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India is the habitat of many freshwater fish species that make a significant contribution to endemism. However, the native species population is declining at a very fast rate due to pollution, habitat loss or degradation, new species introduction, hydrologic alterations, and overfishing. The minor carp, Labeo gonius , is one of the important fish species in the Indian river systems and holds enormous potential in culture fisheries. Therefore, the precise status of population structure is a prerequisite for the management of the species. In the present study, we assessed the potential of mtDNA ATPase 6/8 and D-loop regions as markers to determine the genetic diversity and phylogeography of L. gonius from Indian rivers. We have selected five major Indian rivers for investigation which could represent geographically distant populations of the studied fish. A total of 210 ATPase 6/8 sequences (842 bp) and 203 D-loop region sequences (683 bp) of L. gonius from the five major Indian rivers were submitted to NCBI. Results revealed that ATPase 6/8 has 17 haplotypes and 70 polymorphic sites with an overall haplotype diversity of 0.560 ± 0.036 and nucleotide diversity of 0.00347 ± 0.00. Furthermore, D-loop analysis revealed 58 haplotypes, 67 polymorphic sites, 0.954 ± 0.006 overall haplotype diversity, and 0.01914 ± 0.00 nucleotide diversity. The hierarchical AMOVA analysis indicated that a high proportion of the genetic variation (76.46% and 70.22% for the D-loop and ATPase 6/8 regions, respectively) was attributed to among-population variation under gene pool-1 (considering all the stocks from Ganga, Brahmaputra, Teesta, Narmada, and Mahanadi as a single pool). Furthermore, in gene pool-2, samples were divided into two groups: group 1 (Himalayan rivers)—Ganga, Brahmaputra, and Teesta; and group 2 (peninsular rivers)—Narmada and Mahanadi. Genetic variations in the D-loop and ATPase 6/8 regions were found among populations within groups at 70.65% and 53.48%, respectively. Haplotype network analysis revealed that there were significant differences in distributions and frequencies. The observed unique haplotypes might be useful for differentiating the stocks. In brief, the present study suggested that the D-loop and ATPase 6/8 regions are potential markers and represent a significant contribution to the genetic characterization of the minor carp L. gonius from major Indian rivers. Moreover, the L. gonius population along the east coast especially in the Himalayan rivers (Ganga, Brahmaputra, and Teesta river basin) is found to be genetically more diverse. The results would provide a scientific basis for the assessment of fisheries resources and management of this important species.

The rapid degradation, overexploitation, and encroachment of floodplain wetlands have led to considerable decline in fish diversity and production from these invaluable aquatic resources threatening livelihood of the dependent fishers. The climate change evident in the fast few decades has further aggravated the problem of eutrophication causing water stress and sedimentation leading to rampant macrophyte proliferation affecting ecological and economic functioning of these ecosystems. Macrophyte control and management needs serious attention for sustaining ecosystem services provided by these resources. In this direction, pen culture of grass carp Ctenopharyngodon idella as a biocontrol for macrophytes along with Indian major carps was implemented in a co-management mode in Beledanga, a typical floodplain wetland, a gradually shrinking, macrophyte dominated floodplain wetland in lower Ganga basin. Indian major carps Labeo catla (6.28±0.23g), Labeo rohita (5.1±0.12g), Cirrhinus mrigala (3.5±0.08g) were stocked in the ratio 4:3:3 at the rate of 20 Nos.m −2 in pens (0.1ha each) in triplicate. Grass carp (7.1±0.42g) was stocked in pen at the rate of 20Nos.m −2 in duplicate. The fishes were fed with pelleted feed twice a day at the rate of 2–3% of body weight. The seed was overwintered in pens for a period of 90 days from November 2019 to January 2020. Average weight recorded at the end of culture period was 25.13±1.70g, 18.11±0.63g, 14.53±0.87g, and 39.20±1.90g in L. catla , L. rohita , C. mrigala , and C. idella , respectively. The survival of fish ranged from 70 to 81%. Growth performance and feed utilization efficiency of grass carp were significantly higher ( p <0.05) compared to other carp species. The pen culture was found to be economically viable with a benefit cost ratio of 1.53. The fishes produced were released back into the open wetland as an additional input for culture-based fisheries. The intervention along with niche-based enhanced stocking led to 24% increase in the fish production from the wetland with grass carp contributing 20–22% of the total catch with 32% increase in revenue generated by the sale of fish within a short span of 1 year. The study successfully demonstrated technological suitability and economic feasibility of pen culture in this wetland and role of grass carp as a potential biocontrol species for macrophyte management. Grass carp stocked in open wetland grew to 0.8 to 1kg within 6 months and 2–2.3kg within a year and could utilize 40–45% of the submerged and emergent macrophytes. Integration and optimization of grass carp will not only aid in habitat management of macrophyte-choked wetlands but will also boost their small-scale fisheries by converting standing macrophyte biomass into protein-rich fish biomass. The enhanced production will also cater to nutritional and livelihood security of the dependent fishers.