The anadromous Hilsa shad (Tenualosa ilisha) live in the Bay of Bengal and migrate to the estuaries and freshwater rivers for spawning and nursing of the juveniles. This has led to two pertinent questions: (i) do all Hilsa shad that migrate from marine to freshwater rivers come from the same population? and (ii) is there any relationship between adults and juveniles of a particular habitat? To address these questions, NextRAD sequencing was applied to genotype 31,276 single nucleotide polymorphism (SNP) loci for 180 individuals collected from six strategic locations of riverine, estuarine and marine habitats. FST OutFLANK approach identified 14,815 SNP loci as putatively neutral and 79 SNP loci as putatively adaptive. We observed that divergent local adaptations in differing environmental habitats have divided Hilsa shad into three genetically structured ecotypes: turbid freshwater (Western Riverine), clear freshwater (Eastern Riverine) and brackish-saline (Southern Estuarine-Marine). Our results also revealed that genes involved in neuronal activity may have facilitated the juveniles' Hilsa shad in returning to their respective natal rivers for spawning. This study emphasized the application of fundamental population genomics information in strategizing conservation and management of anadromous fish such as Hilsa shad that intersect diverse ecotypes during their life-history stages.
The migration of anadromous fish in heterogenic environments unceasingly imposes a selective pressure that results in genetic variation for local adaptation. However, discrimination of anadromous fish populations by fine-scale local adaptation is challenging because of their high rate of gene flow, highly connected divergent population, and large population size. Recent advances in next-generation sequencing (NGS) have expanded the prospects of defining the weakly structured population of anadromous fish. Therefore, we used NGS-based restriction site-associated DNA (NextRAD) techniques on 300 individuals of an anadromous Hilsa shad (Tenualosa ilisha) species, collected from nine strategic habitats, across their diverse migratory habitats, which include sea, estuary, and different freshwater rivers. The NextRAD technique successfully identified 15,453 single nucleotide polymorphism (SNP) loci. Outlier tests using the FST OutFLANK and pcadapt approaches identified 74 and 449 SNPs (49 SNPs being common), respectively, as putative adaptive loci under a divergent selection process. Our results, based on the different cluster analyses of these putatively adaptive loci, suggested that local adaptation has divided the Hilsa shad population into two genetically structured clusters, in which marine and estuarine collection sites were dominated by individuals of one genetic cluster and different riverine collection sites were dominated by individuals of another genetic cluster. The phylogenetic analysis revealed that all the riverine populations of Hilsa shad were further subdivided into the north-western riverine (turbid freshwater) and the north-eastern riverine (clear freshwater) ecotypes. Among all of the putatively adaptive loci, only 36 loci were observed to be in the coding region, and the encoded genes might be associated with important biological functions related to the local adaptation of Hilsa shad. In summary, our study provides both neutral and adaptive contexts for the observed genetic divergence of Hilsa shad and, consequently, resolves the previous inconclusive findings on their population genetic structure across their diverse migratory habitats. Moreover, the study has clearly demonstrated that NextRAD sequencing is an innovative approach to explore how dispersal and local adaptation can shape genetic divergence of non-model anadromous fish that intersect diverse migratory habitats during their life-history stages.
The tropical estuarine ecosystem is fascinating for studying the dynamics of water quality and phytoplankton diversity due to its frequently changing hydrological conditions. Most importantly, phytoplankton is the main supplier of ω3 polyunsaturated fatty acids (PUFA) in the coastal food web for fish as they could not synthesize PUFA. This study evaluated seasonal variations of water quality parameters in the Meghna River estuary (MRE), explored how phytoplankton diversity changes according to hydro-chemical parameters, and identified the major phytoplankton groups as the main source of PUFA for hilsa fish. Ten water quality indicators including temperature, dissolved oxygen, pH, salinity, dissolved inorganic nitrogen (DIN = nitrate, nitrite, ammonia) and phosphorus, dissolved silica and chlorophyll-a were evaluated. In addition, phytoplankton diversity was assessed in the water and hilsa fish gut. Principal component analysis (PCA) was used to analyze the spatio-temporal changes in the water quality conditions, and the driving factors in the MRE. Four main components were extracted and explained 75.4% variability of water quality parameters. The most relevant driving factors were dissolved oxygen, salinity, temperature, and DIN (nitrate, nitrite and ammonia). These variabilities in physicochemical parameters and dissolved inorganic nutrients caused seasonal variations in two major groups of phytoplankton. Peak abundance of Chlorophyta (green algae) occurred in water in nutrient-rich environments (nitrogen and phosphorus) during the wet (36%) season, while Bacillariophyta (diatoms) were dominant during the dry (32%) season that depleted dissolved silica. Thus, the decrease of green algae and the increase of diatoms in the dry season indicated the potential link to seasonal changes of hydro-chemical parameters. The green algae (53.7%) were the dominant phytoplankton group in the hilsa gut content followed by diatoms (22.6%) and both are contributing as the major source of PUFAs for hilsa fish according to the electivity index as they contain the highest amounts of PUFAs (60 and 28% respectively).