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

Balitora anlongensis, the first cavefish species of the genus Balitora (Teleostei, Balitoridae) from Guizhou Province, southwest China

This work describes a new species, Balitora anlongensis sp. nov., collected from a cave at Xinglong Town, Anlong County, Guzihou, China. Phylogenetic trees reconstructed based on two mitochondrial and three nuclear genes show that the new species represents an independent evolutionary lineage with large genetic differences, 7.1%–12.0% in mitochondrial gene cytochrome b and 9.2%–12.1% in cytochrome oxidase subunit 1, from congeners. Morphologically, the new species can be distinguished from the 18 species currently assigned to the genus Balitora by a combination of characters, most clearly by having two pairs of maxillary barbels; 8½ branched dorsal-fin rays; 5½ branched anal-fin rays; pectoral fin not reaching pelvic fin origin; dorsal-fin origin in front of pelvic fin origin; eye small (eye diameter approximately equal to outer maxillary barbel length); and fins lacking pigment in live fish. The new species represents the first record of Balitora inhabiting caves in China and increases the number of species in the genus Balitora in its present concept from 18 to 19. The study suggests that more evidence is needed to further clarify the taxonomic composition of the genus Balitora

Analysis of mitochondrial DNA sequences of Turcinoemacheilus genus (Nemacheilidae Cypriniformes) in Iran

Members of Nemacheilidae Family, Turcinoemacheilus genus were subjected to molecular phylogenetic analysis in this study. This genus was reported in 2009 to inhabit in Karoon River drainage, in contrary to previous assumption that it was the endemic species in the Basin of Tigris River. It was sampled from three stations placed in different tributaries in Karoon drainage and evaluated to understand the molecular phylogenetic relationships of Turcinoemacheilus in Iran. The mitochondrial cytochrome b gene (cyt b) and control region were used to infer phylogenetic relationships. PCR amplification of control region was not carried out successfully, possibly due to the high divergence of this sequence in the studied genus. The amplified fragments of cyt b were sequenced then analyzed by the use of phylogenetic software. Only one divergent position was seen in all three samples stations located in amino acid position 365. GTR and p-distances of cytochrome b gene for T. kosswigi computed from different stations of running water in Karoon drainage showed these samples belong to different populations and fall in intraspecific differences. In this study, examination of the molecular phylogeny using Bayesian analysis, maximum parsimony or neighbor-joining define the phylogentics of Turcinoemacheilus genus as a monophyletic clade which is sister-clade of Nemacheilus and Schistura genera. This report is the first report of Turcinoemacheilus molecular data and could describe molecular phylogeny of this genus in loaches

Beta diversity patterns of fish and conservation implications in the Luoxiao Mountains, China

The Luoxiao Mountains play an important role in maintaining and supplementing the fish diversity of the Yangtze River Basin, which is also a biodiversity hotspot in China. However, fish biodiversity has declined rapidly in this area as the result of human activities and the consequent environmental changes. Beta diversity was a key concept for understanding the ecosystem function and biodiversity conservation. Beta diversity patterns are evaluated and important information provided for protection and management of fish biodiversity in the Luoxiao Mountains. The results showed that the spatial turnover component was the main contributor to beta diversity of Hemiramphidae, Amblycipitidae, Catostomidae, Clariidae, Balitoridae and Percichthyidae in the Luoxiao Mountains, which indicated that a number of protected areas would be necessary to conserve fish biodiversity and that these families would need conservation measures. Most protected areas are currently limited to some regions; therefore, in order to protect fish diversity, conservation efforts must target an increase in the number of protected areas which should be spread across each of the regions

Classification, zoogeography and evolution of the fishes of the Cyprinoid families Homalopteridae and Gastromyzonidae.

The Homalopteridae and Gastromyzonidae, which are found in the swift currents of the torrential streaIllil in South Eastern Asia, constitute two remarkable families of Cyprinoid fishes. Habitudinal segregation has induced a great variety of adaptive modifications in them

Species diversity of drifting fish eggs in the Yangtze River using molecular identification

The dam constructions greatly changed the hydrologic conditions in the Yangtze River, and then significantly affected the spawning activities of indigenous river fish. Monitoring the species composition of drifting eggs during spawning season is important for protection issues. In this study, we have sampled drifting fish eggs in nine locations from 2014 to 2016. Eggs were identified using the mitochondrial cyt b gene sequence. A total of 7,933 fish eggs were sequenced successfully and blasted into the NCBI database. Thirty-nine fish species were identified, and were assigned to four families and two orders. Approximately 64% of the species identified, and 67% of the eggs, were classified in the Family Cyprinidae. Abundance and Shannon–Wiener diversity index of species were higher in the main river than in tributaries of the river. However, tributaries may be important spawning grounds for some fish species. The Jaccard’s similarity index and river-way distances among sampled stations were negatively correlated suggesting the environment shapes species composition in the sampled spawning grounds. These results showed that mitochondrial DNA sequence is a powerful and effective tool for fish egg identification in Yangtze River and these data are useful for conservation efforts

Provisional check-list of the fresh-water fishes of China

62 p. : ill. ; 24 cm.Includes bibliographical references and index

Structure of endemic fish assemblages in the upper Yangtze River basin and population differentiation of an endangered endemic fish (Gobiocypris rarus)

Le fleuve Yangtze (Changjiang en chinois) supporte une très riche biodiversité de poissons, avec environ 400 espèces au total. Assimilée à une barrière eco-fonctionnelle, la partie amont du Yangtze présente des conditions environnementales naturelles exceptionnelles, avec une hétérogeneité bien prononcée des habitats, un système de drainage bien développé, une abondance en ressources en eau and une biodiversité importante. Ainsi, on dénombre 286 espèces de poissons dans la partie amont du Yangtze, dont 124 endémiques à cette région. Cependant, cette biodiversité est fortement menacée, notamment du fait de la surexploitation, de la pollution des eaux, des barrages hydroélectriques, des invasions biologiques et des modifications environnementales. Il est de ce fait impératif de mesurer les influences de ces changements environnementaux sur la ressource piscicole, de telle sorte à accélérer la mise en place de mesures de conservation. En conséquent, cette thèse avait pour objectif d'apporter des éléments visant à favoriser la conservation des espèces endémiques de poisons dans la partie amont du fleuve Yangtze. Dans la première partie de la thèse, l'objectif est d'illustrer les mécanismes de structuration des assemblages de poissons pour améliorer les connaissances des processus écologiques de la partie amont du fleuve Yangtze, i.e. déterminer les patrons spatiaux de distribution des poissons endémiques et les relations avec les variables environnementales (publications P1 & P2). Nous avons pu définir cinq assemblages de poissons endémiques dans le haut Yangtze caractérisés par des différences significatives au niveau de la richesse spécifique. Ces assemblages reflètent le gradient longitudinal de la distribution des espèces et de richesse avec une forte corrélation avec la topographie et la géomorphologie du fleuve Yangtze. Chaque assemblage est caractérisé par des espèces endémiques " indicatrices ". Le patron de distribution des poissons endémiques est significativement corrélé avec les facteurs environnementaux de l'utilisation du sol du bassin versant et des caractéristiques du fleuve. Des modèles mixtes utilisant simultanément des paramètres d'utilisation du sol et des caractéristiques du fleuve permettent d'assurer une meilleure prédiction de l'assemblage des poissons endémiques du Yangtze, comparés à des modèles utilisant séparément les 2 groupes de paramètres environnementaux. Enfin, nous suggérons trois points importants pour la conservation des espèces endémiques de poissons du haut Yangtze: sélection de plusieurs sites protégés de diverses espèces; maintient d'une partie courante naturelle pour chaque cours d'eau parmi les affluents; développement de mise en réserve des affluents. Dans la deuxième partie de la thèse, afin d'obtenir une bonne connaissance d'une espèce de poisson endémique en danger (Gobiocypris rarus) et fournir des instructions pour la conservation des autres espèces du haut Yangtze, nous avons utilisé cette espèce comme exemple d'étude de conservation à l'aide de marqueurs microsatellites et morphologiques (publications P3, P4 et P5). L'habitat typique de G. rarus était caractérisé par une seule population stable qui présentait une taille effective relativement large et aucune évidence de structure cryptique au cours des dix dernières années. Les forces maintenant cette diversité génetique était principalement les fluctuations environnementales et les traits d'histoire de vie propres à G. rarus. A une échelle spatiale plus étendue, nous avons trouvé des patrons significatifs de différentiation entre plusieurs populations de G. rarus, d'un point de vue génétique mais aussi morphologique. Particulièrement, deux clusters génétiques reflétant la structure du réseau hydrographique ont été identifiés. L'étude comparée des patrons d'isolation par la distance nous a permis de conclure que G. rarus était capable de migrer de réseau en réseau davantage via les canaux d'irrigations que via l'embouchure des rivières. Nous avons également mis en évidence un dimorphisme sexuel cryptique (i.e. visible uniquement que quelque trait morphologique continu). Finalement, au vue de cette distribution discontinu (tant d'un point de vue génétique que morphologique) et étant donné les menaces écologiques attendu, nous conseillons que la plupart des populations étudiées soit préservées. Plus particulièrement, les populations T1, T2, Q2, M3 et D2 devraient être prioritaire d'un point de vue de la conservation, avec une gestion de l'habitat et de l'espèce particulièrement forte dans ces localités.The Yangtze River, also called Changjiang, supports rich biodiversity, especially diverse fish fauna, i.e., about 400 fish species and subspecies. As an eco-functional barrier of the Yangtze River, the upper Yangtze River exhibits complicated natural environment, pronounced habitat heterogeneity, well-developed drainage system, abundant water resources and rich biodiversity. There were 286 fish species and subspecies distributing in the upper Yangtze River, among which 124 species were endemic. However, these fish resources are experiencing large threats: overexploitation, water pollution, hydropower projects, invasion by exotic species, and global environmental changes. It is imperative to evaluate the influences of the changes in environmental features on the fish resources and to accelerate the progress of conservation projects. Therefore, two parts of content have been studied in this thesis for the conservation of endemic fishes in the upper Yangtze River. Firstly, for the purpose of providing insight into mechanisms structuring fish assemblages and enhancing knowledge on ecological processes in the upper Yangtze River, spatial pattern of endemic fishes in the upper Yangtze River basin and their relationship with environmental features have been studied in P1 and P2 of this thesis. We identified five endemic fish assemblages in the upper Yangtze River basin. Not only species composition but also endemic species richness varied significantly among these five assemblages. They not only reflect the longitudinal gradient pattern but also are closely correlated with the topography and geomorphology of the Yangtze River. Each endemic fish assemblage has its specific indicator species. The endemic fish distribution patterns are significantly correlated with environmental factors such as land-cover features and river characteristics. The mixed models containing both land-cover features and river characteristics are more effective than any individual one in explaining complex endemic fish distribution patterns in the upper Yangtze River basin. Finally, we suggested that three key points for the conservation of endemic fishes in the upper Yangtze River basin should be paid more attention: selection of several protected sites aiming at various species; maintenance of at least one flowing reach in each river; developing the conservation of tributaries. Secondly, in order to obtain enough background of an endangered endemic fish (Gobiocypris rarus) and provide guidelines for other species conservation in the upper Yangtze River basin, the author used this Chinese rare minnow (G. rarus) as an example to do the studies of conservation biology using microsatellite markers and morphological traits in P3, P4 and P5 of this thesis. The type locality of G. rarus held a single stable and healthy population with a relatively large Ne and no cryptic structure during nearly ten years. The forces maintaining their genetic diversity were mainly from environmental fluctuations and life history traits. In addition, there were significant differentiations among wild populations of G. rarus not only in genetic markers but also in morphometric traits. Two obvious genetic clusters were revealed among wild populations of G. rarus, reflecting out water system structure to some extent. An isolation-by-riparian-distance pattern was identified, indicating that G. rarus might migrate through some man-made channels of hydropower projects but not through the mouth of the Minjiang and Tuojiang Rivers to exchange genes. Sexual dimorphism existed in morphometric traits of G. rarus wild populations. Finally, in the view of discontinuous distribution, significant genetic and quantitative differentiation of wild populations, and large threats from human activities, all the studied populations should be protected. Especially, populations T1, T2, Q2, M3 and D2 should be in prior conservation, and a habitat and species management area should be established in its type locality (viz. population D2)

Geographical Speciation Process of the Genus Lepturichthys (Cypriniformes: Balitoridae)

The genus Lepturichthys is endemic in China, including two valid species, L. fimbriata and L. dolichopterus. The former is widely distributed in the Upper and Middle Yangtze River, while the latter only in Minjiang River. In the present study, the mitochondrial cytochrome b gene sequences were analyzed for 20 individuals of L. fimbriata collected from the Upper and Middle Yangtze River and eight individuals of L. dolichopterus collected from Minjiang River. This paper aimed to investigate the geographical speciation process of the genus Lepturichthys. The results showed that the genetic variations among different haplotypes of L. fimbriata ranged from 0.1% to 1.8%, with an average of 0.7%, and from 0.6% to 1.3%, with an average of 0.7% among different haplotypes of L. dolichopterus. The variations between L. fimbriata and L. dolichopterus were also very low, ranging from 0.2% to 1.8%, with an average of 0.9%. Two methods, Neighbor Joining (NJ) and Bayesian analysis (BI), were used for constructing the molecular phylogenetic trees. Both NJ and BI trees indicated that all Lepturichthys specimens formed as a monophyletic group; the L. dolichopterus samples also formed as monophyletic group, having a derived position in the phylogenetic trees, while the L. fimbriata samples formed as a paraphyletic group. Both L. fimbriata and L. dolichopterus are valid species in morphology. Based on molecular and morphological data, we presumed that the geographical speciation process of the genus Lepturichthys could be as following: during the Quaternary Glacial period, L. fimbriata in the Middle and Lower Yangtze River dispersed to the drainages of Southeast China along the Continental Shelf of East China Sea, one population spread to the Minjiang River and envolved as a new species (L. dolichopterus) because of considerable environmental difference, while the remaining L. fimbriata populations in the Yangtze River formed as a paraphyly. The other similar geographical speciation patterns are discussed in the present study as well