Population Genetic Structure of Silver pomfret (Pampus argenteus) along Indian coast

Silver pomfret (Pampus argenteus), is a commercially important pelagic fish in Middle East, Indian and other south East Asian countries, and more over a potential fin fish species for mariculture. The overfishing and overexploitation of this valuable species can reduce their chance of successful reproduction and this may result in changes in species genetic variability and population structure. Despite its importance as a valuable marine resource, little is known about its genetic diversity and population structure of this species in Indian waters. Therefore, there was an urgent need to study the baseline information on genetic stock structuring of this species across its range of natural distribution along Indian waters. Identifying the population structure of commercially important native resources would be the base for genetic upgradation, fisheries management and conservation programs and is significant for every nation. The present study entitled "Population Genetic Structure of Silver pomfret (Pampus argenteus) along Indian coast" aims to determine the fine-scale population structure in P. argenteus collected from five geographical locations along Indian coast using mitochondrial ATPase 6/8 gene and polymorphic microsatellite markers. This study investigates the level of genetic diversity and population genetic structure of the species along the Indian coast and a possibility of population size contraction, since there are indications about the catch decline in the past two decades

Development and validation of microsatellite markers in a protandrous fish species Eleutheronema tetradactylum (Shaw, 1804) through cross-species amplification

The four fingered threadfin Eleutheronema tetradactylum (Shaw, 1804) is a prioritised species for mariculture in India. Their demand in the domestic markets is rapidly growing. Genetic stock structure analysis of fish populations is an important aspect from fisheries management perspective. The present study was conducted to develop microsatellite primers through cross-priming to elucidate the genetic structure of E. tetradactylum. A total of 13 polymorphic microsatellite markers were developed from the resource species, Pacific salmon Polydactylus sexfilis. The observed mean and the effective number of alleles were found to be 11.962 and 6.927 respectively. The mean of observed heterozygosity (Ho) and expected heterozygosity (He) values obtained were 0.784 and 0.798 respectively. These new microsatellite markers can be used as effective tools for studying genetic disparity as well as for elucidating evolutionary relationships among E. tetradactylum populations

Molecular identification of Bigeyes (Perciformes, Priacanthidae) from Indian waters

Thirty-five individuals of six priacanthid fish species were sampled from different localities along the coast of India covering the Arabian Sea and Bay of Bengal. The partial sequence of 16S rRNA and cytochrome oxidase subunit I (COI) genes were analyzed for species identification and phylogenetic relationship among the Indian priacanthids (Priacanthus hamrur, P. prolixus, P. blochii, P. sagittarius, Cookeolus japonicus, and Pristigenys refulgens). The intraspecies genetic distance ranged from 0.000 to 0.002, while distances varied from 0.008 to 0.157 interspecies based on 16S sequences. Using COI data analysis, the intraspecies genetic distance ranged from 0.000 to 0.005, while interspecies distances varied from 0.009 to 0.108. Several sequences labeled Priacanthus hamrur in GenBank are shown to be P. prolixus. We also observed cryptic speciation in Heteropriacanthus cruentatus. Partial sequences of 16S rRNA and COI genes provided phylogenetic information to distinguish thirteen species of priacanthids, indicating the usefulness of molecular markers in species identification

Mitochondrial ATPase 6/8 genes to infer the population genetic structure of silver pomfret fish Pampus argenteus along the Indian waters

Silver pomfret, Pampus argenteus is an economically important seafood species. The fishery resource of pomfret in Indian waters shows a dwindling catch since the last few years and the pomfrets caught were mostly undersized which calls for immediate attempts for management of resources. An accurate definition of population structure is important for management of this species. The genetic stock structure of P. argenteus distributed along Indian coast was identified using analysis of 842 bp of complete ATPase 6/8 genes of mitochondrial DNA. Altogether, 83 silver pomfret (P. argenteus) collected from 4 locations along Indian coast (Gujarat, Kerala, Tamil Nadu and West Bengal) were sequenced. Twenty four haplotypes were identified among 83 individuals with haplotype diversity (0.87) and nucleotide diversity (0.0025). The significant pair-wise FST and AMOVA values, between samples from West Bengal (east coast) and other locations along the west coast (Gujarat and Kerala) indicated the occurrence of distinct population structure in silver pomfret along the coast

Mitochondrial signatures for identification of grouper species from Indian waters

Groupers are important commercial fish in many parts of the world. Accurate identification is critical for effective conservation assessment and fisheries management. Genetic barcodes provide a simple and reproducible method for the identification of species even in the absence of taxonomic expertise. The generation of reference barcodes from properly identified specimens is an important first step in this direction. Here, 36 species belonging to the subfamily Epinephelinae (Family: Serranidae) were collected from landings on the west coast of India and Port Blair, Andaman, and partial nucleotide sequence data of the mitochondrial cytochrome C oxidase subunit I (COI) gene was generated. Barcodes for 13 species were developed from Indian waters for the first time. Analysis using the COI gene produced phylogenetic trees in concurrence with other multi-gene studies. Epinephelus fasciatus and E. areolatus were found to be a species complex, as hypothesized in other studies. The DNA barcodes developed in the study can be used for identifying species within Epinehelinae, where taxonomic ambiguity still exists

Identification and characterisation of microsatellite markers in narrow barred Spanish mackerel Scomberomorous commerson (Lacepede, 1800)

Narrow barred Spanish mackerel, Scomberomorus commerson (Lacepede 1800) is one of the commercially important fish in Indian waters. For sustainable management of the species, it is necessary to understand the genetic stock structure of the species. Accurate delineation of genetic stock structure can be achieved using nuclear microsatellite markers. A study was carried out to identify and validate polymorphic microsatellite markers in S. commerson using information available from closely related fish species. The study could identify 10 polymorphic microsatellite loci which can be effectively utilised for identifying genetic stock structure of the species. Validation of the identified loci was also done by testing the loci in natural populations of the species. The findings of the present study will be useful in devising stock-specific management measures for conservation and sustainable utilisation of this commercially important fish species in Indian waters

DNA barcoding and taxonomic notes on the genus Macolor (Perciformes: Lutjanidae) from Indian waters

The DNA “barcode”, the partial sequence of the mitochondrial gene cytochrome C oxidase subunit I (COI), was assessed for species identification within the genus Macolor. The Midnight Snapper, Macolor macularis Fowler 1931, is compared with its only congener, the Black and White Snapper, Macolor niger (Forsskål 1775), both collected from the south-west coast of India. The examination of fresh specimens of the two species showed diagnostic anatomical and coloration differences and the DNA barcoding showed a genetic divergence of 3.51% between the species. We provide a description and illustrations of DNA-barcoded specimens, assess the reliability of some key marking characters for the two species, and document the DNA barcodes for Indian specimen

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 identification of three deepsea fish species of the genus Chelidoperca (Perciformes: Serranidae) from Indian waters

The deepwater basslets of the genus Chelidoperca has eight nominal species and these are relatively small fishes caught in trawl nets operated at depths greater than 100 m. Mitochondrial cytochrome c oxidase subunit 1 (COI) and 16S rRNA gene sequence variation among three species under the genus Chelidoperca viz., C. investigatoris, C. occipitalis and C. maculicauda from Indian waters and their phylogenetic relationship with other representatives from same genus was studied. Fifteen individuals of Chelidoperca were sampled from different localities in the east and west coasts of India and further, four COI sequences from GenBank were used to reconstruct the phylogenetic relationship in the genus Chelidoperca. Based on COI sequence data analysis, the intraspecies genetic distance ranged from 0.000 to 0.005 while interspecies distance varied from 0.073 to 0.194. With respect to 16S rRNA sequences, the intraspecies genetic distance ranged from 0.000 to 0.002, while interspecies genetic distance varied from 0.062 to 0.118. The mean genetic difference observed between C. investigatoris and the other species used in this study was 11.53%. Results of the study revealed that the genus Chelidoperca is monophyletic