Population structure of the Southeast Asian river catfish Mystus nemurus

Phylogenetics and population genetics of Plotosus canius (Siluriformes: Plotosidae) from Malaysian coastal waters

Plotosus canius (Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental research on biological characteristics of P. canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure of P. canius for the first time through the application of mitochondrial Cytochrome Oxidase I (COI) gene, cross amplification of Tandanus tandanus microsatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395–0.771 and 0.033–0.65 respectively. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (H_o) value of 0.2168, which was lower than the standard heterozygosity in marine populations (H_o = 0.79). This alongside the high Fis values estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotype KR086940, which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. Demographic analyses showed that all populations were in an equilibrium state with no significant evidence of population expansion. To put it briefly, the current study has managed to provide an initial genomic database toward understanding of the genetic characterization, phylogenetic, molecular diversification and population structure in P. canius, and should be necessary highlighted for appropriate management and conservation of species. Further studies must be carried out involving more geographical and sampling sites, larger population size per site, and utilization of species specific microsatellites loci.

A DNA Barcode-Based Evaluation of the Southeast Asian Catfish Genus Hemibagrus Bleeker, 1862 (Teleostei: Siluriformes; Bagridae)

Species of the genus Hemibagrus are large river catfishes found throughout South-east Asia. The complexity of the region’s biogeographical history and the lack of well-defined morphological characters render the taxonomy and phylogenetic reconstruction of Hemibagrus problematical. Early molecular studies of the H. nemurus species group revealed extensive genetic subdivisions, the taxonomic status of which remained unclear. A recent, morphologically-based, revision of the genus provides an opportunity to clarify the taxonomic status of these lineages. We employ a DNA barcode derived from the mitochondrial cytochrome b gene to expand our genetic analyses of the genus and to test the congruence of morphologically and genetically based taxonomies. Secondly, we evaluate phylogenetic relationships among taxa. Thirdly, we describe the phylogeography of Hemibagrus in South-east Asia. The species groups and nominal species proposed in the morphology-based revision generally reflect a hierarchy of monophyletic groups based on phenetic and maximum likelihood reconstructions of mtDNA phylogenies. The most notable exception involves the definition of a morphologically cryptic group from North Borneo. H. nemurus from West Java appears to be a regional population of H. capitulum. The phylogeography of the genus has been principally influenced by the formation of North Borneo and the emergence of the Sunda Islands.

Genetic variation, population structure and identification of yellow catfish, Mystus nemurus (C&V) in Thailand using RAPD, ISSR and SCAR marker

Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were used to investigate the genetic structure of four subpopulations of Mystus nemurus in Thailand. The 7 RAPD and 7 ISSR primers were selected. Of 83 total RAPD fragments, 80 (96.39%) were polymorphic loci, and of 81 total ISSR fragments, 75 (92.59%) were polymorphic loci. Genetic variation and genetic differentiation obtained from RAPD fragments or ISSR fragments showed similar results. Percentage of polymorphic loci (%P), observed number of alleles, effective number of alleles, Nei's gene diversity (H) and Shannon's information index revealed moderate to high level of genetic variations within each M. nemurus subpopulation and overall population. High levels of genetic differentiations were received from pairwise unbiased genetic distance (D) and coefficient of differentiation. Mantel test between D or gene flow and geographical distance showed a low to moderate correlation. Analysis of molecular variance indicated that variations among subpopulations were higher than those within subpopulations. The UPGMA dendrograms, based on RAPD and ISSR, showing the genetic relationship among subpopulations are grouped into three clusters; Songkhla (SK) subpopulation was separated from the other subpopulations. The candidate species-specific and subpopulation-specific RAPD fragments were sequenced and used to design sequence-characterized amplified region primers which distinguished M. nemurus from other species and divided SK subpopulation from the other subpopulations. The markers used in this study should be useful for breeding programs and future aquacultural development of this species in Thailand.

Comparative assessment of genetic variability in the populations of endemic and endangered yellow catfish, Horabagrus brachysoma (Teleostei: Horabagridae), based on allozyme, RAPD, and microsatellite markers

The comparative assessment of genetic diversity using allozymes, random amplified polymorphic DNA (RAPD), and microsatellite markers was conducted in endemic and endangered yellow catfish (Horabagrus brachysoma) sampled from three locations in Western Ghats river systems of India. Among the three markers, microsatellites show more polymorphism, having 100% polymorphic loci, whereas allozymes show the least (56%). In RAPD, 60.5% of fragments were polymorphic. Observed heterozygosity and F(ST) values were very high in microsatellites, compared with the other markers. Microsatellite and RAPD markers reported a higher degree of genetic differentiation than allozymes among the populations depicted by pairwise F(ST)/G(ST), AMOVA, Nei's genetic distance, and UPGMA dendrogram. The three classes of markers demonstrated striking genetic differentiation between pairs of H. brachysoma populations. The data emphasize the need for fishery management, conservation, and rehabilitation of this species.

Genetic variation and phylogenetic relationship between two species of yellow catfish, Horabagrus brachysoma and H. nigricollaris (Teleostei: Horabagridae) based on RAPD and microsatellite markers

The two species of yellow catfish, Horabagrus brachysoma and H. nigricollaris are categorized as 'endangered' and 'critically endangered' respectively in their wild habitat. Proper knowledge of genetic structure and variability of these endangered species are highly essential for the management, conservation and improvement of fish stocks. Therefore, genetic variation and phylogenetic relationships between these species of yellow catfish sampled from Chalakkudy River in the hot spot of biodiversity-Western Ghats region, Kerala, India were analyzed by using Random amplified polymorphic DNA (RAPD) and microsatellite markers. 85 RAPD and five microsatellites loci were detected to analyze the genetic variation and phylogenetic relationships among these species. Out of 85 RAPD loci produced only 52.94% were polymorphic whereas in microsatellite, all 5 loci were polymorphic (100%). Species-specific RAPD bands were found in both species studied. In microsatellite, the number of alleles across the five loci ranged from 1 to 8. The observed heterozygosities in H. brachysoma and H. nigricollaris were 0.463 and 0.443, respectively. Here, both RAPD and microsatellite methods reported a low degree of gene diversity and lack of genetic heterogeneity in both species of Horabagrus which strongly emphasize the need of fishery management, conservation and rehabilitation of these species.

High genetic diversity in cryptic populations of the migratory sutchi catfish Pangasianodon hypophthalmus in the Mekong River

The detection and conservation of spawning units is of crucial importance in highly migratory species. The sutchi catfish Pangasianodon hypophthalmus (Pangasiidae; Teleostei) is a common large-sized tropical fish, which migrates annually to several upstream spawning sites on the Lower Mekong River and feeds on the huge floodplain of the Lower Mekong and Tonle Sap for the other half of the year. We hypothesised that because of the relative size of the feeding and spawning habitat, genetic variability would be high and homogeneous in foraging populations, but that spawning stocks would be distinct in space and time. To test these predictions, 567 individuals from 10 geographic locations separated by up to 1230 km along the Lower Mekong River were genotyped at seven microsatellite loci. The level of genetic diversity was much higher than other freshwater fish and reached values comparable to marine species (mean H(e)=0.757). All samples collected at the potential spawning sites deviated from Hardy-Weinberg expectations, suggesting admixture. Individual-based clustering methods revealed genetic heterogeneity and enabled the detection of three genetically distinct sympatric populations. There was no evidence of recent reduction in effective population size in any population. Contrasting with the vast extent of the feeding grounds, the shortage of spawning grounds seems to have moved sutchi catfish towards diachronous spawning. Hence the sustainable exploitation of this natural resource hinges on the conservation of the limited spawning grounds and open migration routes between the spawning and feeding grounds.