Phylogeny of the East Asian cyprinids inferred from sequences of the mitochondrial DNA control region

With 210 genera and 2010 species, Cyprinidae is the largest freshwater fish family in the world. Several papers, based on morphological and molecular data, have been published and have led to some solid conclusions, such as the close relationships between North American phoxinins and European leuciscins. However, the relationships among major subgroups of this family are still not well resolved, especially for those East Asian groups. In the present paper, the mitochondrial DNA (mtDNA) control region, 896-956 base pairs, of 17 representative species of East Asian cyprinids was sequenced and compared with those of 21 other cyprinids to study their phylogenetic relationships. After alignment, there were 1051 sites. The comparison between pairwise substitutions and HKY distances showed that the mtDNA control region was suitable for phylogenetic study. Phylogenetic analysis indicated that there are two principal lineages in Cyprinidae: Cyprinine and Leuciscine. In Cyprinine, the relationships could be a basal Labeoinae, an intermediate Cyprininae, and a diversified Barbinae (including Schizothroaxinae). In Leuciscine, Rasborinae is at the basal position; Gobioninae and Leuciscinae are sister groups; the East Asian cultrin-xenocyprinin taxa form a large monophyletic group with some small affiliated groups; and the positions of Acheilognathinae and Tincinae are still uncertain.

Mitochondrial d-loop sequence variation and phylogeny of gobiobotine fishes

The mitochondrial DNA control region is amplified and sequenced from 8 genera and 10 species of gobiobotine fishes. The phylogenetic tree of Gobiobotinae and some representative species of other Cyprinid subfamilies obtained by the method of neighborhood joining, maximum likelihood and maximum parsimony with Danio rerio as an outgroup indicates that Gobiobotinae fishes are a monophyletic group which is close to Gobioninae subfamily. Gobiobotinae should be included into subfamily Gobioninae in terms of phylogenetic analysis. The research result supports that Gobiobotinae can be divided into genus Xenophysogobio and Gobiobotia. Xenophysogabio is the most primitive genera in the subfamily.

Mitochondrial cytochrome b sequence variations and phylogeny of the East Asian bagrid catfishes

The mitochondrial DNA cytochrome b gene was sequenced from 8 bagrid catfishes in China. Aligned with cytochrome b sequences from 9 bagrid catfishes in Japan, Korea and Russia retrieved from GenBank, and selected Silurus meridionalis, Liobagrus anguillicauda, Liobagrus reini and Phenacogrammus interruptus as outgroups, we constructed a matrix of 21 DNA sequences. The Kimura's two-parameter distances were calculated and molecule phylogenetic trees were constructed by using the maximum parsimony (MP) and neighbor-joining (NJ) methods. The results show that (i) there exist 3-bp deletions of mitochondrial cytochrome b gene compared with cypriniforms and characiforms; (ii) the molecular phylogenetic tree suggests that bagrid catfishes form a monophyletic group, and the genus Mystus is the earliest divergent in the East Asian bagrid catfishes, as well as the genus Pseudobagrus is a monophyletic group but the genus Pelteobagrus and Leiocassis are complicated; and 60 the evolution rate of the East Asian bagrids mitochondrial cytochrome b gene is about 0.18%-0.30% sequence divergence per million years.

Sequence variations in the mitochondrial DNA control region and their implications for the phylogeny of the Cypriniformes

The mitochondrial DNA control region of six cobitids and two catostomids was sequenced and compared with sequences of other cypriniforms to study their sequence variations. The extended termination associated sequence (ETAS) domain, central domain, and conserved sequence block (CSB) domain were partitioned and the ETAS sequence, CSB-D, CSB-E, ECSB-F, CSB1, CSB2, and CSB3 were identified. It is suggested that the "hairpin" TACAT-ATGTA is the key sequence of ETAS and GACATA is the symbol of CSB1. Phylogenetic analysis based on the CSB domain showed that all cyprinids evolved as one monophyletic group, while the non-cyprinid Cypriniformes could be another monophyly that is in accordance with the hypothesis proposed by Siebert. Further analysis of the phylogeny of the Cobitoidei was also conducted and it is tentatively suggested that their relationships are Catostomidae + (Gyrinocheilidae + (Botiinae + (Homalopteridae + (Cobitinae + Nemacheilinae)))).

Phylogeny of the specialized schizothoracine fishes (Teleostei : Cypriniformes : Cyprinidae)

Phylogeny of the specialized schizothoracine fishes (Teleostei: Cypriniformes: Cyprinidae). Zoological Studies 40(2). 147-157. To elucidate phylogenetic relationships within the specialized schizothoracine fishes, we used 41 variable osteological and external characters among this groups, three species of Schizothorax, and 1 fossil species. When the 3 species of Schizothorax were designated as an outgroup and all 41 characters were set as unordered with equal weighting, the data matrix yielded a single most-parsimonious tree with a tree length of 71 steps, a consistency index of 0.6761, and a retention index of 0.7416. Meanwhile, a bootstrap test was conducted to verify the reliability of the results. The matrix was also analyzed for different conditions: all characters were ordered and the fossil species was added as an outgroup. The phylogenetic analyses presented herein support the following hypotheses. 1) All species of the specialized schizo-thoracines fishes form a monophyletic group. 2) Monophyly of the genus Ptychobarbus is not supported by the bootstrap test or when these characters are ordered. 3) The genus Gymnodiptychus forms a monophyletic group. 4) All species of Ptychobarbus and Gymnodiptychus form a monophyletic group with Diptychus as its sister group.

Phylogeny of the Amphiliidae (Teleostei : Siluriformes)

The freshwater African catfish family Amphiliidae had been reviewed based on the 73 osteological characters with Diplomystidae, dagger Hypsidoridae, Amblycipitidae, Sisoridae, and Bagridae as out-groups. Because the family position of Leptoglanis (Bagridae/Amphiliidae) is under debate, this genus has been taken as an out-group too. Results of the study indicate that: 1) the Amphiliidae is not a monophyletic group and must now be restricted to the genera Amphilius and Paramphilius; the two subfamilies Amphiliinae and Doumeinae are separated by the sisorids Euchiloglanis (with most of the glyptosternid fishes) and Glyptothorax (with most of the non-glyptosternid fishes); 2) no synapomorphies were found for the subfamily Amphiliinae. 3) The five genera of subfamily Doumeinae constitute a monophyletic group, Andersonia being the sister-group of the four other genera; subfamily Doumeinae + Leptoglanis form the family Doumeidae. The glyptosternids no longer belong to the Sisoridae (family restricted to the non-glyptosternids) and represent the new family Glyptosternidae. (C) 1999 Editions scientifiques et medicales Elsevier SAS.

Phylogeny of SARS-CoV based on high-dimensional information geometry

We proposed a novel methodology, which firstly, extracting features from species' complete genome data, using k-tuple, followed by studying the evolutionary relationship between SARS-CoV and other coronavirus species using the method, called "High-dimensional information geometry". We also used the mothod, namely "caculating of Minimum Spanning Tree", to construct the Phyligenetic tree of the coronavirus. From construction of the unrooted phylogenetic tree, we found out that the evolution distance between SARS-CoV and other coronavirus species is comparatively far. The tree accurately rebuilt the three groups of other coronavirus. We also validated the assertion from other literatures that SARS-CoV is similar to the coronavirus species in Group I.

Molecular phylogeny and species identification of pufferfish of the genus Takifugu (Tetraodontiformes, Tetraodontidae)

The phylogenetic relationships and species identification of pufferfishes of the genus Takifugu were examined by use of randomly amplified polymorphic DNA (RAPD) and sequencing of the amplified partial mitochondrial 16S ribosomal RNA genes. Amplifications with 200 ten-base primers under predetermined optimal reaction conditions yielded 1962 reproducible amplified fragments ranging from 200 to 3000 bp. Genetic distances between 5 species of Takifugu and Lagocephalus spadiceus as the outgroup were calculated from the presence or absence of the amplified fragments. Approximately 572 bp of the 16S ribosonial RNA gene was amplified, using universal primers, and used to determine the genetic distance values. Topological phylogenic trees for the 5 species of Takifugu and outgroup were generated from neighbor-joining analysis based on the data set of RAPD analysis and sequences of mitochondrial 16S rDNA. The genetic distance between Takifugu rubripes and Takifugu pseudommus was almost the same as that between individuals within cacti species, but much smaller than that between T. rubripes, T. pseudommus, and the other species. The molecular data gathered from both analysis of mitochondria and nuclear DNA strongly indicated that T. rubripes and T. pseudommus should be regarded as the same species. A fragment of approximately 900 bp was amplified from the genome of all 26 T. pseudommus individuals examined and 4 individuals of intermediate varieties between T. rubripes and T. pseudommus. Of the 32 T. rubripes individuals, only 3 had the amplified fragment. These results suggest that this fragment may be useful in distinguishing between T. rubripes and T. pseudommus.

Morphology and Molecular Phylogeny of Trimyema koreanum n. sp., a Ciliate from the Hypersaline Water of a Solar Saltern

A new ciliate, Trimyema koreanum n. sp., isolated from hypersaline water (salinity of 293 parts per thousand) from a solar saltern in Korea, was investigated using live observation, protargol impregnation, and gene sequencing. Trimyema koreanum is about 30 x 13 mu m in vivo, has usually 23 longitudinal ciliary rows forming two distinct ciliary girdles visible both in vivo and in protargol impregnation. A third indistinct ciliary girdle as well as a girdle of mucocysts is distinguishable only in impregnated cells. We suggest T. koreanum as a new species, differing from the most similar species, T. marinum, by the presence of two distinct ciliary girdles (T. marinum usually has six ciliary girdles clearly visible in living cells and three anterior spirals that encircle the cell completely). Although the number of known 18S rRNA sequences in the genus Trimyema was limited, the Trimyema group including T. koreanum forms a strong clade. The phylogenetic position confirms that the isolate belongs to the genus Trimyema and is different from previously sequenced species. Trimyema koreanum is able to consume both prokaryotes and small eukaryotes (specifically, the alga Dunaliella sp.).

Mitochondrial DNA phylogeny of two morphologically enigmatic fishes in the subfamily Schizothoracinae (Teleostei : Cyprinidae) in the Qinghai-Tibetan Plateau

The complete mitochondrial DNA (mtDNA) cytochrome b gene (1140 bp) was sequenced in Herzenstein macrocephalus and Gymnocypris namensis and in 13 other species and sub-species (n = 22), representing four closely related genera in the subfamily Schizothoracinae. Conflicting taxonomies of H. macrocephalus and G. namensis have been proposed because of the character instability among individuals. Parsimony, maximum likelihood and Bayesian methods produced phylogenetic trees with the same topology and resolved several distinctive clades. Previous taxonomic treatments, which variously placed these two species of separate genera or as sub-species, are inconsistent with the mtDNA phylogeny. Both H. macrocephalus and G. namensis appear in a well-supported clade, which also includes nine species of Schizopygopsis, and hence should be transferred to the genus Schizopygopsis. Morphological changes are further illustrated, and their adaptive evolution in response to the local habitat shifts during the speciation process appears to be responsible for conflicting views on the systematics of these two species and hence the contrasting taxonomic treatments. These species are endemic to the Qinghai-Tibetan Plateau, a region with a history of geological activity and a rich diversity of habitats that may have result in the parallel and reversal evolution of some morphological characters used in their taxonomies. Our results further suggest that speciation and morphological evolution of fishes in this region may be more complex than those previously expected. (c) 2007 The Authors Journal compilation (c) 2007 The Fisheries Society of the British Isles.