Molecular phylogeny of elasmobranchs inferred from mitochondrial and nuclear markers

The elasmobranchs (sharks, rays and skates) being the extant survivors of one of the earliest offshoots of the vertebrate evolutionary tree are good model organisms to study the primitive vertebrate conditions. They play a significant role in maintaining the ecological balance and have high economic value. Due to over-exploitation and illegal fishing worldwide, the elasmobranch stocks are being decimated at an alarming rate. Appropriate management measures are necessary for restoring depleted elasmobranch stocks. One approach for restoring stocks is implementation of conservation measures and these measures can be formulated effectively by knowing the evolutionary relationship among the elasmobranchs. In this study, a total of 30 species were chosen for molecular phylogeny studies using mitochondrial cytochrome c oxidase subunit I, 12S ribosomal RNA gene and nuclear Internal Transcribed Spacer 2. Among different genes, the combined dataset of COI and 12S rRNA resulted in a well resolved tree topology with significant bootstrap/posterior probabilities values. The results supported the reciprocal monophyly of sharks and batoids. Within Galeomorphii, Heterodontiformes (bullhead sharks) formed as a sister group to Lamniformes (mackerel sharks): Orectolobiformes (carpet sharks) and to Carcharhiniformes (ground sharks). Within batoids, the Myliobatiformes formed a monophyly group while Pristiformes (sawfishes) and Rhinobatiformes (guitar fishes) formed a sister group to all other batoids.     

Role of 677C→T polymorphism a single substitution in methylenetetrahydrofolate reductase (MTHFR) gene in North Indian infertile men

Failure or severe difficulty in conceiving a child is surprisingly common, worldwide problem. Half of these cases are due to male factors with defects in sperm (1 in 15 men) being the single most common cause. Also about 60–75 % of male infertility cases are idiopathic, since the molecular mechanisms underlying the defects remain unknown. DNA methylation is crucial for spermatogenesis and high methylenetetrahydrofolate reductase (MTHFR) activity in adult testis than other organs in mouse, signifies its critical role in spermatogenesis. According to recent findings there is a correlation of epigenetic regulation of several imprinted genes with disturbed spermatogenesis and fertility. Consequently any change in the MTHFR gene sequence can modify the spermatogenesis including transmission of infertility to the carriers. The aim of the study is to analyze the distribution of the single nucleotide polymorphism C677T in the MTHFR gene in 637 North Indian infertile patients and 364 fertile North Indian men as controls by using PCR–RFLP technique and Chi Square test for statistical analysis. The average MTHFR 677CC, 677CT, 677TT genotype frequencies of total infertile men were 70.17, 24.17, 5.65 % in infertile men and 75.27, 21.7, 2.74 % in controls, respectively. The average frequency of the MTHFR 677T allele was 17.73 % in infertile men as compared to 13.59 % in controls. The statistical difference was significant. Disease risk was found 2.27-folds increased in patients who were carrying T allele. We found an association of C677T polymorphism with male infertility and that it may be a genetic risk factor for male infertility in North Indian population.     

Biosorption of Cd(II) and Pb(II) onto brown seaweed, Lobophora variegata (Lamouroux): kinetic and equilibrium studies

The present work deals with the biosorption performance of raw and chemically modified biomass of the brown seaweed Lobophora variegata for removal of Cd(II) and Pb(II) from aqueous solution. The biosorption capacity was significantly altered by pH of the solution delineating that the higher the pH, the higher the Cd(II) and Pb(II) removal. Kinetic and isotherm experiments were carried out at the optimal pH 5.0. The metal removal rates were conspicuously rapid wherein 90% of the total sorption occurred within 90 min. Biomass treated with CaCl₂ demonstrated the highest potential for the sorption of the metal ions with the maximum uptake capacities i.e. 1.71 and 1.79 mmol g⁻¹ for Cd(II) and Pb(II), respectively. Kinetic data were satisfactorily manifested by a pseudo-second order chemical sorption process. The process mechanism consisting of both surface adsorption and pore diffusion was found to be complex. The sorption data have been analyzed and fitted to sorption isotherm of the Freundlich, Langmuir, and Redlich–Peterson models. The regression coefficient for both Langmuir and Redlich–Peterson isotherms were higher than those secured for Freundlich isotherm implying that the biosorption system is possibly monolayer coverage of the L. variegata surface by the cadmium and lead ions. FT-IR studies revealed that Cd(II) and Pb(II) binding to L. variegata occurred primarily through biomass carboxyl groups accompanied by momentous interactions of the biomass amino and amide groups. In this study, we have observed that L. variegata had maximum biosorption capacity for Cd(II) and Pb(II) reported so far for any marine algae. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The identity and distribution of striped bagrid catfish,Mystus tengara (Hamilton 1822) revealed through integrative taxonomy

Molecular Biology Reports - The taxonomic status and geographical distribution of M. tengara are vague. No genetic diversity and phylogenetic study have been done till now to resolve its identity...     

On the biosorption,by brown seaweed, <Emphasis Type=Italic>Lobophora variegata</Emphasis>, of Ni(II) from aqueous solutions: equilibrium and thermodynamic studies

The biosorption equilibrium isotherms of Ni(II) onto marine brown algae Lobophora variegata, which was chemically-modified by CaCl₂ were studied and modeled. To predict the biosorption isotherms and to determine the characteristic parameters for process design, twenty-three one-, two-, three-, four- and five-parameter isotherm models were applied to experimental data. The interaction among biosorbed molecules is attractive and biosorption is carried out on energetically different sites and is an endothermic process. The five-parameter Fritz–Schluender model gives the most accurate fit with high regression coefficient, R ² (0.9911–0.9975) and F-ratio (118.03–179.96), and low standard error, SE (0.0902–0.0.1556) and the residual or sum of square error, SSE (0.0012–0.1789) values to all experimental data in comparison to other models. The biosorption isotherm models fitted the experimental data in the order: Fritz–Schluender (five-parameter) > Freundlich (two-parameter) > Langmuir (two-parameter) > Khan (three-parameter) > Fritz–Schluender (four-parameter). The thermodynamic parameters such as ΔG ⁰, ΔH ⁰ and ΔS ⁰ have been determined, which indicates the sorption of Ni(II) onto L. variegata was spontaneous and endothermic in nature.     

Characterization of genetic diversity and population structure in wheat using array based SNP markers

Genetic diversity is crucial for successful adaptation and sustained improvement in crops. India is bestowed with diverse agro-climatic conditions which makes it rich in wheat germplasm adapted to various niches. Germplasm repository consists of local landraces, trait specific genetic stocks including introgressions from wild relatives, exotic collections, released varieties, and improved germplasm. Characterization of genetic diversity is done using morpho-physiological characters as well as by analyzing variations at DNA level. However, there are not many reports on array based high throughput SNP markers having characteristics of genome wide coverage employed in Indian spring wheat germplasm. Amongst wheat SNP arrays, 35K Axiom Wheat Breeder’s Array has the highest SNP polymorphism efficiency suitable for genetic mapping and genetic diversity characterization. Therefore, genotyping was done using 35K in 483 wheat genotypes resulting in 14,650 quality filtered SNPs, that were distributed across the B (~?50%), A (~?39%), and D (~?10%) genomes. The total genetic distance coverage was 4477.85 cM with 3.27 SNP/cM and 0.49 cM/SNP as average marker density and average inter-marker distance, respectively. The PIC ranged from 0.09 to 0.38 with an average of 0.29 across genomes. Population structure and Principal Coordinate Analysis resulted in two subpopulations (SP1 and SP2). The analysis of molecular variance revealed the genetic variation of 2% among and 98% within subpopulations indicating high gene flow between SP1 and SP2. The subpopulation SP2 showed high level of genetic diversity based on genetic diversity indices viz. Shannon’s information index (I)?=?0.648, expected heterozygosity (He)?=?0.456 and unbiased expected heterozygosity (uHe)?=?0.456. To the best of our knowledge, this study is the first to include the largest set of Indian wheat genotypes studied exclusively for genetic diversity. These findings may serve as a potential source for the identification of uncharacterized QTL/gene using genome wide association studies and marker assisted selection in wheat breeding programs.

     

Stock structure analysis of ‘Bombay duck’ (Harpadon nehereus Hamilton, 1822) along the Indian coast using truss network morphometrics

Harpadon nehereus, commonly known as ‘Bombay duck’, is a fish with a discontinuous distribution along the Indian peninsula. The fisheries are dominant on the north‐east and north‐west coast but are absent in commercial landings below 15° north latitude. Heretofore stock assessment studies had not considered the various spawning stock components that replenish this fishery, therefore the present study. Fish samples were collected from four locations: two each from the northeast and the northwest coasts. Twenty‐four morphometric variables were measured using a box‐truss network method. Factor analysis of these variables differentiated the east and the west coast fish populations. Multiple comparisons on the factor scores indicated two independent stocks on the east coast, whereas the fishery on the west coast is replenished by a single stock. The important morphometric traits that accounted for most of the stock variations were related to swimming adaptations of the fish. Future stock assessments can consider the population on the west coast as a single stock when formulating management plans. To harvest the resource in a sustainable manner, the maritime states on the west coast should adopt collaborative efforts towards managing this fishery.     

New Distributional Record for the Two Gobies (Gobiidae) from the North-Eastern Arabian Sea,Indian Ocean

Journal of Ichthyology - Gobiopsis canalis, checkered goby is one of the rare species of the genus Gobiopsis, with information available from few specimens only. In the present study, this species...     

Length‐weight relationships of five needlefish species from Kerala waters,south‐west coast of India

Length‐weight relationships (LWRs) were estimated for five needlefish species such as Ablennes hians (Valenciennes, 1846), Tylosurus crocodilus (Péron & Lesueur, 1821), Tylosurus acus melanotus (Bleeker, 1850), Strongylura leiura (Bleeker, 1850), and Strongylura strongylura (van Hasselt, 1823). Specimens were collected on weekly basis from Cochin Fisheries Harbour (Lat. 09056′327″N, Long. 76015′764″E), Munambam Fisheries Harbour (Lat. 10010′965″N, Long. 76010′258″E), Kalamukku (Lat. 09059′924″N, Long. 76014′564″E) and Chellanam (Lat. 09047′950″N, Long. 76016′551″E), between October 2015 to August 2017. Fish were captured by traditional long liner (hook no. IX‐XIV) and ring seiner (mesh size 8–24 mm). The estimated allometric co‐efficient b values ranged from 3.063 (Tylosurus acus melanotus) to 3.962 (Strongylura leiura) and r² values ranged from 0.850 (Tylosurus acus melanotus) to 0.992 (Tylosurus crocodilus). All the LWRs were highly significant, with p < .001. In addition, the study provides the first estimate of LWR for Tylosurus acus melanotus and new estimate for other four species of needlefish.     

Reproductive strategy of milk shark, <Emphasis Type="Italic">Rhizoprionodon acutus</Emphasis> (Ruppell 1837), along north-eastern Arabian Sea

The reproductive characteristic of Rhizoprionodon acutus were investigated using 684 specimens collected along Gujarat coast (India) of the north-eastern Arabian Sea. The sex ratio between male and female (1:1.13) was not found to be significantly different. Male and female sharks were found to mature at total lengths of 61.5 cm and 61.3 cm, respectively. Large and ripe follicles were observed throughout the year, which indicates that the breeding season extends all through the year. However, a significant increase in maximum follicle diameter was observed during February and March in the first quarter and during October and November in the last quarter of the year, which indicates that a portion of the population shows temporal preferences for breeding. This is also corroborated by the increase in the number of mature females with visible eggs in their ovary. Increase in the number of ready to spawn pregnant females was observed during March to May, followed by an increase in the number of postpartum females during May to June. The larger mean size of embryos was also recorded during May and, therefore, it can be presumed that a major parturition event happens during May. The uterine fecundity was found to be significantly influenced by maternal body size and varied from three to seven embryos per litter. Unlike male sharks, the female sharks showed significant variation in the monthly hepato-somatic index (HSI) which was significantly higher in January, after which it showed a gradual decreasing trend probably due to maternal nutrient investment during gestation.