Cloning and sequencing of the growth hormone gene of large yellow croaker and its phylogenetic significance

Using conserved primers and the PCR reaction, the growth hormone (GH) gene and the 3'-UTR of the large yellow croaker (Pseudosciaena crocea) were amplified and sequenced. The gene structure was analyzed and compared to the GH genes of 5 other percoid fish downloaded from Genbank. Also the GH gene of the large yellow croaker and the genes from 14 Percoidei and 2 Labroidei species were aligned using Clustal X. A matrix of 564 bp was used to construct the phylogenetic tree using maximum parsimony and neighbor-joining methods. Phylogenetic trees by the two methods are identical in most of the clades with high bootstrap support. The results are also identical to those from morphological data. In general, this analysis does not support the monophyly of the families Centropomidae and Carangidae. But our GH gene tree indicates that the representative species of the families Sparidae and Sciaenidae are a monophyletic group.

Phylogenetic relationships of glyptosternoid fishes (Siluriformes : Sisoridae) inferred from mitochondrial cytochrome b gene sequences

To explore phylogenetic relationships among glyptosternoid fishes, we determined nucleotide sequences of the complete mitochondrial cytochrome b gene region (1138 base pair). Thirteen species of glyptosternoid fishes and six species of non-glyptosternoids represent 10 sisorid genera were examined. Molecular phylogenetic trees were constructed using the maximum parsimony, minimum evolution, maximum likelihood, and Bayesian methods. Bayesian and maximum likelihood analyses support the monophyly of glyptosternoids, but our hypothesis of internal relationships differs from previous hypothesis. Results indicated that glyptosternoid is a monophyletic group and genera Glyptosternum and Exostoma are two basal species having a primitive position among it. Genera Euchiloglanis and Pareuchiloglanis form a sister-group. Then they form a sister-group with Pseudexostoma plus Oreoglanis. Our result also found that Pareuchiloglanis anteanalis might be considered as the synonyms of Parechiloglanis sinensis, and genus Euchiloglanis might have only one valid species, Euchiloglanis davidi. (C) 2003 Elsevier Inc. All rights reserved.

Phylogenetic relationships of the subclass Peritrichia (Oligohymenophorea, Ciliophora) inferred from small subunit rRNA gene sequences

The phylogenetic relationships among peritrichs remain unresolved. In this study, the complete small subunit rRNA (SSrRNA) gene sequences of seven species (Epistylis galea, Campanella umbellaria, Carchesium polypinum, Zoothamnium arbuscula, Vaginicola crystallina, Ophrydium versatile, and Opercularia microdiscum) were determined. Trees were constructed using distance-matrix, maximum-likelihood and maximum-parsimony methods, all of which strongly supported the monophyly of the subclass Peritrichia. Within the peritrichs, 1) E. galea grouped with Opercularia microdiscum and Campanella umbellaria but not the other Epistylis species, which indicates that the genus Epistylis might not be monophyletic; 2) the topological position of Carchesium and Campanella suggested that Carchesium should be placed in the family Zoothammidae, or be elevated to a higher taxonomic rank, and that Campanella should be independent of the family Epistylididae, and probably be given a new rank; and 3) Opisthonecta grouped strongly with Asty/ozoon, which suggested that Opisthonecta species were not the ancestors of the stalked peritrichs.

Sequence analysis of cytochrome b gene indicates that East Asian group of cyprinid subfamily Leuciscinae (Teleostei : Cyprinidae) evolved independently

The sequences of mitochondrial cytochrome b gene of cyprinid subfamily Leuciscinae are analyzed. Phylogenetic trees generated with methods of neighbor-joining, maximum likelihood and maximum parsimony with Phenacogrammus as an outgroup indicate that Leuciscinae is not a monophyletic group but includes two discrete subgroups. The East Asian group of the subfamily Leuciscinae, including the genera Ctenopharyngodon, Elopichthys, Luciobrama, Mylopharyngodon, Ochetobius, and Squaliobarbus, is close to Aristichthys and Hypophthalmichthys, and they form a monophyletic group which is distant from the leuciscine genera in Europe, Siberia and North America, such as Phoxinus, Leuciscus, Abramis, Rutilus, Chondrostoma, Alburnus, Opsopoedus, Lythrurus, and Pimephales. Our study suggests that the diversified East Asian group of the subfamily Leuciscinae should have an independent origination.

Sequence variations of the S7 ribosomal protein gene in primitive cyprinid fishes: Implication on phylogenetic analysis

Cyprinidae is the largest fish family in the world and contains about 210 genera and 2010 species. Appropriate DNA markers must be selected for the phylogenetic analyses of Cyprinidae. In present study, the 1st intron of the S7 ribosomal protein (r-protein) gene is first used to examine the relationships among cyprinid fishes. The length of the 1st intron obtained by PCR amplification ranges from 655 to 859 by in the 16 cyprinid species investigated, and is 602 by in Myxocyprinus asiaticus. Out of the alignment of 925 nucleotide sites obtained, the parsimony informative sites are 499 and occupy 54% of the total sites. The results indicate that the 1st intron sequences of the S7 r-protein gene in cyprinids are rich in informative sites and vary remarkably in sequence divergence from 2.3% between close species to 66.6% between distant species. The bootstrap values of the interior nodes in the NJ (neighbor-joining) and MP (most-parsimony) trees based on the present S7 r-protein gene data are higher than those based on cytochrome b and the d-loop region respectively. Therefore, the 1st intron sequences of the S7 r-protein gene in cyprinids are sensitive enough for phylogenetic analyses, and the 1st intron is an appropriate genetic marker for the phylogenetic reconstruction of the taxa in different cyprinid subfamilies. However, attempts to discuss whether the present S7 r-protein gene data can be applied to the phylogeny of the taxa at the level of the family or the higher categories in Cypriniformes need further studies.

Phylogenetic relationships of the subclass Peritrichia (Oligohymenophorea, Ciliophora) with emphasis on the genus Epistylis, inferred from small subunit rRNA gene sequences

The peritrichs have been recognized as a higher taxon of ciliates since 1968. However, the phylogenetic relationships among them are still unsettled, and their placement within the class Oligohymenophorea has only been supported by the analysis of the small subunit rRNA gene sequence of Opisthonecta henneguyi. DNA was isolated directly from field-sampled species for PCR, and was used to resolve relationships within the genus Epistylis and to confirm the stability of the placement of peritrichs. Small subunit rRNA gene sequences of Epistylis plicatilis, Epistylis urceolata, Epistylis chysemydis, Epistylis hentscheli, Epistylis wenrichi, and Vorticella campanula were sequenced and analyzed using both distance-matrix and maximum-parsimony methods. In phylogenetic trees, the monophyly of both the genus Epistylis and the subclass Peritrichia was strongly supported, while V. campanula clustered with Vorticella microstoma. The topology in which E. plicatilis and E. hentscheli formed a strongly supported sister clade to E. urceolata, E. chrysemydis, and E. wenrichi was consistent with variations in the thickness of the peristomial lip. We concluded that the peristomial area, especially the. peristomial lip, might be the important phylogenetic character within the genus Epistylis.

The Relationship between Decision Trees and the Scale of Train Data Set

Decision Trees need train samples in the train data set to get classification rules. If the number of train data was too small, the important information might be missed and thus the model could not explain the classification rules of data. While it is not affirmative that large scale of train data set can get well model. This Paper analysis the relationship between decision trees and the train data scale. We use nine decision tree algorithms to experiment the accuracy, complexity and robustness of decision tree algorithms. Some results are demonstrated.