limited to the middle and lower reaches of the Yangtze River from Yichang to Shanghai, China, and the adjoining Poyang and Dongting Lakes. Its population size has decreased remarkably during the last several decades due to the heavy impact of human activities, including overfishing of prey species, water development projects that cause attendant habitat loss and degradation, water pollution, and accidental deaths caused by harmful fishing gear and collisions with motorized vessels. It was estimated that the number of remaining individuals was down to approximately 1800 in 2006, a number that is decreasing at a rate as high as 5% per year. Three conservation measures - in situ and ex situ conservation and captive breeding have been applied to the protection of this unique porpoise since the early 1990s. Seven natural and two "semi-natural" reserves have so far been established. Since 1996, a small group of finless porpoises has been successfully reared in a facility at the Institute of Hydrobiology of the Chinese Academy of Sciences; three babies were born in captivity on July 5, 2005, June 2, 2007 and July 5, 2008. These are the first freshwater cetaceans ever born in captivity in the world. Several groups of these porpoises caught in the main stream of the Yangtze River, or rescued, have been introduced into the Tian'e-Zhou Semi-natural Reserve since 1990. These efforts have proven that, not only can these animals survive in the area, they are also to reproduce naturally and successfully. More than 30 calves had been born in the reserve since then, with one to three born each year. Taking deaths and transfers into account, there were approximately 30 individuals living in the reserve as of the end of 2007. Among eight mature females captured in April 2008, five were confirmed pregnant. This effort represents the first successful attempt at off-site protection of a cetacean species in the world, and establishes a solid base for conservation of the Yangtze finless porpoise. A lesson must be drawn from the tragedy of Chinese River Dolphin (Lipotes vexillifer), which has already been declared likely extinct. Strong, effective and appropriate protective measures must be carried out quickly to prevent the Yangtze finless porpoise from becoming a second Chinese River Dolphin, and save the biodiversity of the Yangtze River as a whole

Investigations into the perplexing interrelationship of the Genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodontidae)

The phylogenetic relationships within the genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodontidae) remain unresolved. Because of the use of Takifugu as model organisms, the resolution of these relationships is crucial for the interpretation of evolutionary trends in biology. Pufferfishes of this genus are comprised of a comparatively small number of species and are mainly distributed along the coastal region of the western part of the Sea of Japan and the coastline of China. Mitochondrial gene sequences were employed to test the phylogenetic hypotheses within the genus. Seventeen species of the genus were examined. Molecular phylogenetic trees were constructed using the maximum parsimony, neighbor-joining, maximum likelihood and Bayesian methods. Our hypothesis of internal relationships within the genus differs from previous hypotheses. Our results indicate that (1) the genus Takifugu is a monophyletic assemblage; (2) the genus is divided into 6 subgroups based on the molecular data; and (3) there is low genetic diversity among the species within this genus. In addition, speciation within Takifugu appears to be driven by hybridization and isolation by distribution. Our results also suggested that the taxonomy in the genus should be clarified based on both molecular and morphological data.The phylogenetic relationships within the genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodontidae) remain unresolved. Because of the use of Takifugu as model organisms, the resolution of these relationships is crucial for the interpretation of evolutionary trends in biology. Pufferfishes of this genus are comprised of a comparatively small number of species and are mainly distributed along the coastal region of the western part of the Sea of Japan and the coastline of China. Mitochondrial gene sequences were employed to test the phylogenetic hypotheses within the genus. Seventeen species of the genus were examined. Molecular phylogenetic trees were constructed using the maximum parsimony, neighbor-joining, maximum likelihood and Bayesian methods. Our hypothesis of internal relationships within the genus differs from previous hypotheses. Our results indicate that (1) the genus Takifugu is a monophyletic assemblage; (2) the genus is divided into 6 subgroups based on the molecular data; and (3) there is low genetic diversity among the species within this genus. In addition, speciation within Takifugu appears to be driven by hybridization and isolation by distribution. Our results also suggested that the taxonomy in the genus should be clarified based on both molecular and morphological data

Predominant occurrence of apical cell divisions in Oedogoniam pakistanense and its phylogenetic significance

A rare terrestrial species, Oedogonium pakistanense, was first recorded from Hubei Province, south-central China. Morphological characters. including the predominant occurrence of apical cell division and unique lateral apical caps, are described. The growth of the filaments in O. pakistanense from China is usually the result of the repeated divisions of the apical cells and intercalary divisions are rare. It is suggested that this species may represent an evolutionary transition between Oedogonium and Oedocladium, the latter being a terrestrial genus with branched filaments and cell division more often terminal than intercalary.A rare terrestrial species, Oedogonium pakistanense, was first recorded from Hubei Province, south-central China. Morphological characters. including the predominant occurrence of apical cell division and unique lateral apical caps, are described. The growth of the filaments in O. pakistanense from China is usually the result of the repeated divisions of the apical cells and intercalary divisions are rare. It is suggested that this species may represent an evolutionary transition between Oedogonium and Oedocladium, the latter being a terrestrial genus with branched filaments and cell division more often terminal than intercalary

Spatiotemporal heterogeneity of plankton communities in Lake Donghu, China, as revealed by PCR-denaturing gradient gel electrophoresis and its relation to biotic and abiotic factors

The 16S and 18S rRNA genes of planktonic organisms derived from five stations with nutrient gradients in Lake Donghu, China, were studied by PCR-denaturing gradient gel electrophoresis (DGGE) fingerprinting, and the relationships between the genetic diversity of the plankton community and biotic/abiotic factors are discussed. The concentrations of total nitrogen (TN), total phosphorus (TP), NH4-N and As were found to be significantly related (P < 0.05) to morphological composition of the plankton community. Both chemical and morphological analyses suggested that temporal heterogeneity was comparatively higher than spatial heterogeneity in Lake Donghu. Although the morphological composition was not identical to the DGGE fingerprints in characterizing habitat similarity, the two strongest eutrophic stations (I and II) were always initially grouped into one cluster. Canonical correspondence analysis suggested that the factors strongly correlated with the first two ordination axes were seasonally different. The concentrations of TN and TP and the densities of rotifers and crustaceans were generally the main factors related to the DGGE patterns of the plankton communities. The study suggested that genetic diversity as depicted by metagenomic techniques (such as PCR-DGGE fingerprinting) is a promising tool for ecological study of plankton communities and that such techniques are likely to play an increasingly important role in assessing the environmental conditions of aquatic habitats.The 16S and 18S rRNA genes of planktonic organisms derived from five stations with nutrient gradients in Lake Donghu, China, were studied by PCR-denaturing gradient gel electrophoresis (DGGE) fingerprinting, and the relationships between the genetic diversity of the plankton community and biotic/abiotic factors are discussed. The concentrations of total nitrogen (TN), total phosphorus (TP), NH4-N and As were found to be significantly related (P < 0.05) to morphological composition of the plankton community. Both chemical and morphological analyses suggested that temporal heterogeneity was comparatively higher than spatial heterogeneity in Lake Donghu. Although the morphological composition was not identical to the DGGE fingerprints in characterizing habitat similarity, the two strongest eutrophic stations (I and II) were always initially grouped into one cluster. Canonical correspondence analysis suggested that the factors strongly correlated with the first two ordination axes were seasonally different. The concentrations of TN and TP and the densities of rotifers and crustaceans were generally the main factors related to the DGGE patterns of the plankton communities. The study suggested that genetic diversity as depicted by metagenomic techniques (such as PCR-DGGE fingerprinting) is a promising tool for ecological study of plankton communities and that such techniques are likely to play an increasingly important role in assessing the environmental conditions of aquatic habitats

A high sensitivity iron-dependent bioreporter used to measure iron bioavailability in freshwaters

A Nostoc sp. PCC 7120 iron bioreporter containing iron-regulated schizokinen transporter gene alr0397 promoter fused to the luxAB genes was examined to optimize its response to bioavailable iron. Doseresponse relationships between luciferase activity and free ferric ion (Fe3+) concentrations pFe (-lg [Fe3+]) were generated by measuring luciferase activities of the bioreporter in trace metalbuffered Fraquil medium with various incubation times. The results were best demonstrated by sigmoidal curves (pFe 18.821.7, Fe3+ = 10-18.810-21.7 M) with the linear range extending from pFe 19.621.5 (Fe3+ = 10-19.610-21.5 M) after a 12-h incubation time. Optimal conditions for the use of this bioreporter to sense the iron bioavailability were determined to be: a 12-h exposure time, initial cell density of OD730 nm = 0.06, high nitrate (100 mu M), high phosphate (10 mu M), moderate Co2+ (0.122.5 nM), Zn2+ (0.1612 nM), Cu2+ (0.0450 nM), and wide range of Mn2+ concentration (0.922300 nM). The applicability of using this iron bioreporter to assess iron availability in the natural environment has been tested using water samples from eutrophic Taihu, Donghu, and Chaohu lakes. It is indicated that the bioreporter is a useful tool to assess bioavailable iron in various water quality samples, especially in eutrophic lakes with high bioavailable iron.A Nostoc sp. PCC 7120 iron bioreporter containing iron-regulated schizokinen transporter gene alr0397 promoter fused to the luxAB genes was examined to optimize its response to bioavailable iron. Doseresponse relationships between luciferase activity and free ferric ion (Fe3+) concentrations pFe (-lg [Fe3+]) were generated by measuring luciferase activities of the bioreporter in trace metalbuffered Fraquil medium with various incubation times. The results were best demonstrated by sigmoidal curves (pFe 18.821.7, Fe3+ = 10-18.810-21.7 M) with the linear range extending from pFe 19.621.5 (Fe3+ = 10-19.610-21.5 M) after a 12-h incubation time. Optimal conditions for the use of this bioreporter to sense the iron bioavailability were determined to be: a 12-h exposure time, initial cell density of OD730 nm = 0.06, high nitrate (100 mu M), high phosphate (10 mu M), moderate Co2+ (0.122.5 nM), Zn2+ (0.1612 nM), Cu2+ (0.0450 nM), and wide range of Mn2+ concentration (0.922300 nM). The applicability of using this iron bioreporter to assess iron availability in the natural environment has been tested using water samples from eutrophic Taihu, Donghu, and Chaohu lakes. It is indicated that the bioreporter is a useful tool to assess bioavailable iron in various water quality samples, especially in eutrophic lakes with high bioavailable iron

Sinigarra napoense, a new genus and species of labeonin fishes (Teleostei: Cyprinidae) from Guangxi Province, South China

A new garrain genus and species are described from the Zuo-Jiang of the Zhu-Jiang (Pearl River) drainage in Guangxi Province, South China. Sinigarra, new genus, is characterized by having the lower lip modified into a mental adhesive disc posteriorly discontinuous with the mental region. It is distinguished from all other disc-bearing genera, namely Garra, Placocheilus, Discocheilus and Discogobio, by having the anterior edge of the mental adhesive disc not modified to form an anteromedian crescentic fold, an upper lip present, but separated from the upper jaw, and indistinct papillae scarcely scattered over the rostral cap and lower lip or absent.A new garrain genus and species are described from the Zuo-Jiang of the Zhu-Jiang (Pearl River) drainage in Guangxi Province, South China. Sinigarra, new genus, is characterized by having the lower lip modified into a mental adhesive disc posteriorly discontinuous with the mental region. It is distinguished from all other disc-bearing genera, namely Garra, Placocheilus, Discocheilus and Discogobio, by having the anterior edge of the mental adhesive disc not modified to form an anteromedian crescentic fold, an upper lip present, but separated from the upper jaw, and indistinct papillae scarcely scattered over the rostral cap and lower lip or absent

Cloning and sequence analysis of Sox genes in a tetraploid cyprinid fish, Tor douronensis

A PCR survey for Sox genes in a young tetraploid fish Tor douronensis (Teleostei: Cyprinidae) was performed to access the evolutionary fates of important functional genes after genome duplication caused by polyploidization event. Totally 13 Sox genes were obtained in Tor douronensis, which represent SoxB, SoxC and SoxE groups. Phylogenetic analysis of Sox genes in Tor douronensis provided evidence for fish-specific genome duplication, and suggested that Sox19 might be a teleost specific Sox gene member. Sequence analysis revealed most of the nucleotide substitutions between duplicated copies of Sox genes caused by tetraploidization event or their orthologues in other species are silent substitutions. It would appear that the sequences are under purifying selective pressure, strongly suggesting that they represent functional genes and supporting selection against all null allele at either of two duplicated loci of Sox4a, Sox9a and Sox9b. Surprising variations of the intron length and similarities of two duplicated copies of Sox9a and Sox9b, suggest that Tor douronensis might be an allotetraploidy.A PCR survey for Sox genes in a young tetraploid fish Tor douronensis (Teleostei: Cyprinidae) was performed to access the evolutionary fates of important functional genes after genome duplication caused by polyploidization event. Totally 13 Sox genes were obtained in Tor douronensis, which represent SoxB, SoxC and SoxE groups. Phylogenetic analysis of Sox genes in Tor douronensis provided evidence for fish-specific genome duplication, and suggested that Sox19 might be a teleost specific Sox gene member. Sequence analysis revealed most of the nucleotide substitutions between duplicated copies of Sox genes caused by tetraploidization event or their orthologues in other species are silent substitutions. It would appear that the sequences are under purifying selective pressure, strongly suggesting that they represent functional genes and supporting selection against all null allele at either of two duplicated loci of Sox4a, Sox9a and Sox9b. Surprising variations of the intron length and similarities of two duplicated copies of Sox9a and Sox9b, suggest that Tor douronensis might be an allotetraploidy

A niche model to predict Microcystis bloom decline in Chaohu Lake, China

Cyanobacterial blooms occur frequently in lakes due to eutrophication. Although a number of models have been proposed to forecast algal blooms, a good and applicable method is still lacking. This study explored a simple and effective mathematical-ecological model to evaluate the growth status and predict the population dynamics of Microcystis blooms. In this study, phytoplankton were collected and identified from 8 sampling sites in Chaohu Lake every month from July to October, 2010. The niche breadth and niche overlap of common species were calculated using standard equations, and the potential relative growth rates of Microcystis were calculated as a weighted-value of niche overlap. In July, the potential relative growth rate was 2.79 (a.u., arbitrary units) but then rapidly declined in the following months to -3.99 a.u. in September. A significant correlation (R =0.998, P < 0.01) was found in the model between the net-increase in biomass of Microcystis in the field and the predicted values calculated by the niche model, we concluded that the niche model is suitable for forecasting the dynamics of Microcystis blooms. Redundancy analysis indicated that decreases in water temperature, dissolved oxygen and total dissolved phosphorus might be major factors underlying bloom decline. Based on the theory of community succession being caused by resource competition, the growth and decline of blooms can be predicted from a community structure. This may provide a basis for early warning and control of algal blooms.Cyanobacterial blooms occur frequently in lakes due to eutrophication. Although a number of models have been proposed to forecast algal blooms, a good and applicable method is still lacking. This study explored a simple and effective mathematical-ecological model to evaluate the growth status and predict the population dynamics of Microcystis blooms. In this study, phytoplankton were collected and identified from 8 sampling sites in Chaohu Lake every month from July to October, 2010. The niche breadth and niche overlap of common species were calculated using standard equations, and the potential relative growth rates of Microcystis were calculated as a weighted-value of niche overlap. In July, the potential relative growth rate was 2.79 (a.u., arbitrary units) but then rapidly declined in the following months to -3.99 a.u. in September. A significant correlation (R =0.998, P < 0.01) was found in the model between the net-increase in biomass of Microcystis in the field and the predicted values calculated by the niche model, we concluded that the niche model is suitable for forecasting the dynamics of Microcystis blooms. Redundancy analysis indicated that decreases in water temperature, dissolved oxygen and total dissolved phosphorus might be major factors underlying bloom decline. Based on the theory of community succession being caused by resource competition, the growth and decline of blooms can be predicted from a community structure. This may provide a basis for early warning and control of algal blooms

Cloning and characterization of interferon stimulated genes Viperin and ISG15, and their promoters from snakehead Channa argus

By suppression subtractive hybridization, rapid amplification of cDNA ends and gene walking methods, interferon stimulated genes (ISGs), Viperin and ISG15, and their promoters have been cloned and characterized from snakehead Channa argus. The Viperin cDNA was found to be 1474 nt and contain an open reading frame (ORF) of 1059 nt that translates into a putative peptide of 352 amino acid (aa). The putative peptide of Viperin shows high identity to that in teleosts and mammals except for the N-terminal 70 aa. The ISG15 cDNA was found to be 758 nt and contain an ORF of 468 nt that translates into a putative peptide of 155 aa. The putative peptide of ISG15 is composed of two tandem repeats of ubiquitin-like (UBL) domains, and a canonical conjugation motif (LRGG) at C-terminal. Viperin and ISG15 promoter regions were characterized by the presence of interferon stimulating response elements (ISRE) and gamma-IFN activation sites (GAS). ISRE is a feature of IFN-induced gene promoter and partially overlaps interferon regulatory factor (IRF) 1 and IRF2 recognition sites. GAS is responsible for the gamma-IFN mediated transcription. One conserved site for NF-kappa B was found in the promoter region of Viperin. This is the first report of conservative binding motif for NF-kappa B in accordance with the consensus sequence (GGGRN-NYYCC) among teleost ISG promoters. Moreover, there were also TATA, CAAT and Sp1 transcription factor sites in Viperin and ISG15 promoters. In 5' untranslated region (UTR), snakehead ISG15 gene contains a single intron, which differs from Viperin gene. The transcripts of Vipeirn and ISG15 mRNA were mainly expressed in head kidney, posterior kidney, spleen and gill. The expression levels in liver were found to increase obviously in response to induction by IFN-inducer poly I : C.By suppression subtractive hybridization, rapid amplification of cDNA ends and gene walking methods, interferon stimulated genes (ISGs), Viperin and ISG15, and their promoters have been cloned and characterized from snakehead Channa argus. The Viperin cDNA was found to be 1474 nt and contain an open reading frame (ORF) of 1059 nt that translates into a putative peptide of 352 amino acid (aa). The putative peptide of Viperin shows high identity to that in teleosts and mammals except for the N-terminal 70 aa. The ISG15 cDNA was found to be 758 nt and contain an ORF of 468 nt that translates into a putative peptide of 155 aa. The putative peptide of ISG15 is composed of two tandem repeats of ubiquitin-like (UBL) domains, and a canonical conjugation motif (LRGG) at C-terminal. Viperin and ISG15 promoter regions were characterized by the presence of interferon stimulating response elements (ISRE) and gamma-IFN activation sites (GAS). ISRE is a feature of IFN-induced gene promoter and partially overlaps interferon regulatory factor (IRF) 1 and IRF2 recognition sites. GAS is responsible for the gamma-IFN mediated transcription. One conserved site for NF-kappa B was found in the promoter region of Viperin. This is the first report of conservative binding motif for NF-kappa B in accordance with the consensus sequence (GGGRN-NYYCC) among teleost ISG promoters. Moreover, there were also TATA, CAAT and Sp1 transcription factor sites in Viperin and ISG15 promoters. In 5' untranslated region (UTR), snakehead ISG15 gene contains a single intron, which differs from Viperin gene. The transcripts of Vipeirn and ISG15 mRNA were mainly expressed in head kidney, posterior kidney, spleen and gill. The expression levels in liver were found to increase obviously in response to induction by IFN-inducer poly I : C

Comparison of evolutionary rates in the mitochondrial DNA cytochrome b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei : Cypriniformes)

It is widely accepted that mitochondrial DNA (mtDNA) control region evolves faster than protein encoding genes with few exceptions. In the present study, we sequenced the mitochondrial cytochrome b gene (cyt b) and control region (CR) and compared their rates in 93 specimens representing 67 species of loaches and some related taxa in the Cobitoidea (Order Cypriniformes). The results showed that sequence divergences of the CR were broadly higher than those of the cyt b (about 1.83 times). However, in considering only closely related species, CR sequence evolution was slower than that of cyt b gene (ratio of CR/cyt b is 0.78), a pattern that is found to be very common in Cypriniformes. Combined data of the cyt b and CR were used to estimate the phylogenetic relationship of the Cobitoidea by maximum parsimony, neighbor-joining, and Bayesian methods. With Cyprinus carpio and Danio rerio as outgroups, three analyses identified the same four lineages representing four subfamilies of loaches, with Botiinae on the basal-most clade. The phylogenctic relationship of the Cobitoidea was ((Catostomidae + Gyrinocheilidae) + (Botiinae + (Balitorinae + (Cobitinae + Nemacheilinae)))), which indicated that Sawada's Cobitidae (including Cobitinae and Botiinae) was not monophyletic. Our molecular phylogenetic analyses are in very close agreement with the phylogenetic results based on the morphological data proposed by Nalbant and Bianco, wherein these four subfamilies were elevated to the family level as Botiidae, Balitoridae, Cobitidae, and Nemacheilidae. (c) 2005 Elsevier Inc. All rights reserved.It is widely accepted that mitochondrial DNA (mtDNA) control region evolves faster than protein encoding genes with few exceptions. In the present study, we sequenced the mitochondrial cytochrome b gene (cyt b) and control region (CR) and compared their rates in 93 specimens representing 67 species of loaches and some related taxa in the Cobitoidea (Order Cypriniformes). The results showed that sequence divergences of the CR were broadly higher than those of the cyt b (about 1.83 times). However, in considering only closely related species, CR sequence evolution was slower than that of cyt b gene (ratio of CR/cyt b is 0.78), a pattern that is found to be very common in Cypriniformes. Combined data of the cyt b and CR were used to estimate the phylogenetic relationship of the Cobitoidea by maximum parsimony, neighbor-joining, and Bayesian methods. With Cyprinus carpio and Danio rerio as outgroups, three analyses identified the same four lineages representing four subfamilies of loaches, with Botiinae on the basal-most clade. The phylogenctic relationship of the Cobitoidea was ((Catostomidae + Gyrinocheilidae) + (Botiinae + (Balitorinae + (Cobitinae + Nemacheilinae)))), which indicated that Sawada's Cobitidae (including Cobitinae and Botiinae) was not monophyletic. Our molecular phylogenetic analyses are in very close agreement with the phylogenetic results based on the morphological data proposed by Nalbant and Bianco, wherein these four subfamilies were elevated to the family level as Botiidae, Balitoridae, Cobitidae, and Nemacheilidae. (c) 2005 Elsevier Inc. All rights reserved