Genomic Basis of Local Adaptation in Brackish Water Fish Populations Across the Niger Delta Salinity Gradient: An Environmental Genomics Approach

Understanding the genomic architecture of local adaptation to salinity gradients provides fundamental insights into speciation processes and informs management of fish populations in estuarine systems increasingly modified by climate-driven hydrological changes. This research uses an environmental genomics approach to characterise the genomic basis of local adaptation to salinity in three euryhaline fish species (Mugil cephalus, Sardinella maderensis, and Siganus rivulatus) across the salinity gradient of the Niger Delta. Population samples were collected at twelve sites spanning salinities from 0 to 35 practical salinity units in Rivers, Bayelsa, and Delta States. Whole-genome resequencing was performed on 240 individuals per species. Population structure was characterised using principal component analysis, admixture modelling, and FST outlier analysis. Genotype-environment association analysis using lfmm and BayPass identified genomic regions associated with local salinity variation. Candidate adaptive loci were functionally annotated against reference genomes. Parallel evolution analyses tested whether the same genomic regions showed repeated associations with salinity adaptation across species. Population structure in all three species showed a salinity-concordant gradient with marked differentiation between marine-dominated and freshwater-influenced populations. Between 84 and 312 candidate adaptive loci per species were identified, with enrichment for genes associated with ion transport, osmotic regulation, and gill epithelium function. Significant parallel evolution was detected at genes encoding Na+/K+ ATPase and aquaporin isoforms across all three species, suggesting convergent genomic solutions to salinity adaptation. This research establishes an environmental genomics framework for monitoring adaptive capacity of Niger Delta estuarine fish under projected freshwater input changes. Keywords: local adaptation, environmental genomics, salinity gradient, Niger Delta, estuarine fish.