Trophic interactions and the diet composition of sympatric finfish predators in the tropical demersal ecosystem in the Bay of Bengal.

The dietary composition, foraging strategies, and interspecific trophic interactions were identified for four major demersal carnivorous finfishes, namely, croaker Otolithes ruber, hairtail Trichiurus lepturus, threadfin bream Nemipterus japonicus, and lizardfish Saurida undosquamis, along the north-western part of Bay of Bengal from 2014 to 2016. Two species, Trichiurus lepturus and Saurida undosquamis, were identified as finfish feeders due to the high number of teleost (clupeids and engraulids) prey. One species, Nemipterus japonicus, had a significantly different diet of metapenaeids and charybdids, and was identified as a shellfish feeder. The final species, Otolithes ruber, preyed equally on crustaceans and teleosts, and was identified as a shellfish-finfish feeder. The feeding activity of all four species was lower during peak spawning periods and tended to increase with maturity. Feeding preferences varied with seasons. The trophic level ranged from 3.49 to 4.01, classifying the four species as medium-carnivores or meso-predators. Niche breadth ranged from 0.170 to 0.421, with seasonal and ontogenetic variations. Individual or subgroup specialization was observed on dominant prey, but intraspecific diet variations indicated all four species to be opportunistic predators. There was substantial prey overlap for Saurida undosquamis with Otolithes ruber and Trichiurus lepturus, which increased ontogenetically and coincided with their peak spawning. Sharing of abundant prey resources together with temporal and ontogenetic resource partitioning at intra- and interspecific levels possibly lowered dietary competition, thereby facilitating the coexistence of these demersal predators. This study provides new information on feeding interactions from a tropical demersal ecosystem that can be applied for the ecosystem-based management of trawl fisheries.

Exploring biophysical links of catch rate from mid-water trawl fishery in the north-west coast of India, Eastern Arabian Sea: A remote sensing approach.

Fish frequently shift their distribution ranges as a result of changes in preferred environmental factors. Knowledge on distribution of fish in relation to their environmental optima is crucial for improving the understanding of fishing grounds and planning sustainable exploitation. This study investigated the monthly variability in environmental factors impacting the catch rate and the spatio-temporal distribution patterns of fish along northwest coast of India (NWCI) from 2017 to 2019. The time series images of sea surface temperature (SST), sea surface height anomaly (SSHa), chlorophyll-a concentration (CHL), and euphotic depth (Zeu) indicate close coupling between bio-physical variables in the region. Generalized Additive Model (GAM) applied to the catch rate of mid-water trawlers found that CHL and Zeu were the most influential variables for ribbonfish distribution, while CHL and SST influence squid distribution and SST and SSHa influence cuttlefish distribution. The total deviation explained 37.70 %, 10.70 %, and 22.28 % in the final model for simulating the spatio-temporal distribution of ribbonfish, squid, and cuttlefish, respectively. Environmental factors were significant in the final GAM model (p < 0.05). Spatio-temporal distribution patterns of fishery resources from mid-water trawlers showed that they were related to biophysical changes in the northwest coast of India. The high catch rate was observed in the northern latitudes during the post-monsoon (October), the major fishing season in the region. However, it shrank and shifted to southern latitudes during the winter (January). This study could be adapted to nearby countries in the Arabian Sea region for an effective and useful tool to monitor and manage the fishery resources. Furthermore, it could aid in decision-making for policymakers and resource managers to formulate strategies for holistic marine fishery management and sustainable resource exploitation.

Comparative transcriptome analysis of Indian domestic duck reveals candidate genes associated with egg production.

Egg production is an important economic trait and a key indicator of reproductive performance in ducks. Egg production is regulated by several factors including genes. However the genes involved in egg production in duck remain unclear. In this study, we compared the ovarian transcriptome of high egg laying (HEL) and low egg laying (LEL) ducks using RNA-Seq to identify the genes involved in egg production. The HEL ducks laid on average 433 eggs while the LEL ducks laid 221 eggs over 93 weeks. A total of 489 genes were found to be significantly differentially expressed out of which 310 and 179 genes were up and downregulated, respectively, in the HEL group. Thirty-eight differentially expressed genes (DEGs), including LHX9, GRIA1, DBH, SYCP2L, HSD17B2, PAR6, CAPRIN2, STC2, and RAB27B were found to be potentially related to egg production and folliculogenesis. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that DEGs were enriched for functions related to glutamate receptor activity, serine-type endopeptidase activity, immune function, progesterone mediated oocyte maturation and MAPK signaling. Protein-protein interaction network analysis (PPI) showed strong interaction between 32 DEGs in two distinct clusters. Together, these findings suggest a mix of genetic and immunological factors affect egg production, and highlights candidate genes and pathways, that provides an understanding of the molecular mechanisms regulating egg production in ducks and in birds more broadly.

Characterization of the complete mitochondrial genome of Barilius malabaricus and its phylogenetic implications.

Bariliine fishes are important components of the ornamental as well as subsistence fishery sectors in India. Many of the species in the genus Barilius are threatened by habitat loss and therefore need to be met with conservation initiatives. Effective conservation measures, however, require clarification of species identities and resolution of the validity of many species currently treated as synonymous or sub-species. The complete mitochondrial genome data provide better insight into phylogenetic information than the short fragment or single gene based analysis. Thus, we have sequenced the complete mitochondrial genome of Barilius malabaricus, one of the important fish species in the fresh water ornamental sector, for better understanding its phylogenetic status. The 16,519 bp mitochondrial genome consists of 37 genes which classifies as 22 tRNA, 13 protein coding and 2 ribosomal RNA genes and a control region. Overall, the mitochondrial genome bears the typical gene order and composition as in other fishes. Further, the COI, cytochrome b and 16S rRNA gene sequences revealed that, B. malabaricus is genetically closer to B. canarensis and B. bakeri compared to other Barilius species. Also, the Barilius species of west flowing rivers in Western Ghats were consistently recovered as a clade distinct from other species. We therefore suggest to retain the genus name Barilius for the species from the Western Ghats until a comprehensive analysis based on both morphological and molecular markers reveals the relationship between species now variously placed in the genera Barilius and Opsarius in greater detail.

Resurrection and Re-description of Pampus candidus (Cuvier), Silver Pomfret from the Northern Indian Ocean.

Pomfrets (Genus Pampus) are commercially important fish in the Indo-Pacific region. The systematics of this genus is complicated because of morphological similarities between species. The silver pomfret from Indian waters has long been considered to be Pampus argenteus. Morphological and molecular examination of specimens from the Arabian Sea and Bay of Bengal regions suggested the silver pomfret from the region represents two species that are distinct both from each other and from P. argenteus from the South China Sea. Based on detailed morphological, meristic and molecular examinations, the most common species from the Indian Ocean was found to correspond with the descriptions of Stromateus candidus (Cuvier), which is resurrected from the synonymy of P. argenteus and redescribed here as Pampus candidus (new combination). The second species, which has restricted distribution in Indian waters needs further studies to arrive at taxonomic conclusions and is hence not described in the current study. Lectotypes are also designated for Pampus candidus.

Molecular markers reveal only two mud crab species of genus Scylla (Brachyura: Portunidae) in Indian coastal waters.

The taxonomic ambiguity of the Indian mud crab (genus Scylla de Hann 1833) is still a cause of concern as several papers have been published with misleading identification. This is the first attempt to resolve the taxonomic uncertainty of the mud crab commonly available in Indian coastal waters using molecular genetic markers (ITS-1 and sequencing of COI gene) combined with traditional morphometry. Additionally, we developed a PCR method by which Indian mud crab species can be identified rapidly and effectively. The results clearly indicate that the green morph of the Indian mud crab is Scylla serrata and the brown morph is S. olivacea. The S. serrata commonly mentioned in the literature from India is S. olivacea; the S. tranquebarica noted by many Indian researchers should belong to S. serrata. Caution should be taken when interpreting or implementing the biological, molecular, and aquaculture data in the literature.

Population genetic structure of Penaeus monodon, in relation to monsoon current patterns in Southwest, East and Andaman coastal waters of India.

The black tiger shrimp (Penaeus monodon), a commercially important penaeid species, is widely distributed across the Indo-Pacific region. Genetic diversity in P. monodon collected from eight geographical regions in Southwest, East and Andaman coastal waters of India (N=418) was investigated using 10 polymorphic microsatellite loci. Average observed heterozygosity at sampled loci were high, ranging from 0.643 (Coromandel Coast) to 0.753 (South Andaman). Pairwise F(ST) (ranged from 0.005 to 0.078) and R(ST) (ranged from 0.005 to 0.171) estimates revealed surprisingly strong and statistically significant genetic structure among tiger shrimp populations. A synthetic map generated by multidimensional scaling shows an apparent cline in allele frequencies paralleling the roughly circular flow of surface currents in the Bay of Bengal. Significant heterozygote deficiencies were noted in most population samples at most loci. Andaman Island sites showed the highest diversity. Recognition of high genetic diversity and distinct population structuring of P. monodon in Indian seas has important implications for future domestication of this species in India, for two reasons: identification of the best wild founding stocks for aquaculture and, subsequently, the potential impacts of release of domesticates to the wild, either accidentally or deliberately (i.e. for stock enhancement).

Allozyme variation in a threatened freshwater fish, spotted murrel (Channa punctatus) in a South Indian river system.

Samples of the spotted murrel (Channa punctatus) were collected from three rivers of Tamil Nadu and Kerala. The allozyme variation of C. punctatus was investigated by polyacrylamide gel electrophoresis. Eighteen enzymes were detected, but only 10 (EST, PGM, G3PDH, G6PDH, SOD, GPI, ODH, GDH, XDH, and CK) showed consistent phenotypic variations. Allele frequencies were estimated at the 18 polymorphic loci representing 10 enzymes. Two rare alleles, EST-4*C and G6PDH-2*C, were noted in the Tamirabarani and Kallada populations but were absent in the Siruvani population. The allele frequencies of the Tamirabarani and Kallada populations were similar, except for a few loci. Among the three populations, the maximum genetic distance (0.026) and FST (0.203) were found between the geographically distant Siruvani and Kallada populations. Overall the study showed that among the three populations, the Tamirabarani and Kallada have similar genetic structures.