Genetic population structure of a highly migratory Hilsa Shad, Tenualosa ilisha, in three river systems, inferred from four mitochondrial genes analysis

This is the first study to clearly demonstrate genetic divergence in the highly migratory Hilsa shad, Tenualosa ilisha and the presence of population structure, as well as speculated migratory routes among the natural hilsa populations of Hoogli, Brahmaputra and Padma (in India) river systems, compared with that of marine samples from Kakdwip and Digha, collected during 2013-16. Sequence data of four mitochondrial regions, Cytochrome b (CytB), ATPase6&8 (ATPase), 12s and 16s rRNA (rRNA) were used for the study. It was found that ATPase6&8 and rRNA were under selection pressure and out of 45 population pairs analyzed, highest significant pairs (16) were observed with ATPase, followed equally (12) by rRNA and CytB datasets. Comparison of these samples with those collected in 1999-2000 revealed temporal stability of sampled populations, with low genetic differentiation between temporal samples from same locality, except for Brahmaputra samples. Among the samples collected (2013-16), between samples from Brahmaputra and Padma, several shared haplotypes indicated genetic homogeneity and significant level of migration was also observed. The F-ST values showed that samples collected from both moonsoon and winter runs, at brackish water location in Hoogly River, Godakhali, were found to be two separate distinct genetic stocks. Migratory patterns from the sea to these freshwater river systems have also been speculated from mitochondrial DNA data, which needs confirmation from tagging studies. These results have strong implications for the conservation and sustainable management of hilsa fishery, as a consequence to its over-exploitation, which directly influences the overall species diversity.