Studies investigating genotype to phenotype relationships have demonstrated that genetic variation is biologically important; however, the evolutionary significance of these relationships and variation maintenance remains poorly understood. Here, three wild populations of the small teleost fish Fundulus heteroclitus: one locally heated by thermal effluent from a nuclear power plant (TE) and two reference populations that do not experience local heating (10 km north and 3.5 km south) were used. This experimental design was intended to test the central hypothesis that the TE population is locally adapted when compared to the north and south reference sites. Temperature specific metabolic and thermal tolerance traits, tissue specific (heart and brain) mRNA expression, and genetic variation (single nucleotide polymorphisms, SNPs) are compared among populations. Few differences exist among populations in physiological traits, mRNA expression, or SNPs. Instead, large inter-individual variation in metabolic and thermal tolerance traits is irrespective of population. This large variation is explained by tissue and acclimation temperature specific mRNA expression patterns, with different mRNAs in heart and brain tissue from similar pathways explaining trait variation. Whole genome sequencing for the same individuals that physiological traits and mRNA expression were measured in allowed direct (genome wide association, GWAS) and indirect (expression quantitative trait loci, eQTL) associations with physiological traits to be examined. Many significant eQTL explain single and multivariate mRNA expression patterns. These tissue specific eQTL are dominated by trans-acting factors (found on different chromosomes than the mRNAs they impact). This thesis contributes new knowledge on the evolutionary importance of biological variation. </p
