Microsatellite Genotyping Corroborated Loss of Genetic Diversity in Clarias batrachus as a Result of Lack of Regulatory Reforms in Aquaculture.

In India, over the past 50 years, aquaculture practices of species such as those used for Clarias batrachus were developed without adequate regulatory oversight. In these situations, it is important to consider the influence that genetic factors can have on such vulnerable aquaculture species. Population genetic structure can be evaluated through the use of neutral molecular markers, and this can aid in predicting the risk of the demise of populations and for framing management strategies to conserve remaining populations. The study presented here reports on the genetic status of C. batrachus populations through the analysis of data collected using 22 microsatellite markers from seven natural and one hatchery population. The mean values for observed heterozygosity across loci within populations ranged from 0.242 to 0.485. Measures of genetic differentiation were low overall, with mean values for FST of 0.270, FIS of 0.113 and FIT of 0.353. An AMOVA analysis revealed that percentages of variation among and within populations were 27.16 and 6.86, respectively, and Bayesian clustering analyses showed a population subdivision consisting of five clusters with admixture of haplotypes from other populations leading to genetic bottleneck. We also examined how hatchery management factors leading to excessive exchanges of fish between river systems through could impact the structure of the C. batrachus populations. Overall, this study shows how the systematic use of molecular markers can facilitate the development of management policies for these populations and for the development of a comprehensive set of rules for hatcheries and aquaculture practices, including avoidance of excessive homozygosity by avoiding repeated use of feral broodstock and their interrogation.

Refutation of media reports on introduction of the red bellied piranha and potential impacts on aquatic biodiversity in India.

The presence of a new, potentially deadly exotic fish resembling the Red Bellied Piranha, Pygocentrus nattereri was reported in India by print media from various aquatic resources. These reports raised dramatic concerns over public health issues and threats to the aquatic biodiversity of India. Considering the potential severity of the issue and concerns raised by the media, we undertook a study to evaluate the reliability of identification reports of the suspected fish, any relationships to other species of piranha and to address any possible threats to the aquatic biodiversity of India. For this study, samples were collected from most of the major river systems and lakes in India and evaluated for taxonomic identifications of the suspect fish and phylogenetic relationships to other fish species. Our results clearly show that the suspect fish is in fact Piaractus brachypomus, a species commonly referred as "Pacu", and not the red bellied piranha, P. nattereri. Comparisons of both fish do show striking similarities that may account for the misreporting in the media. Furthermore, P. brachypomusas is still an exotic fish, and as such may still have potentially harmful impacts on the native aquatic fauna of India. Quick attention to this issue and the imposition of control measures, including market bans, should be considered to prevent further loss of biodiversity.

Evidence for a species complex in Indialona ganapati (Chydoridae).

Indialona ganapati (Petkovski 1966 ), is one of the three known cladoceran endemic species from India. It is also the only one of these species that is monotypic and endemic to central India. In this study we report on habitat shifts for this species as well as presence of parthenogenetic and ephippial females throughout the year, phenomena that are uncommon in most species of the family Chydoridae. These factors prompted us to undertake a study evaluating the taxonomic status of this species in collections from India using morphological and molecular methods. This included recognition of some degree of morphometric diversity based on sexual differentiation and reproductive patterns which were not correlated with speciation events. Analysis of our data does, however, suggest that I. ganapati can be split into two recent clades. Also, phylogenetic as well as haplotype network analysis of our data suggests the presence of a sibling species complex of I. ganapati in the river Godavari. This suggests that reconsideration of taxonomic status of this species may be appropriate. In addition, this study underscores the potential utility of using COI gene based 'barcode' DNA sequences for recognizing the existence of cryptic species among the cladocera.

Multiple tests on saffron find new adulterant materials and reveal that Ist grade saffron is rare in the market.

Among spices, Saffron is among the most extensively interrogated for purity and authenticity. Numerous methods have been recommended for authentication of Saffron samples and for detection of adulterants for codex compliance. However, none of these methods can fulfill both of these important quality criteria. This study describes a three step approach to achieving this goal by including the established ISO3632 method and two additional methods based on microscopic examination and DNA barcoding. We provide results showing the utility of these methods both independently and in combination for quality evaluation of 36 commercial saffron samples. Our results show that use of the ISO3632 approach alone can reveal the color and aroma but not the genetic origin of the material or distinguish between synthetic components versus natural ingredients. Also, the microscopic observation method can give a preliminary indication of saffron authenticity, but used alone it is unable to quantify purity. Finally, a relatively new method based on the use of DNA barcodes can authenticate the biological origin of the saffron, but here results may be misleading if auto-adulterating materials are present. Overall, our study reveals that through the combined use of all three methods, saffron authentication can substantially improved.

Genetic structure of populations and conservation issues relating to an endangered catfish, Clarias batrachus, in India.

The Asian catfish, Clarias batrachus (Linnaeus, 1758), is a highly valued species endemic to India that is currently in drastic decline in most of its natural habitat. The present study was undertaken to document the genetic structure of populations of this species using mitochondrial DNA markers, specifically from the cytochrome B and D-loop regions. Specimens from eight wild populations were collected and analyzed from different regions in India. The genetic variation within and among populations was evaluated using a range of descriptive statistics. The analysis described here provides a broad and consistent view of population structure and demographic history of populations of C. batrachus. Although there was some genetic structuring consistent with regional differences, all eight populations examined here showed relatively low levels of genetic variation in terms of both haplotype and nucleotide diversities in the different analyses used. However, a number of private haplotypes were discovered, and this may provide valuable information for future selective breeding program and conservation management. The results may aid in the design and implementation of strategies for the future management of this endangered catfish C. batrachus in India.

High rates of substitution of the native catfish Clarias batrachus by Clarias gariepinus in India.

The clariid catfish, Clarias batrachus commonly known as Magur, has declined drastically from natural habitats in India during the last decade. This fish is highly preferred fish by Indian consumers and has high market demand. As a result traders often substitute C. batrachus with a morphologically similar but supposedly banned exotic catfish, C. gariepinus, in India. This study uses rigorous morphological comparisons confirmed by DNA barcode analysis to examine the level of substitution of C. batracus by C. gariepinus in India. Our results indicate that up to 99% (in many cases) of the market samples sold as Magur or C. batrachus were in fact C. gariepinus.

DNA barcoding using skin exuviates can improve identification and biodiversity studies of snakes.

Snakes represent a taxonomically underdeveloped group of animals in India with a lack of experts and incomplete taxonomic descriptions being the main deterrents to advances in this area. Molecular taxonomic approaches using DNA barcoding could aid in snake identification as well as studies of biodiversity. Here a non-invasive sampling method using DNA barcoding is tested using skin exuviates. Taxonomically authenticated samples were collected and tested for validation and comparisons to unknown snake exuviate samples. This approach was also used to construct the first comprehensive study targeting the snake species from Maharashtra state in India. A total of 92 skin exuviate samples were collected and tested for this study. Of these, 81 samples were successfully DNA barcoded and compared with unknown samples for assignment of taxonomic identity. Good quality DNA was obtained irrespective of age and quality of the exuviate material, and all unknown samples were successfully identified. A total of 23 species of snakes were identified, six of which were in the list of Endangered species (Red Data Book). Intra- and inter-specific distance values were also calculated, and these were sufficient to allow discrimination among species and between species without ambiguity in most cases. Two samples were suspected to represent cryptic species based on deep K2P divergence values (>3%), and one sample could be identified to the genus level only. Eleven samples failed to amplify COI sequences, suggesting the need for alternative PCR primer pairs. This study clearly documents how snake skin exuviates can be used for DNA barcoding, estimates of diversity and population genetic structuring in a noninvasive manner.

Genetic fragmentation in India's third longest river system, the Narmada.

India's third longest river, the Narmada, is studied here for the potential effects on native fish populations of river fragmentation due to various barriers including dams and a waterfall. The species we studied include a cyprinid fish, Catla catla, and a mastacembelid, Mastacembelus armatus, both of which are found in the Narmada. Our goal was to use DNA sequence information from the D-loop region of the mitochondrial DNA to explore how this fragmentation could impact the genetic structure of these fish populations. Our results clearly show that these barriers can contribute to the fragmentation of the genetic structure of these fish communities, Furthermore, these barriers enhance the effects of natural isolation by distance and the asymmetry of dispersal flows. This may be a slow process, but it can create significant isolation and result in genetic disparity. In particular, populations furthest upstream having low migration rates could be even more subject to genetic impoverishment. This study serves as a first report of its kind for a river system on the Indian subcontinent. The results of this study also emphasize the need for appropriate attention towards the creation of fish passages across the dams and weirs that could help in maintaining biodiversity.