Genomic analysis and phylogenetic characterization of Himalayan snow trout, Schizothorax esocinus based on mitochondrial protein-coding genes.

BACKGROUND: Mitochondrial DNA (mtDNA) has become a significant tool for exploring genetic diversity and delineating evolutionary links across diverse taxa. Within the group of cold-water fish species that are native to the Indian Himalayan region, Schizothorax esocinus holds particular importance due to its ecological significance and is potentially vulnerable to environmental changes. This research aims to clarify the phylogenetic relationships within the Schizothorax genus by utilizing mitochondrial protein-coding genes. METHODS: Standard protocols were followed for the isolation of DNA from S. esocinus. For the amplification of mtDNA, overlapping primers were used, and then subsequent sequencing was performed. The genetic features were investigated by the application of bioinformatic approaches. These approaches covered the evaluation of nucleotide composition, codon usage, selective pressure using nonsynonymous substitution /synonymous substitution (Ka/Ks) ratios, and phylogenetic analysis. RESULTS: The study specifically examined the 13 protein-coding genes of Schizothorax species which belongs to the Schizothoracinae subfamily. Nucleotide composition analysis showed a bias towards A + T content, consistent with other cyprinid fish species, suggesting evolutionary conservation. Relative Synonymous Codon Usage highlighted leucine as the most frequent (5.18%) and cysteine as the least frequent (0.78%) codon. The positive AT-skew and the predominantly negative GC-skew indicated the abundance of A and C. Comparative analysis revealed significant conservation of amino acids in multiple genes. The majority of amino acids were hydrophobic rather than polar. The purifying selection was revealed by the genetic distance and Ka/Ks ratios. Phylogenetic study revealed a significant genetic divergence between S. esocinus and other Schizothorax species with interspecific K2P distances ranging from 0.00 to 8.87%, with an average of 5.76%. CONCLUSION: The present study provides significant contributions to the understanding of mitochondrial genome diversity and genetic evolution mechanisms in Schizothoracinae, hence offering vital insights for the development of conservation initiatives aimed at protecting freshwater fish species.

Effects of intracoelomic transmitter implantation on metabolic rate, swimming performance, growth and survival in juveniles of two salmonids.

In this study, we investigated the effects of acoustic tag implantation on standard and routine metabolic rate (SMR and RMR, estimated via oxygen consumption), critical swimming speed (Ucrit ), survival and growth in juveniles of rainbow trout Oncorhynchus mykiss and lake trout Salvelinus namaycush. Tag burdens ranged from 1.8% to 7.5% across the two species. Growth rates in acoustic-tagged fish were equal to or higher than those in other treatments. Acoustic-tagged S. namaycush had a marginally lower Ucrit than controls but that effect was not replicated in the O. mykiss experiment. Tagging did not have clear effects on metabolic rate but there was an interaction whereby SMR and RMR tended to increase with time since surgery in tagged O. mykiss but not in other treatments (the same trend did not occur in S. namaycush). Survival was high across treatments (mean 98% survival among O. mykiss, 97.5% among S. namaycush). There were no statistically significant effects of tag burden (percentage of body mass) except for a weak negative relationship with growth rate (across species) and a weak positive relationship with Ucrit but only in the O. mykiss. Collectively, our findings suggest there were minor, context-dependent effects of acoustic tagging in juvenile S. namaycush and O. mykiss during an eight-week laboratory experiment. Further research will be required to assess whether tagging can cause meaningful behavioural effects in these species in captivity or in the wild and whether there is a tag burden threshold above which deleterious effects consistently occur.

Distribution of temperature tolerance quantitative trait loci in Arctic charr (Salvelinus alpinus) and inferred homologies in rainbow trout (Oncorhynchus mykiss).

We searched for quantitative trait loci (QTL) affecting upper temperature tolerance (UTT) in crosses between the Nauyuk Lake and Fraser River strains of Arctic charr (Salvelinus alpinus) using survival analysis. Two QTL were detected by using two microsatellite markers after correcting for experiment-wide error. A comparative mapping approach localized these two QTL to homologous linkage groups containing UTT QTL in rainbow trout (Oncorhynchus mykiss). Additional marginal associations were detected in several families in regions homologous to those with QTL in rainbow trout. Thus, the genes underlying UTT QTL may antedate the divergence of these two species, which occurred by approximately 16 MYA. The data also indicate that one pair of homeologs (ancestrally duplicated chromosomal segments) have contained QTL in Arctic charr since the evolution of salmonids from a tetraploid ancestor 25-100 MYA. This study represents one of the first examples of comparative QTL mapping in an animal polyploid group and illustrates the fate of QTL after genome duplication and reorganization.

Alternative mating strategies in Atlantic salmon and brown trout.

By screening variable number of tandem repeat (VNTR) loci, multiple paternity within clutches has been found in wild populations of southern European Atlantic salmon (Salmo salar) and brown trout (Salmo trutta). For Atlantic salmon, we determined the relative contribution of alternative male phenotypes to the next generation. Individual males that are morphologically juvenile yet sexually mature fertilized a large proportion of eggs, and they thereby contributed to an increase of genetic variability in wild populations via (1) balancing the sex ratio, (2) increasing outbreeding, and (3) enlarging the effective population size, in part a consequence of (1) and (2). In addition, these precocious males ensured that interspecific spawns involving Atlantic salmon females and brown trout males (a fairly common occurrence in southern Europe where the two species are sympatric) resulted mostly in Atlantic salmon progeny. For brown trout, preliminary genetic results indicated that multiple paternity, when present, was not due to alternative mating strategies by males, but rather to successive fertilizations by adult suitors.

The importance of employing homologous serum free of thyronines in radioimmunoassays to assess circulating thyroid hormones in rainbow trout

A pesar de ser abundante, la información relacionada con los valores de tironinas circulantes en la trucha arcoiris, es confusa. El presente estudio demuestra la importancia de mantener especies sero-homólgoas durante la medición de tironinas con RIE para eviatar falsos resultados. La utilización de suero homólogo (trucha) libre de tironinas en la curva estándar permite la estandarización de radioinmunoensayos exactos y específcos para cuantificar los niveles circulates de T3 y T4 en 10 microl de suero de trucha arcoiris. El límite de detección fue de 50 pg para ambas tironinas. Los coeficientes de variación inter e intra ensayo fueron menores al 10 por ciento. Los valores promedio para T3 y T4 + - DEM en la población de truchas estudiadas (n=34) fueron 23.6 + - 1.2 y 12.0 + - 2.3 ng/ml respectivamente. Se obsevó una correlación positiva y significativa (p < 0.005) entre el peso corporal y T3 confirmando la participación activa de esta tironina en el proceso de crecimiento.

Isolation of a putative retrovirus pol gene fragment from trout.

1. A 220 bp DNA fragment was obtained from three different species of salmonids during PCR analysis using a primer sequence based on human beta-2 microglobulin. All of the 220 bp fragments showed strong homology to each other. 2. Several of the DNA sequences also contained protein reading frames. Searching DNA and protein databases revealed significant homology to a segment of the pol gene (reverse transcriptase) from various retroviruses. Phylogenetic analysis at both the DNA and the protein levels showed clustering of the fish sequences and the closest viral sequence was the Moloney murine leukaemia virus (MoMuLV). Southern analysis indicated that there are several copies of the gene dispersed throughout the salmonid genome. 3. Preliminary results suggest that these sequences may be unique to the family Salmonidae. This would suggest that this retrovirus was incorporated in the DNA of an ancestral salmonid prior to the evolution and divergence of this family of fish.