Phylogenetic relationships of Danio within the order cypriniformes: A framework for comparative and evolutionary studies of a model species

The evolutionary relationships of species of Danio and the monophyly and phylogenetic placement of the genus within the family Cyprinidae and subfamily Rasborinae provide fundamentally important phyloinformatics necessary for direct evaluations of an array of pertinent questions in modern comparative biology. Although the genus Danio is not one of the most diverse within the family, Danio rerio is one of the most important model species in biology. Many investigations have used this species or presumed close relatives to address specific questions that have lasting impact on the hypothesis and theory of development in vertebrates. Largely lacking from this approach has been a holistic picture of the exact phylogenetic or evolutionary relationships of this species and its close relatives. One thing that has been learned over the previous century is that many organismal attributes (e.g., developmental pathways, ecologies, behaviors, speciation) are historically constrained and their origins and functions are best explained via a phylogenetic approach. Herein, we provide a molecular evaluation of the phylogenetic placement of the model species Danio rerio within the genus Danio and among hypothesized closely related species and genera. Our analysis is derived from data using two nuclear genes (RAG1, rhodopsin) and five mitochondrial genes (ND4, ND4L, ND5, COI, cyt b) evaluated using parsimony, maximum likelihood, and Bayesian analyses. The family Cyprinidae is resolved as monophyletic but the subfamily Rasborinae (priority over Danioinae) is an unnatural assemblage. Danio is identified as a monophyletic group sister to a clade inclusive of the genera Chela, Microrasbora, Devario, and Inlecypris, not Devario nor Esomus as hypothesized in previous studies. Danio rerio is sister to D. kyathit among the species of Danio evaluated in this analysis. Microrasbora and Rasbora are non-monophyletic assemblages; however, Boraras is monophyletic.

Phylogeny of Oedogoniales (Chlorophyceae, Chlorophyta) inferred from 18S rDNA sequences with emphasis on the relationships in the genus Oedogonium based on ITS-2 sequences

The phylogeny of Oedogoniales was investigated by using nuclear 18S rDNA sequences. Results showed that the genus Oedocladium, as a separated clade, was clustered within the clade of Oedogonium; whereas the genus Bulbochaete was in a comparatively divergent position to the other two genera. The relationship among the species of Oedogonium was discussed, focusing on ITS-2 phylogeny analyzed combining with some morphological characteristics. Our results showed that all the dioecious nannandrous taxa involved in this study were resolved into one clade, while all the monocious taxa were clustered into another clade as a sister group to the former. The report also suggests that the dioecious macrandrous taxa form a paraphyly and could be more basally situated than the dioecious nannandrous and the monoecious taxa by means of molecular phylogeny and morphotype investigations.

Micronutrient niacin addition to enhance biological treatment of textile wastewater

Micronutrients play an important role in biological processes for wastewater treatment. Many industrial wastewaters lack in nutrients required for microbial growth, and this is one of the problems at many activated sludge plants treating them. In this study, the effects of the micronutrient niacin on the COD removal rates of textile wastewater, together with the effect of Mixed Liquor Suspended Solids (MLSS) on niacin, were studied. Certain improvement effects were found on the removal rates of COD, when 0.5 similar to 2.0 mg/L niacin was added to the textile wastewater. The optimal concentration of niacin was 1.0 mg/L, which was continuously added during textile wastewater treatment, and removal rates were 1.31 times compared to those of the control system. The concentration of MLSS was probably one of the factors influencing treatment efficiency, and the biological performance of treatment system could be optimized through micronutrient niacin supplements.

Phylogenetic relationships of the Chinese sisorid catfishes: a nuclear intron versus mitochondrial gene approach

Several recent molecular phylogenetic studies of the sisorid catfishes (Sisoridae) have challenged some aspects of their traditional taxonomy and cladistic hypotheses of their phylogeny. However, disagreement with respect to relationships within this family in these studies highlights the need for additional data and analyses. Here we subjected 15 taxa representing 12 sisorids genera to comprehensive phylogenetic analyses using the second intron of low-copy nuclear S7 ribosomal protein (rpS7) gene and the mitochondrial 16S rRNA gene segments both individually and in combination. The competing sisorid topologies were then tested by using the approximately unbiased (AU) test and the Shimodaira-Hasegawa (SH) test. Our results support previously suggested polyphyly of Pareuchiloglanis. The genus Pseudecheneis is likely to be nested in the glyptosternoids and Glaridoglanis might be basal to the tribe Glyptosternini. However, justified by AU and SH test, the sister-group relationship between Pseudecheneis and the monophyletic glyptosternoids cannot be rejected based on the second intron of rpS7 gene and combined data analyses. It follows that both gene segments are not suitable for resolving the phylogenetic relationships within the sisorid catfishes. Overall, the second intron of rpS7 gene yielded poor phylogenetic performance when compared to 16S rRNA gene, the evolutionary hypothesis of which virtually agreed with the combined data analyses tree. This phenomenon can be explained by the insufficient length and fast saturation of substitutions in the second intron of rpS7 gene, due to substitution patterns such as frequent indels (insertion/deletion events) of bases in the sequences during the evolution.

Relationships between the biomass of algal crusts in fields and their compressive strength

In the desert areas of China investigated by the authors, various biological crusts were predominately associated with three blue-green algal (cyano bacterial) species, Microcoleus vaginatus Gom., Phormidium tenue (Menegh.) Gom. and Seytonema javanicum (Mitz.) Born et Flah. Their biomass and their compressive strength were measured simultaneously in the field in this study. It was also found that the compressive strength of algal crusts was enhanced with the increasing of algal biomass from an undetectable level to a value as high as 9.6mg g(-1) dry soil. However, when the algal biomass decreased, the compressive strength did not descend immediately, but remained relatively steady. The higher the algal biomass became, the thicker were the algal crusts formed. Given the same biomass, the highest compressive strength of man-made algal crusts in fields was found at an algal ratio of 62.5% M. vaginatus, 31.25% P. tenue and 6.25% S. javanicum, and it reached 0.89kgcm(-2). When the biomass of the crusts increased above the value of 8.16 mg chl ag(-1) dry soil, the compressive strength would not ascend easily. It indicated that the compressive strength of man-made algal crusts appeared temporarily saturated in the field. (c) 2006 Elsevier Ltd. All rights reserved.

Relationships between microcystins and environmental parameters in 30 subtropical shallow lakes along the Yangtze River, China

1. A survey of 30 subtropical shallow lakes in the middle and lower reaches of the Yangtze River area in China was conducted during July-September in 2003-2004 to study how environmental and biological variables were associated with the concentration of the cyanobacterial toxin microcystin (MC). 2. Mean MC concentration in seasonally river-connected lakes (SL) was nearly 33 times that in permanently river-connected lakes (RL), and more than six times that in city lakes (NC) and non-urban lakes (NE) which were not connected to the Yangtze River. The highest MC (8.574 mu g L-1) was detected in Dianshan Lake. 3. MC-RR and MC-LR were the primary toxin variants in our data. MC-RR, MC-YR and MC-LR were significantly correlated with Ch1 a, biomass of cyanobacteria, Microcystis and Anabaena, indicating that microcystins were mainly produced by Microcystis and Anabaena sp. in these lakes. 4. Nonlinear interval maxima regression indicated that the relationships of Secchi depth, total nitrogen (TN) : total phosphorus UP) and NH4+ with MC were characterised by negative exponential curves. The relationships between MC and TN, TP, NO3- + NO2- were fitted well with a unimodal curve. 5. Multivariate analyses by principal component and classifying analysis indicated that MC was mainly affected by Microcystis among the biological factors, and was closely related with temperature among physicochernical factors.

DNA polymorphism of the plankton community and its relationships to species composition in the Three Gorges Reservoir Region of the Yangtze River

We examined DNA polymorphism of the plankton community in the Three Gorges Reservoir Region of Yangtze River and studied its relationships to species composition. Samples of the plankton community were collected from nine sampling sites and analyzed by random amplified polymorphic DNA (RAPD). Nine of 60 screened primers generated a total of 88 observable 180 to 1400 by bands, all of which were polymorphic. Cluster analysis of the resulting binary format from DNA banding patterns grouped the target communities into three clusters. The topology of the constructed diagram from species composition data was generally similar to that based on RAPD markers.

Geographical distribution of testate amoebae in Tibet and northwestern Yunnan and their relationships with climate

In Asia, especially in China, our knowledge of the distribution of testate amoebae is still limited. In this paper, the geographical distribution of testate amoebae in Tibetan Plateau and northwestern Yunnan Plateau, southwest China and their relationships with the climatic factors have been studied. We found testate amoebae shifted in the most dominant species and increased in species (or genus) richness from northwest to southeast. Further, the linear regression analyses revealed that both species richness and genus richness have higher positive correlations with the mean temperature of the warmest month and annual mean precipitation as contrasted with the mean altitude, which showed weak negative correlation. This indicates that the temperature and precipitation are more significant influences on the richness than the altitude. The cluster analysis based on the community structure, defined by Sorenson's coefficient matrix, suggested four groups from the 10 physiographical regions. This geographical distribution pattern was also closely related with the climatic regionalization. The present climatic regionalization pattern of the study area originated from the uplift of Tibetan Plateau and mainly occurred in or after the late Pleistocene. Therefore, the geographical distribution of testate amoebae in our study area may have experienced complicated and drastic changes corresponding to the variation of the climate caused by the geological events.

The phylogenetic relationships of the gobioninae (Teleostei : Cyprinidae) inferred from mitochondrial cytochrome b gene sequences

The Gobioninae are a group of morphologically and ecologically diverse Eurasian freshwater cyprinid fishes. The intergeneric relationships of this group are unresolved and the possible monophyly of this subfamily remains to be established. We used complete mitochondrial cytochrome b gene sequences from most genera within the gobionine group, in addition to a selection of cyprinid outgroups, to investigate the possible monophyly of this group and resolve the interrelationships within the group. Our results support the monophyly of the Gobioninae and identify four monophyletic groups within the subfamily; the Hemibarbus group, the Sarcocheilichthys group, the Gobio group, and the Pseudogobio group. The morphologically aberrant genera Gobiobotia, Xenophysogobio and Gobiocypris are included in the Gobioninae, with the latter a sister group of Gnathopogon.

Phylogenetic relationships among Trichodinidae (Ciliophora : Peritricha) derived from the characteristic values of denticles

The phylogenetic relationships among trichodinids remain obscure. As an important diagnostic marker, the morphology of the denticles in the adhesive disc as well as the adoral spiral has been widely used in generic discrimination and species identification of trichodinids. We studied the characters of denticles of the ten genera of Trichodinidae and the sole genus Urceolaria of Urceolariidae by using a quantitative method. The characteristic values were used to generate Manhattan distance, on which the dendrogram was based to construct with the Unweighted Paired Group Method using the Arithmetic mean (UPGMA). The investigations show that all the genera of the family Trichodinidae were clearly separate from the outgroup Urceolaria, and within the Trichodinidae: (i) Dipartiella grouped with Trichodinella and Tripartiella and lay in the closest position to the outgroup with a low dissimilarity, suggesting Dipartiella might be the most primitive genus in the family; (ii) Hemitrichodina clustered in a single clad and lay in the farthest position to the outgroup with the highest dissimilarity, indicating that it might be the most advanced genus; and (iii) the other 6 genera, Trichodina, Paratrichodina, Semitrichodina, Vauchomia, Pallitrichodina and Trichodoxa clustered in a big clad with very low dissimilarity, showing that they are closely related to each other. We discuss the evolutionary trend of the denticle and conclude that the denticles of the adhesive disc should be an apomorphic feature of the trichodinids and their changes could reflect the evolutionary tendencies of these ciliates.

Influence of environmental variables on macroinvertebrates in a macrophyte-dominated Chinese lake, with emphasis on the relationships between macrophyte heterogeneity and macroinvertebrate patterns

The benthic community structure in Baoan Lake was examined in relation to lake water physicochemical characteristics and biological parameters. Seventy macroinvertebrate taxa were identified, and mollusks constituted the dominant group and accounted for more than 80% of the total abundance. Assemblages were composed mainly of scrapers (81.5%) and collector-gatherers (roughly 10%). Three plant variables (richness, total cover, and total biomass) were strongly correlated with the faunal gradient (p<0.05). Other predicator variables were Cl-, SiO2, and chemical oxygen demand. Because of the importance of macrophytes in structuring benthic assemblage in this lentic system, the spatial heterogeneity of macrophytes also influenced the pattern of macroinvertebrates. Seven lake regions were uniquely characterized according to primary macrophyte composition and biomass. There were significant differences for macroinvertebrate taxa richness, abundance, and biodiversity among the seven macrophyte regions.

Distribution of the macroinvertebrate communities in the Xiangxi River system and relationships with environmental factors

Surveys of macroinvertebrates were carried out in the Xiangxi River system during July of 2001. Among the 121 taxa collected, Ephemeroptera, Trichoptera, and Diptera dominated (41.7, 26.0, and 24.5% of the total relative abundance, respectively). Two-way indictor species analysis and detrended correspondence analysis divided the 49 sites into four groups based on species composition and relative abundance. Canonical correspondence analysis indicated that elevation, SiO2, pH, conductivity, hardness, and NO2-N were significant environmental factors affecting the distribution of macroinvertebrates.

Phylogenetic relationships of labeonine cyprinids of the disc-bearing group (Pisces : Teleostei)

Phylogenetic relationships of labeonine cyprinids of the disc-bearing group (Pisces. Teleostei). Zoological Studies 44 (1): 130-143. The disc-bearing group is composed of 4 currently recognized cyprinid genera: Discocheilus, Discogobio, Garra, and Placocheilus. This group is defined as having a lower lip modified to form a mental adhesive disc whose posterior margin is not continuous with the mental region, and includes 91 widely distributed species in tropical Africa and Asia. So far, it is represented in China by 28 species (about 1/3 of the total number) of all 4 genera. A phylogenetic analysis, based on 29 morphological characters scored from first-hand observations of 23 of the Chinese species examined, revealed that the disc-bearing group forms a monophyletic clade in which Garra is the basal lineage, and Placocheilus constitutes a subclade with the sister pair of Discocheilus and Discogobio. In such a phylogenetic framework, the validity of each genus of the disc-bearing group was evaluated. It was confirmed that Discocheilus, Discogobio and Placocheilus represent 3 valid cyprinid genera. Evidence provided in this phylogenetic analysis, incorporated with conclusions reached in the known literature, reveals that the monophyly and validity of Garra need to be further studied using observations of more Garra species. Additional characters should also be examined, as the characters utilized in this study and in Abebe's with Getahun's (1999) study are insufficient to resolve the monophyly of Garra.

The rotifer assemblage in a shallow, eutrophic Chinese lake and its relationships with cyanobacterial blooms and crustacean zooplankton

Rotifer assemblage in the subtropical eutrophic Lake Chaohu was investigated monthly from September 2002 to August 2003. Forty-nine species belonging to 18 genera and 14 families were recorded. The highest densities of rotifer were observed during summer when there were heavy cyanobacterial blooms. There was a significant positive correlation between total rotifer density and the biomass of cyanobacteria. However, no correlations were found between the densities of rotifer and crustacean zooplankton, possibly owing to the paucity of large-bodied planktonic crustaceans. It is likely that the occurrence of cyanobacterial blooms not only caused the shift of dominant crustacean zooplankton from large species to smaller ones but also weakened the negative interaction between crustaceans and rotifers.

Phylogenetic relationships of the Chinese cyprinid genus Rhinogobio Bleeker (Teleostei : Cyprinidae) based on sequences of the mitochondrial DNA control region, with comments on character adaptations

Rhinogobio is a cyprinid genus restricted to the river drainages of China. Sequences of the mitochondrial DNA control region were determined for four Rhinogohio species and one outgroup species, Coreius heterodon, to investigate the phylogenetic relationships within the genus. The control region of the Rhinogobio species ranges from 922 to 930 base pairs and comprises 930 base pairs in Coreius. Our phylogenetic analysis indicates two distinct lineages in the genus Rhinogobio. The first includes only R. ventralis. In the second lineage there are three species, two closely related species R. cylindricus and R. hunanensis, and their sister species R. typus. An analysis of character adaptations suggests an evolutionary trend in this genus towards a relatively lower body and caudal peduncle depth, a shorter dorsal fin, and a more anterior anus. In addition, there is a trend towards shorter barbels and relatively larger eyes. Some or all of these traits may be associated with a habitat shift from fast-flowing turbid rivers to slower-flowing clear river habitats.