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Mitochondrial genomes of Squalidus mantschuricus, S. chankaensis, and S. longifilis have been determined using Sanger sequencing (GenBank Accession No. MT767745–MT767747). The three mitochondrial genomes consist of 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region with the length of 16,605, 16,611, and 16,607 bp. Phylogenetic analysis of the three species showed that S. mantschuricus is nested within a fully supported terminal clade with S. argentatus, and S. chankaensis is a sister group of S. mantschuricus, S. argentatus, and S. wolterstorffi. Squalidus longifilis is positioned in a clade with S. multimaculatus and S. gracilis.

Mitochondrial genomes of two individuals of Tachanovsky’s gudgeon Ladislavia taczanowskii have been determined on the basis of Sanger dideoxy sequencing. The gene compositions of two genomes contain 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region with the same length 16,614 bp. The phylogenetic tree reveals that the monotypic genus Ladislavia is a sister group of the subfamily Gobioninae within the family Gobionidae.

Two complete mitochondrial genomes of Gobio acutipinnatus and G. microcephalus are assembled, and they have the same length with slightly high A + T contents (54.88% and 56.57%) in base composition...

International audience; The interrelationships among mugilids (Mugiliformes: Mugilidae) remain highly debated. Using a mitochondrial gene-based phylogeny as criterion, a revised classification with 25 genera in the Mugilidae has recently been proposed. However, phylogenetic relationships of major mitochondrial lineages remain unresolved and to gain a general acceptance the classification requires confirmation based on multilocus evidence and diagnostic morphological characters. Here, we construct a species-tree using twelve nuclear and three mitochondrial loci and infer the evolution of 71 morphological characters. Our multilocus phylogeny does not agree with previous morphology-based hypotheses for the relationships within Mugilidae, confirms the revised classification with 25 genera and further resolves their phylogenetic relationships. Using the well-resolved multilocus phylogeny as the criterion, we reclassify Mugilidae genera into three new subfamilies (Myxinae, Rhinomugilinae, and Cheloninae) and one new, recombined, subfamily (Mugilinae). The Rhinomugilinae subfamily is further divided into four tribes. The revised classification of Mugilidae is supported by morpho-anatomical synapomorphies or a combination of characters. These characters are used to erect a key to the subfamilies and genera.

In this study, we determined complete mitochondrial genomes of Saurogobio gracilicaudatus, S. xiangjiangensis, S. gymnocheilus, and S. lissilabris so that these data could contribute to reconstruct interspecific phylogenetic relationships within the genus Saurogobio. The four mitochondrial genomes showed A + T bias (55.2–57.0%) of base compositions with the length from 16,594 to 16,608 bp. Phylogenetic relationships among Saurogobio fishes and their close relatives showed that the genus Saurogobio was a monophyletic group and it could be divided into two major groups.

Freshwater fishes in the genus Paraleucogobio include two species, Paraleucogobio notacanthus and Paraleucogobio strigatus. In this study, we determined complete mitochondrial genomes of P. notacan...

Abbottina binhi has been misidentified as Abbottina rivularis in China for a long time. In this study, we determined three mitochondrial genomes of A. rivularis and A. binhi such that these data should contribute to molecular identifications of the two species. The size of new mitochondrial genomes was 16,609 or 16,599 bp with A + T bias of 55.7–56.5% in the base compositions. Our reconstructed phylogeny showed that A. rivularis and A. binhi formed a sister taxon relationship, and they together were a monophyletic group.

Cerithideopsilla is a genus of potamidid snails found in high abundance on sedimentary intertidal flats and beneath mangrove trees on continental shores in the tropical and subtropical Indo-West Pacific region and Mediterranean Sea. Taxonomic revisions have recognized four species, but recent molecular studies have hinted at a higher diversity. Here, we analyse 377 individuals sampled from across the known range and use a combination of molecular phylogenetic (mitochondrial COI and 16S rRNA, and nuclear 28S rRNA genes), statistical (generalized mixed Yule-coalescent GMYC method) and morphological (shell form) criteria to delimit 16 species. These form four species groups, corresponding with the traditionally recognized species C. alata, C. ‘djadjariensis’ (for which the valid name is C. incisa), C. cingulata and C. conica. Distribution maps were compiled using museum specimens identified by diagnostic shell characters. In combination with the molecular phylogenetic trees, these suggest an allopatric speciation mode, with diversification centred on the East Asian coastline and northern Australia, and a pronounced gap in the ‘eastern Indonesian corridor’, an area of low oceanic productivity. There is, however, frequently geographical overlap between sister species and we suggest from several sources of evidence (e.g. presence of C. conica in isolated saline lakes 900 km from the sea) that post-speciation transport by migratory birds has occurred. Nine of the 16 species occur between the Gulf of Tonkin and Hong Kong, so southern China is significant for both the evolution and conservation of Cerithideopsilla species. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 114, 212–228.

Tidal marshes are an important habitat and nursery area for fish. In the past few decades, rapid economic development in the coastal areas of China has led to the interruption and destruction of an increasing number of tidal marshes. The growing interest in tidal marsh restoration has increased the need to understand the relationship between geomorphological features and fish assemblages in the design of marsh restoration projects. We studied temporal variations in, and the effects of creek geomorphological features on, the estuarine tidal creek fish community. Using modified channel nets, we sampled fish monthly from March 2007 to February 2008 from seven tidal creeks along an intertidal channel system in Chongming Dongtan National Nature Reserve. Fourteen creek geomorphological variables were measured or derived to characterize intertidal creek geomorphological features. The Gobiidae, with 10 species, was the most speciesrich family. The most abundant fish species were Liza affinis, Chelon haematocheilus, and Lateolabrax maculatus. The fish community was dominated by juvenile marine transients, which comprised about 80% of the total catch. The highest abundance of fish occurred in June and July, and the highest biomass occurred in December. Canonical redundancy analyses demonstrated that depth, steepness, cross-sectional area, and volume significantly affected the fish species assemblage. L. affinis favored small creeks with high elevations. Synechogobius ommaturus, Acanthogobius luridus, and Carassius auratus preferred deep, steep creeks with a large cross-sectional area and volume. These findings indicate that the geomorphological features of tidal creeks should be considered in the conservation and sustainable management of fish species and in the restoration of salt marshes.

Freshwater fishes of the subfamily Gobioninae (Cypriniformes: Cyprinidae) are composed of three major clades, the tribes Gobionini and Sarcocheilichthyini, and a Hemibarbus–Squalidus group. In this study, we determined ten complete fish mitogenomes from eight of all twelve genera in the tribe Gobionini. The ten mitogenomes displayed similar patterns in gene arrangements, codon use and gene overlaps with the length of 16,605–16,617 bp and base compositions slightly A + T bias of 56.1–58.0%. Our phylogeny of the tribe Gobionini revealed that the genera Gobio, Xenophysogobio, Gobiobotia, Saurogobio and Pseudogobio were monophyletic, and other genera Abbottina, Biwia, Microphysogobio and Platysmacheilus were paraphyletic or polyphyletic. The findings indicate that the genera classifications of Gobionini are needed to be further confirmed.

A group of small and transparent Asian noodlefishes (Osmeriformes: Salangidae) are commercially important fishery species, however, interrelationships among these fishes remain unresolved in previous studies using mitochondrial markers. We re-examine phylogenetic relationships of Salangidae by including complete taxon sampling, based on seven nuclear loci and one mitochondrial gene using a multilocus coalescence-based species-tree method. Our results show a well-resolved phylogeny of Salangidae that does not agree with previous hypotheses. The topology test suggests that our hypothesis represents the most likely phylogeny. Using the inferred species-tree as criterion, we recombine the rank of subfamilies and genera in the Salangidae, and erect a new genus Neosalangichthys. Our revised classification of Salangidae is well supported by reinterpreting previously proposed diagnostic characters. Finally, re-defined synapomorphic characters are used to erect a key to the genera of Salangidae.

This study examined the hematological profiles and responses to exhaustive exercise in 'all-fish' growth hormone (GH) transgenic common carp (Cyprinus carpio L) compared to non-transgenic controls. Transgenic fish had significantly smaller erythrocytes (length, width, surface area and volume), with a larger surface to volume ratios than non-transgenics. There were no significant differences in hematocrit, blood hemoglobin concentrations, plasma glucose, lactate, cholesterol and protein concentrations between the two strains at rest, but the transgenic fish had significantly lower resting mean corpuscular hemoglobin concentrations (MCHC) or higher plasma triglyceride concentrations than controls. Exhaustive exercise did not induce significant changes in hematocrit, hemoglobin concentrations and MCHC in either strain. The patterns of elevation and recovery in plasma glucose and lactate were the same for transgenic and control fish, although lactate levels were lower in the transgnic fish than controls at 1 h and 2 h post-exercise. There was a significant elevation in plasma cholesterol and triglyceride concentrations for 1 h post-exercise in transgenics but not in non-transgenic controls. Plasma protein concentrations were not altered by exhaustive exercise in transgenics but were lower from 2 h post-exercise in non-transgenic controls. These findings suggest that the 'all-fish' GH transgene significantly affects the erythrocyte morphology and the patterns in hematological response to exhaustive exercise of common carp, especially for lipid metabolism. The greater reliance on triglycerides and a greater erythrocyte surface to volume ratio may help transgenic carp to recover from exhaustive exercise, but further research on muscle metabolism and aerobic metabolic rate are needed in order to confirm this conclusion. (C) 2010 Elsevier B.V. All rights reserved.

Non-vegetated creek edges were investigated to explore spatial nekton use patterns in a low salinity intertidal salt marsh creek network of the Yangtze River estuary along a stream-order gradient with four creek orders. Non-vegetated creek edges were arbitrarily defined as the approximately 3 m extending from the creek bank (the marsh–creek interface) into open water. Nekton was sampled using seine nets during daytime high slack water during spring tides for two or three days each in May through July 2008. Twenty-three nekton species (16 fishes and 7 crustaceans) were caught during the study. Fishes were dominated by gobies (Mugilogobius abei, Periophthalmus magnuspinnatus, Periophthalmus modestus, Synechogobius ommaturus), mullets (Chelon haematocheilus, Liza affinis) and Chinese sea bass (Lateolabrax maculatus). Crustaceans were dominated by mud crab (Helice tientsinensis) and white prawn (Exopalaemon carinicauda). Rank abundance curves revealed higher evenness of nekton assemblages in lower-order creeks compared to higher-order creeks. Fish abundance tended to increase with increasing creek order. Crustacean abundance was higher in the first–third order creeks than in the fourth-order creek. Dominant nekton species displayed various trends in abundance and length–frequency distributions along the stream-order gradient. The spatial separation of nekton assemblages between the first–third order creeks and the fourth-order creek could be attributed to geomorphological factors (distance to mouth and cross-sectional area). These findings indicate that both lower- and higher-order creek edges play important yet different roles for nekton species and life history stages in salt marshes.

The treefrog genus Hyla (Anura: Hylidae) consists of at least 31 species found in North America, Central America, Europe, and Asia and is the only genus of hylids that occurs outside the New World. Despite intensive work on the phylogeny of the genus in the past few years, several problems still exist regarding relationships within Hyla. These problems include the unusual placements of H. gratiosa and H. walkeri in some recent studies and the relatively limited taxon sampling of Asian species. In the present study, we revisit the phylogeny of Hyla to address some of these problems. First, we tested the unexpected placements of H. gratiosa and H. walkeri by sampling additional individuals of these species. Our results show that the unusual placements of H. gratiosa and H. walkeri in previous studies were most likely due to a mislabelled tissue sample and a misidentified specimen, respectively. Second, we included two species of Asian Hyla not included in previous phylogenies. Our study provides ad...

Aim We studied elevational species richness patterns of Schizothorax fishes and identified the roles of ecological and evolutionary factors in shaping the patterns of elevational diversity. Location The Tibetan Plateau and its adjacent regions. Methods We assembled distribution and altitude data for all Schizothorax species using the literature. We merged ecological and evolutionary approaches to test the relationships between species richness and ecological factors (climate, area, the mid-domain effect) or evolutionary factors (diversification rates and time of colonization). Results We found that species richness of Schizothorax fishes peaked at mid-elevations. Rainfall, area, the mid-domain effect and diversification rate were weak predictors of the richness pattern. Temperature showed a nonlinear relationship with species richness. Temperature and time of colonization were the most important variables in explaining the elevational diversity pattern. Main conclusion Our findings indicate that the time-for-speciation effect and niche conservatism play important roles in variation of species richness.

Although the impact of plant invasions on benthic communities, especially burrowing crabs, has received increasing attention, the results from past studies are mixed. The exotic plant Spartina alterniflora has become the most abundant species in the salt marshes of the Yangtze River estuary since it was first found just over a decade ago, but its effects on crabs in the salt marshes is largely unknown. To examine whether the invasions of this exotic plant affected native crabs, we compared the biomass and abundance of the dominant burrowing crab Sesarma dehaani in an exotic Spartina marsh, native Phragmites australis marsh and mudflats of the Yangtze River estuary, China. To explain the differences of S. dehaani populations between different habitats, feeding preference of S. dehaani for Spartina and Phragmites was investigated. Results showed crab abundance and biomass in the Spartina marsh were significantly greater than those in the Phragmites marsh and mudflats. Soil water content and plant community characteristics in the Spartina marsh also significantly differed in the Phragmites marsh and mudflats. Moreover, the feeding preference experiment showed that crabs consumed Spartina more than twice as much as Phragmites. In summary, this study showed that Spartina provided compatible habitats for native crab S. dehaani through offering suitable food source and moderate environmental conditions.

Tidal marshes provide nursery habitats for many commercial nektonic species; thus, determining trophic linkages between tidal marshes and aquatic consumers is important for sustain- ing fishery production in estuarine ecosystems. We examined stable isotopes (δ 13 C, δ 15 N) in 4 com- mercial nekton species (Chelon haematocheilus, Synechogobius ommaturus, Lateolabrax maculatus and Exopalaemon carinicauda) in the tidal marshes of the Yangtze River estuary, China. We esti- mated the frequency and range of potential contribution (0 to 100%) from different food sources (benthic microalgae, suspended particulate organic matter, the invasive C4 plant Spartina alterniflora and native C3 plants Phragmites australis and Scirpus mariqueter) to the nektonic consumers, and then pooled the contributions for primary producers with similar isotope values (giving 3 groups: microalgae, invasive C4 plant and native C3 plants). Marsh vascular plants and microalgae were at the base of the food web supporting these nektonic species. For C. haematocheilus and S. ommatu- rus, vascular plants constituted a larger fraction of their carbon source than microalgae. S. alterniflora contributed more than 50% of their total organic carbon and was more important than the native C3 plants. For L. maculatus and E. carinicauda, intermediate δ 13 C values precluded definitive assign- ment of a major carbon source. We have shown that tidal marshes provide important food sources for some dominant estuarine nektonic species, and that the exotic plant S. alterniflora has been incorpo- rated into aquatic food webs of the Yangtze River estuary.

The structure and temporal variations of the fish community in salt marshes of Chinese estuaries are poorly understood. Fish utilization of a salt marsh intertidal creek in the Yangtze River estuary was studied based on quarterly sampling surveys in July and November, 2004, and February and May, 2005. Fishes were collected by consecutive day and night samplings using fyke nets during the ebbing spring tides. A total of 25,010 individuals were caught during the study. 17 families and 33 species were documented, and the most species-rich family was Gobiidae. Three species, Synechogobius ommaturus, Chelon haematocheilus and Lateolabrax maculatus together comprised 95.65% of the total catch, which were also the most important commercial fishery species in the Yangtze River estuary. The fish community was dominated by juvenile individuals of estuarine resident species. Time of year significantly affected fish use of salt marshes, but no significant effects of diel periodicity on the fish community were found except for fish sampling in July. These findings indicate that salt marshes in the Yangtze River estuary may play important nursery roles for fish community.

Members of Candidia, Nipponcrysis, Parazacco, Opsariichthys, and Zacco are a group of East Asian freshwater fishes, and these five genera form a monophyletic group within the subfamily Oxygastrinae (Cypriniformes: Cyprinidae). In this study, we first determined complete mitogenomes of Candidia pingtungensis, Opsariichthys acutipinnis, O. chengtui, and Zacco acanthogenys. The four mitogenomes with the length of 16 611-16 615 bp displayed the same patterns in gene arrangements and the use of start and stop codons for protein-coding genes. Our phylogeny divided Candidia, Nipponcrysis, Parazacco, Opsariichthys, and Zacco into two major groups that the former three genera consisted of a group and the latter two genera formed another group. The phylogeny also revealed that C. pingtungensis was nested within Nipponcrysis. Our findings indicate that the taxonomy status of Candidia and Nipponcrysis is still needed to be confirmed.

Comparing elevational gradients across a wide spectrum of climatic zones offers an ideal system for testing hypotheses explaining the altitudinal gradients of biodiversity. We document elevational patterns of lizard and snake species richness, and explore how land area and climatic factors may affect species distributions of lizards and snakes. Our synthesis found 42 lizard species and 94 snake species known from the Hengduan Mountains. The lizards are distributed between 500 and 3500 m, and the snakes are distributed between 500 and 4320 m. The relationship between species richness and elevation for lizards and snakes is unimodal. Land area explains a significant amount of the variation in lizard and snake species richness. The cluster analysis reveals pronounced distinct assemblages for lizards and snakes to better reflect the vertical profiles of climate in the mountains. Climatic variables are strongly associated with lizard and snake richness along the elevational gradient. The data strongly implicate water availability as a key constraint on lizard species richness, and annual potential evapotranspiration is the best predictor of snake species richness along the elevational gradient in the Hengduan Mountains.

We used partial DNA sequences of cytochrome b and 16S mitochondrial genes to determine the phylogenetic placement of salangid fishes and the generic relationships within the salangids. Our molecular data strongly support the monophyly of salangid fishes, the inclusion of salangids in the Osmeridae, and the sister group relationship between salangids and osmerids. Our analyses suggest that Plecoglossus can be separated from all the other salangids and osmerids. Mallotus and Hypomesus are clustered within Osmerinae, rather than allied with Salanginae. As regards the relationships within the salangids, our analyses are incongruent with all previous classification hypotheses. Our phylogenetic analyses support the sister group relationships between Protosalanx and Neosalanx, and between Salanx and Hemisalanx. More evidences show that Leucosoma is more closely related to the Salanx-Hemisalanx clade, while Salangichthys forms part of an unresolved basal polytomy.

Aim To document patterns in diversity, altitudinal range and body size of freshwater fishes along an elevational gradient in the Yangtze River basin. Location The Yangtze River basin, China. Methods We used published data to compile the distribution, altitudinal range and body size of freshwater fishes. Correlation, regression, clustering and graphical analyses were used to explore patterns in diversity, altitudinal range and body size of freshwater fishes in 100-m elevation zones from 0 to 5200 m. Results Species richness patterns across the elevational gradient for total, non-endemic and endemic fishes were different. The ratio of endemics to total richness peaked at mid elevation. Land area on a 500-m interval scale explained a significant amount of the variation in species richness. Species density displayed two peaks at mid-elevation zones. The cluster analysis revealed five distinct assemblages across the elevation gradient. The relationship between elevational range size and the midpoint of the elevational range revealed a triangular distribution. The frequency distribution of log maximum standard length data displayed an atypical right-skewed pattern. Intermediate body sizes occurred across the greatest range of elevation while small and large body sizes possessed only small elevational amplitudes. The size-elevation relationship between the two major families revealed a very strong pattern of body size constraint among the Cobitidae with no corresponding elevational constraint and a lot of body size and elevational diversification among the Cyprinidae. Main conclusion The data failed to support either Rapoport's rule or Bergmann's rule.

In a Chinese eutrophic shallow lake, the spatial, temporal and vertical distributions of meiofauna in different lake zones along a eutrophic gradient were analyzed. The spatial distribution of meiofauna among sampling stations changed with nutrient levels. Nematoda were most abundant at the majority of sampling stations comprising 70.6 - 93.2 % meiofaunal abundance except for a hypereutrophic station. The seasonal patterns in abundance of nematodes, oligochaetes, rotifers, chironomids and different nematode feeding groups differed among stations, which revealed that the temporal variations of these meiofaunal groups and the nematode feeding groups may vary with different nutrient loadings. The vertical distributions of meiofaunal groups, nematode species, and nematode trophic groups in the upper and lower sediment layers were similar, suggesting a consistent vertical distribution pattern across different trophic conditions. Nematode species richness, Shannon-Wiener species diversity index, trophic diversity and Maturity Index were significantly correlated with nutrient levels (total phosphorus and nitrogen in lake water and total phosphorus in sediment). Our results suggest the importance of nematode community analyses in the assessment of freshwater eutrophication.

We synthesized information on freshwater fish biodiversity in the Yangtze River basin. We documented 361 species and subspecies that had been recorded and described from the basin. Of these, 177 species are endemic. The basin is usually divided into three parts, i.e. the upper reaches, the middle reaches and the lower reaches. This study indicated that the ‘three reaches’ approach was not supported by fish distribution patterns. Hydrological alterations are perhaps the largest threat to fish biodiversity in the basin. Fishes in the upper reaches will be seriously affected by the construction of the Three Gorges Dam and other dams, and action should be taken for priority conservation. The most immediate restoration need is reconnection of the Yangtze River with its lakes. The cluster of lakes in the Central Yangtze should be protected to maintain habitats for spawning, feeding and migration of migratory fishes. Our study indicates a need to identify areas of high fish biodiversity and to select nature reserves to mitigate the loss of fish biodiversity in the Yangtze River basin.

Effects of reclaiming estuarine tideland on soil fauna biodiversity were studied in the Yangtze river estuary of China, focusing on nematodes. The responses of the nematode community to the disturbance caused by reclamation can be summarized as: (1) there was no distinct decline in the density of nematodes, but the community structure changed greatly; (2) the proportions of plant feeders and omnivorous nematodes increased after reclamation, whereas the proportions of bacterial feeders and predators decreased; (3) more apparent patchiness of nematode distribution was found in the reclaimed terrestrial environment than in intertidal marshes. Generally, agrocenoses have been characterized by low proportions of predator-omnivores. Our study indicated that omnivorous dorylaimids can be markedly abundant in agroecosystems, depending on the annual crop rotation and tillage practices. The predominant trophic group in cultivated land shifted between omnivorous nematodes and plant feeders, implying that the food chain path changed with agricultural processes. The maturity index (MI) provides little information in the present study, probably because the MI value embraced information of many disturbances including vegetation succession and changes in soil features. The faunal profile, representing both enrichment and structural conditions, is believed to be effective and more informative for analyzing the nematode successional trends.

The Amur sleeper Perccottus glenii (Perciformes, Gobioidei, Odontobutidae) is well known as an invasive fish in the river basins of Eastern and Central Europe, but its genetic background is unavailable across its native habitats in northeast Asia. In this study, we used the mitochondrial cytochrome b gene by sampling 19 populations of P. glenii across its native distributional areas of Liaohe and Amur River basins to explore its evolutionary history. Phylogenetic analyses identified three major clades within P. glenii , among which Clade A and Clade B were co-distributed in the Liaohe and Amur River basins, and Clade C was restricted to the latter. Molecular dating showed that the splits of Clades A, B and C have happened in the late Early–early Middle Pleistocene and the most recent common ancestors of these clades have been presented in the late Middle–early Late Pleistocene. The P. glenii showed very high levels of genetic structure among populations (ΦST = 0.801), probably due to the characters of its life histories with very limited dispersal ability. The admixture of different clades in some populations of P. glenii probably reflects historical secondary contact. These findings indicate that Pleistocene climatic oscillation and river capture were major determinants for genetic variations and evolutionary history of the P. glenii .

The first complete mitochondrial genome (mitogenome) of Rana sensu stricto (sensu Frost, 2013) was determined using Rana kunyuensis as a representative species. The mitogenome was 22,255 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and duplicated control regions. The mitogenome of R. kunyuensis showed novel gene order arrangement with a translocation of tRNALeu(CUN) and ND5 in comparison with published anuran mitogenomes to date. This mitogenome should contribute to understand the evolution of anuran mitochondrial gene order arrangements.

F-4 generation of human growth hormone (hGH) gene-transgenic red common carp, and the non-transgenic controls were fed for 8 weeks on purified diets with 20%, 30% or 40% protein. Analysis of whole-body amino acids showed that the proportions of lysine, leucine, phenylalanine, valine and alanine, as percentages of body protein, increased significantly, while those of arginine, glutamic acid and tyrosine decreased, with increases in dietary protein level in at least one strain of fish. Proportions of the other amino acids were unaffected by the diets. The proportions of lysine and arginine were significantly higher, while those of leucine and alanine were lower in the transgenics than in the controls in at least one diet group. Proportions of the other amino acids were unaffected by strain. The results suggest that the whole-body amino acid profile of transgenic carp, when expressed as proportions of body protein, was in general, similar to that of the non-transgenic controls. (C) 2000 Elsevier Science B.V. All rights reserved.

Rhynchocypris lagowskii sensu lato (Cypriniformes: Cyprinidae) has been revealed as a species complex including two species, i.e. R. lagowskii sensu stricto and a cryptic species R. cf. lagowskii. We determined the first complete mitochondrial genome (mitogenome) of R. cf. lagowskii by comparing with a published mitogenome of R. lagowskii sensu stricto. The two species displayed similar pattern of mitochondrial gene arrangements and similar base compositions of the heavy strain with a bias in the A + T content. There were the nucleotide sequence similarity of 91.8% for mitogenomes and pairwise p-distance of 6.9% for COI genes between R. cf. lagowskii and R. lagowskii sensu stricto and these results supported the two species as different species.

The taxonomy and systematics of Phoxinus (Cypriniformes: Cyprinidae) is still not well-resolved. In this study, we determined the first complete mitochondrial genome (mitogenome) of Phoxinus tumensis. The mitogenome was 17,050 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region. All genes were encoded on the heavy strain except for ND6 and eight tRNA genes. The overall base composition of the heavy strain was 27.9% for A, 25.5% for C, 28.4% for T and 18.2% for G. The control region was revealed to contain tandem repeats. The mitogenome data of P. tumensis should contribute to clarify the systematics of Phoxinus fishes.

International audience; A comprehensive mitochondrial phylogeny of the family Mugilidae (Durand et al., Mol. Phylogenet. Evol. 64 (2012) 73-92 [1]) demonstrated the polyphyly or paraphyly of a proportion of the 20 genera in the family. Based on these results, here we propose a revised classification with 25 genera, including 15 genera currently recognized as valid (Agonostomus, Aldrichetta, Cestraeus, Chaenomugil, Chelon, Crenimugil, Ellochelon, Joturus, Mugil, Myxus, Neomyxus, Oedalechilus, Rhinomugil, Sicamugil and Trachystoma), 7 resurrected genera [Dajaus (for Agonostomus monticola), Gracilimugil (for Liza argentea), Minimugil (for Sicamugil cascasia), Osteomugil (for several species currently under Moolgarda and Valamugil, including M. cunnesius, M. engeli, M. perusii, and V. robustus), Planiliza (for Indo-Pacific Chelon spp., Indo-Pacific Liza spp., and Paramugil parmatus), Plicomugil (for Oedalechilus labiosus), and Squalomugil (for Rhinomugil nasutus)] and 3 new genera: Neochelon gen. nov. (for Liza falcipinnis), Parachelon gen. nov. (for L. grandisquamis) and Pseudomyxus gen. nov. (for Myxus capensis). Genus Chelon was shown to include exclusively Chelon spp. and Liza spp. from the Atlantic and the Mediterranean, and Liza spp. species endemic to eastern southern Africa. Genus Crenimugil should now include C. crenilabis, Moolgarda seheli and V. buchanani. Genus names Liza, Moolgarda, Paramugil, Valamugil and Xenomugil should be abandoned because they are no longer valid. Further genetic evidence is required to confirm or infirm the validity of the genus Paracrenimugil Senou 1988. The mitochondrial phylogeny of the 25 genera from the present revision is the following: [(Sicamugil, (Minimugil, Rhinomugil)); Trachystoma; ((Myxus, Neomyxus), (Cestraeus, Chaenomugil, (Agonostomus, Dajaus, Joturus), Mugil)); (Aldrichetta, Gracilimugil); Neochelon gen. nov.; (Pseudomyxus gen. nov., (Chelon, Oedalechilus, Planiliza, Parachelon gen. nov.)); ((Squalomugil, (Ellochelon, Plicomugil)), (Crenimugil, Osteomugil))]. Agonostomus monticola and several species with large distribution ranges (including Moolgarda seheli, Mugil cephalus and M. curema) consist of separate lineages whose geographic distribution suggests they are cryptic species, thus warranting further taxonomic work in the Mugilidae at the infra-generic level.

Few studies have explored the role of Cenozoic tectonic evolution in shaping patterns and processes of extant animal distributions within East Asian margins. We select Hynobius salamanders (Amphibia: Hynobiidae) as a model to examine biogeographical consequences of Cenozoic tectonic events within East Asian margins. First, we use GenBank molecular data to reconstruct phylogenetic interrelationships of Hynobius by Bayesian and maximum likelihood analyses. Second, we estimate the divergence time using the Bayesian relaxed clock approach and infer dispersal/vicariance histories under the ‘dispersal–extinction–cladogenesis’ model. Finally, we test whether evolutionary history and biogeographical processes of Hynobius should coincide with the predictions of two major hypotheses (the ‘vicariance’/‘out of southwestern Japan’ hypothesis). The resulting phylogeny confirmed Hynobius as a monophyletic group, which could be divided into nine major clades associated with six geographical areas. Our results show that: (1) the most recent common ancestor of Hynobius was distributed in southwestern Japan and Hokkaido Island, (2) a sister taxon relationship between Hynobius retardatus and all remaining species was the results of a vicariance event between Hokkaido Island and southwestern Japan in the Middle Eocene, (3) ancestral Hynobius in southwestern Japan dispersed into the Taiwan Island, central China, ‘Korean Peninsula and northeastern China’ as well as northeastern Honshu during the Late Eocene–Late Miocene. Our findings suggest that Cenozoic tectonic evolution plays an important role in shaping disjunctive distributions of extant Hynobius within East Asian margins.

The first complete mitochondrial genome (mitogenome) of Plesiopidae (Teleostei: Perciformes) was determined using the Eastern hulafish Trachinops taeniatus as a representative species of the family. The mitogenome was 16,821 bp in length, including 13 typical vertebrate protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region. The gene arrangement was similar to other fishes except for the reversal position of tRNAAla and tRNAAsn. The overall base composition was 27.4% for A, 27.5% for C, 27.4% for T and 17.7% for G. This mitogenome should contribute to resolving phylogenetic position of Plesiopidae.

We first determined complete mitochondrial genomes of Rana dybowskii and Rana cf. chensinensis (Anura: Ranidae). The mitogenomic lengths of R. dybowskii and R. cf. chensinensis were 18,864 and 18,808 bp, respectively. The two mitogenomes have similar gene compositions including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region. Rana dybowskii and R. cf. chensinensis mitogenomes displayed same gene order arrangements and similar base compositions with an A + T bias. Mitogenomic data of the two species contributed to provide molecular marker for their conservative genetics and clarified their phylogenetic position under mitogenome-based phylogeny of the genus Rana.

The first complete mitochondrial genome (mitogenome) of Cerithioidea (Gastropoda: Caenogastropoda) was determined using a freshwater snail Semisulcospira libertina (Cerithioidea: Semisulcospiridae) as a representative species of the superfamily. The mitogenome was 15,432 bp in length, including 13 typical invertebrate protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The overall base composition was 31.4% for A, 17.8% for C, 34.8% for T and 16.0% for G with a A + T bias. The mitogenome of S. libertina displayed novel gene order arrangement compared with published Caenogastropoda mitogenomes to date. This mitogenome contributed in resolving phylogenetic position and interrelationships of Cerithioidea.

This study extended the geographic coverage of a previous study to explore population genetic structure and demographic history in the Ariake icefish Salanx ariakensis from three populations of continental coastlines and one island population in the north-western Pacific based on a partial sequence of the mitochondrial cytochrome b gene. The S. ariakensis showed high genetic diversity and strong genetic structure. Phylogenetic analysis showed a shallow gene tree with no clear phylogeographical structure. Contiguous range expansion and restricted gene flow were inferred to be main population events by nested-clade analysis. Significant genetic differentiations between populations could be attributable to negligible gene flow by coalescent analysis. High nucleotide diversity of each population was due to geographic mixing of heterogenous haplotypes during lowering sea levels of the Pleistocene. These findings indicate that cycles of geographic isolation and secondary contact happened in the Pleistocene glacial-interglacial cycles shaping genetic structure and population demography of S. ariakensis.

This study examines phylogenetic placement of the enigmatic Western Australian Lepidogalaxias, and extends previous studies by including eight new taxa to enable re-examination phylogenetic relationships of lower euteleostean fishes at the ordinal level, based on mitochondrial genomes from 39 ingroup taxa and 17 outgroups. Our results suggest that Lepidogalaxias occupies a basal position among all euteleosts, in contrast with earlier hypotheses that variously suggested a closer relationship to esocid fishes, or to the galaxiid Lovettia. In addition our evidence shows that Osmeriformes should be restricted Retropinnidae, Osmeridae, Plecoglossidae and Salangidae. This reduced Osmeriformes is supported in our results as the sister group of Stomiiformes. Galaxiidae, which is often closely linked to Osmeriformes, emerges as sister group of a combined Osmeriformes, Stomiiformes, Salmoniformes, Esociformes and Argentiformes, and we give Galaxiiformes the rank of order to include all remaining galaxioid fishes (Galaxias and allied taxa, Aplochiton and Lovettia). Our results also support a sister group relationship between Salmoniformes and Esociformes, which are together the sister group of Argentiniformes.

Cryptic species are common in gobioid fishes, as revealed by recent molecular studies. This study collected molecular and morphological data to delimit species boundaries and to reveal the historical biogeography of Odontamblyopus lacepedii sensu lato by sampling 87 specimens from 16 locations in the northwestern Pacific. Phylogenetic trees based on mitochondrial NADH dehydrogenase subunit 5 sequences identified three major clades. Clear morphological separations among these clades were detected by examining morphological characters used in taxonomic diagnosis. Therefore, these clades were delineated as three separate species: O. lacepedii sensu stricto (in the East China Sea, Yellow Sea, Gulf of Bohai, and Ariake Bay); O. sp. (in the southern East China Sea and southern Yellow Sea); and O. rebecca (in the Gulf of Tonkin, northern South China Sea, and southern East China Sea). Estimated divergence times were 0.61 +/- 0.15 Ma between O. lacepedii and O. sp., and 2.31+/-0.36 Ma between O. rebecca and O. lacepedii+O. sp. These findings indicate that isolation of marginal seas and habitat fragmentation during major falls in sea level in the late Pliocene and Pleistocene may have been responsible for genetic breaks among Odontamblyopus species in the northwestern Pacific.

Phylogenetic placement of Pseudorasbora elongate remains unresolved. We determined the first complete mitochondrial genome of P. elongate that its mitogenome data should contribute to clarify the systematics of Pseudorasbora fishes. The mitogenome was 16,607 bp in length, including 13 typical protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region. The overall base composition of the heavy strain was 31.1% for A, 24.8% for C, 28.2% for T and 15.9% for G, with the A + T bias of 59.3%.

The first complete mitochondrial genome (mitogenome) of Opistognathidae (Teleostei: Perciformes) has been determined using the Southern Smiler, Opistognathus jacksoniensis, as a representative species of the family. This mitogenome was 16,650 bp in length, including 13 typical vertebrate protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA genes and 1 control region. All genes were encoded on the heavy strain except for ND6 and eight tRNA genes. The overall base composition of the heavy strain was 27.4% for A, 30.2% for C, 25.7% for T and 16.7% for G. The mitogenome data of O. jacksoniensis should contribute to clarify phylogenetic position of Opistognathidae under mitogenome-based phylogenetic reconstruction of perciform fishes.

The genus Helice is comprised of four species, H. formosensis, H. latimera, H. tientsinensis, and H. tridens. A recent molecular analysis identified H. formosensis and H. tientsinensis as junior synonyms of H. latimera. We used three mitochondrial and two nuclear genes to further delineate species boundaries in Helice and to add to knowledge of the historical biogeography of the genus. The molecular data revealed deep divergences between the H. formosensis-latimera-tientsinensis complex and H. tridens. Clear genetic separations with incomplete lineage sorting and convincing morphological divergences were detected among H. formosensis, H. latimera, and H. tientsinensis, and a coalescence analysis revealed negligible gene flow among these species, except for weak unidirectional gene flow from H. formosensis to H. latimera. The estimated divergence time of 1.42-1.92 Ma between the H. formosensis-latimera-tientsinensis complex and H. tridens is consistent with the opening of the Tsushima/Korea Strait (1.71-1.52 Ma). The divergence time (approximately 22-730 ka) among H. formosensis, H. latimera, and H. tientsinensis indicates that the Taiwan Strait acted as a biogeographic barrier during major falls in sea level during the Pleistocene. Our findings indicate that H. formosensis, H. latimera, and H. tientsinensis are valid species, and that straits (Tokara Strait, Tsushima/Korea Strait, and Taiwan Strait), the Okinawa Trough, and currents (Kuroshio Current, Tsushima Current, and Taiwan Strait Warm Current) have acted as geographic barriers resulting in allopatric speciation among onshore marine animals in the northwestern Pacific.

Nematoda is a metazoan group with extremely high diversity only next to Insecta. Caenorhabditis elegans is now a favorable experimental model animal in modern developmental biology, genetics and genomics studies. However, the phylogeny of Nematoda and the phylogenetic position of the phylum within animal kingdom have long been in debate. Recent molecular phylogenetic studies gave great challenges to the traditional nematode classification. The new phylogenies not only placed the Nematoda in the Ecdysozoan and divided the phylum into five clades, but also provided new insights into animal molecular identification and phylogenetic biodiversity studies. The present paper reviews major progress and remaining problems in the current molecular phylogenetic studies of Nematoda, and prospects the developmental tendencies of this field.