Introduction
Conservation of genetic diversity is critical for the continual survival of the fisheries industry and plays a pivotal role in the socio-economic development of our nation. Owing to the challenges associated with the ever-increasing demands for resources and the need to conserve fresh water bodies, the onus for ecological conservation now lies with local and regional biodiversity regulators and policy-makers. This demands a decisive shift from piecemeal steps to a comprehensive and practical multidisciplinary approach for conservation gambits (Adrian et al ., 2019). The fisheries segment provides employment to 14 million individuals in India, and a lack of species conservation could have serious ramifications on employment in the sector. Conservation plans to perk up the declining wild fish populations have been delayed by an unstable taxonomy.
Mahseer is a popular game and food fish of India. It provides unparalleled recreation to anglers from all over the world as a sport fish superior to the salmon. However, anthropogenic activities such as dam-building and over-fishing have adversely affected the Mahseerpopulation across the country. Once an abundant species, theMahseer population has been decreasing in natural waters and the different Mahseer species are now either categorized as “threatened” or “endangered”. Moreover, T tor  has been recently classified as a data deficient species (Rayamajhi et al. 2018); there is, therefore, an urgent need to validate the conspecificity of the species from the river Mahananda (northern Bengal) with records of T. tor  from other parts of India. However, the presence of only a few haplotypes of Mahseer species (Tor tor ), indiscernible morphological features, and paucity of research on accurate classification (Jayaram, 1999) have led to confusion in accurate taxonomic classification of this fish.
The advent of molecular biology and DNA markers has helped the progress of pisciculture by enabling the study of genetic variability, breeding patterns, institution of parentage identifying strain and species and high-resolution genetic linkage maps.
As genetic markers are important tools for the study of fish species and population characterization, the development of molecular methods has permitted genomic analysis and made the analysis of existing variations possible. Similarly, gene frequencies of mitochondrial genes are also indicative of phylogeny and close associations. Cytochrome oxidase I (COI) , a mitochondrial gene, is a popular target for species identification and barcoding; it has been reported that approximately 98% of reported marine fish species can be identified by COIbarcoding. This approach has been employed to catalogue and record fish in many geographic regions (Asgharian et al. , 2011; Aquilinoet al. , 2011 and Cawthorn et al ., 2011). However, there is a dearth of genetic studies conducted on Mahseer species in India. Older studies have mainly explored taxonomy based only on morphological characteristics and therefore, there is a need to perform molecular studies [such as those by Nguyen et al. (2008)] to aid in the conservation of this endangered species. There is paucity of studies on Mahseer genetic structure reported across the Indian waters (Sati et al ., 2013) and in Rajasthan state. An examination of the mitochondrial genetic information of nine Mahseer species belonging to the Tor, Neolissochilus, and Naziritor genera was performed by Khare et al. in 2014. Their study highlighted the need for integrating molecular and morphological data to accomplish taxonomic revision of the Tor and Naziritor genera.
The mitochondrial genome has been effectively used for phylogenetic analysis and to solve taxonomic ambiguity in Mahseer species (Pavan-Kumar et al ., 2016). Therefore, we undertook this study to perform phylogenetic analysis on Mahseer species indigenous to southern Rajasthan using mitochondrial DNA sequences.
In the present study, we have analysed haplotype diversity ofMahseer (Tor sp.) from southern Rajasthan using theCOI gene frequencies. Accurate taxonomic identification using molecular markers is an indispensable step towards the protection of this endangered fish.