No abstract

In this study, the phylogenetic relationships among 13 pangasiids and six schilbids of Thailand were reconstructed based on the almost complete mitochondrial cytochrome b (cyt b), 12S rRNA, tRNA-Val and 16S rRNA, as well as the partial nuclear recombination-activating gene 1 (rag1) sequences by using the maximum likelihood and the Bayesian inference methods of phylogenetic reconstruction. The reconstructed phylogeny based on the concatenated sequence data set recovered Pangasiidae and Schilbidae as reciprocally monophyletic groups. Within Pangasiidae, four major clades were recovered, which according to the cyt b genetic distances can be categorized into four genera: Pangasius, Pseudolais, Helicophagus and Pangasianodon. The genus Pangasianodon was strongly supported as the most basal taxon within pangasiids, whereas Pseudolais + Helicophagus were recovered as a sister group of Pangasius. Within the latter, the giant pangasius Pangasius sanitwongsei was recovered as a sister group of the spot pangasius Pangasius larnaudii, Pangasius krempfi as a sister group of Pangasius nasutus + Pangasius conchophilus and Pangasius polyuranodon as a sister species of Pangasius macronema. Other internal phylogenetic relationships, however, were unresolved. Within Schilbidae, Pseudeutropius was supported as the most basal lineage. Eutropiichthys was recovered as a sister group of Clupisoma. The enigmatic Clupisoma sinense was recognized as more closely related to Laides longibarbis than to Clupisoma prateri. Thus, based on the cyt b genetic distances, a recategorization of C. sinense to the genus Laides is suggested. On the basis of a relaxed clock fossil calibration, the divergence of pangasiids and schilbids was estimated to have occurred 14·93 million years before present (b.p.) during the Miocene epoch. The separation between Pangasiidae and Schilbidae took place c. 13·12 Mb.p. during the early middle Miocene. The estimated divergence time of pangasiids is similar to the age of the calibrated fossil, Cetopangasius chaetobranchus, which was discovered in north-central Thailand. This suggests that the oldest pangasiid ancestor diverged into diverse genera in the area.

In order to support studies of short mackerel population genetic structure in the Gulf of Thailand and phylogenetic relationships, the mitochondrial genome of the short mackerel, Rastrelliger brachysoma, has recently been determined by a partial cloning technique, long PCR with three pairs of newly designed primers and primer walking sequencing. The complete mitochondrial genome is 16,539 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes) and a control region (CR) as in other bony fishes. Within the 845-bp CR, we identified several conserved motifs. The phylogeny obtained by Bayesian analyses based on two nucleotide datasets corresponding to the cytb and nd2 mitochondrial genes strongly support the inclusion of R. brachysoma within the monophyletic tribe of Scombrini in the family Scombridae. The obtained phylogeny also reveals high-statistical support for the existence of two distinct groups indicating that Scombroidei and Xiphioidei are two separate suborders.

The black mud crab, Scylla serrata (Forskål 1775), is the most economically important edible crab in South-East Asia. In the present study, the complete mitochondrial genome of black mud crab, S. serrata, was determined with the sequential polymerase chain reaction and primer walking sequencing. The complete mitochondrial genome was 15,721 bp in length with an A+T content of 69.2 % and contained 37 mitochondrial genes (13 protein coding genes (PCGs), 2 ribosomal RNA genes and 22 transfer RNA genes) and a control region (CR). The analysis of the CR sequence shows that it contains a multitude of repetitive fragments which can fold into hairpin-like or secondary structures and conserved elements as in other arthropods. The gene order of S. serrata mainly retains as the pancrustacean ground pattern, except for a single translocation of trnH. The gene arrangement of S. serrata appears to be a typical feature of portunid crabs. Phylogenetic analyses with concatenated amino acid sequences of 12 PCGs establishes that S. serrata in a well-supported monophyletic Portunidae and is consistent with previous morphological classification. Moreover, the phylogenomic results strongly support monophyletic Pancrustacea (Hexapoda plus "Crustaceans"). Within Pancrustacea, this study identifies Malacostraca + Entomostraca and Branchiopoda as the sister group to Hexapoda, which confirms that "Crustacea" is not monophyletic. Cirripedia + Remipedia appear to be a basal lineage of Pancrustacea. The present study also provides considerable data for the application of both population and phylogenetic studies of other crab species.

The complete mitochondrial control regions (CR) of three mackerels (Rastrelliger spp.) were examined and analyzed. The CR contained three domains, in which three termination-associated sequences (TAS-I, TAS-II and TAS-III), two central conserved sequence blocks (CSB-E, CSB-D), three conserved sequence blocks (CSB-I, CSB-II, and CSB-III) and a putative promoter were detected. Molecular indices analyses of the aligned complete CR sequences showed high level of haplotype diversities and genetic divergences among the three species. The intraspecific divergence among species of this genus ranked from 0.25% to 1.62% and interspecific divergence from 1.90% to 4.30%. The phylogenetic tree shows monophyly with R. brachysoma as a basal species of Rastrelliger. Applying the average divergence rate for fish control regions, the results suggest that the time of separation among Rastrelligers could have occurred in the middle Pleistocene era.