Genomic Basis of Local Adaptation in Nile Tilapia Populations Across Environmentally Contrasting River Systems in Nigeria

Understanding the genomic basis of local adaptation in freshwater fish has profound implications for fisheries management and conservation genetics in the face of environmental change. This study investigates the genomic architecture of local adaptation in Nile tilapia populations sampled from eleven river systems across Nigeria, spanning a pronounced environmental gradient from hypereutrophic, warm, degraded lowland rivers in the Niger Delta to cooler, oligotrophic highland streams in the Jos Plateau. Whole-genome resequencing was performed at high coverage for 220 individuals. Population structure, demographic history, and signatures of selection were analysed using population genomics approaches including selective sweep detection, environmental association analysis, and gradient forest modelling. Functional annotation of candidate loci under selection was performed against the Nile tilapia reference genome. Results identified 247 genomic regions showing signatures of diversifying selection corresponding to environmental gradients in temperature, dissolved oxygen, and conductivity. Environmental association analysis linked temperature and dissolved oxygen gradients to candidate genes involved in haemoglobin oxygen affinity, thermal stress response, and metabolic rate regulation. Demographic modelling revealed pronounced historical population contractions in Jos Plateau populations, consistent with Pleistocene climate fluctuations constraining highland range occupancy. Evidence of recent adaptive introgression from highland into lowland populations at several immunological loci suggests ongoing evolutionary response to emerging pathogen pressures. The study makes a significant original contribution to the population genomics of tropical freshwater fish adaptation and provides a genomic evidence base for conservation unit designations in Nigerian tilapia fisheries management. Keywords: local adaptation, genomics, Nile tilapia, freshwater fish, Nigeria.