Evolution by natural selection acts on natural populations amidst migration, gene-by-environmental interactions, constraints and tradeoffs, which affect the rate and frequency of adaptive change. We asked how many and how rapidly loci change in populations subject to severe, recent, environmental changes as well as the role of geographical cline in shaping patterns of variation. To address these questions, we used genomic approaches to identify randomly selected SNPs with evolutionarily significant patterns in three natural populations of the estuarine fish, Fundulus heteroclitus, which inhabit and have adapted to highly polluted Superfund sites as well as in six clean reference sites.
Three statistical tests identified 1.4-2.5% of SNPs were significantly different from the neutral model in each polluted population as compared to geographically flanking clean reference sites. These non-neutral patterns in populations adapted to highly polluted environments suggest that these loci or closely linked loci are evolving by natural selection. Selection due to geographic cline was explored using combined FST-outlier and cline shape analyses; 40% of the SNPs exhibit a reliable clinal pattern. One SNP identified as an outlier in all polluted populations using the tests to examine for natural selection due to pollution is in proximal promoter of the xenobiotic metabolizing enzyme, cytochrome P4501A (CYP1A). This enzyme’s gene has been identified previously as being refractory to induction to prototypic inducers in the three highly polluted populations. To explore the functional importance of this SNP, the inducibility of the promoter was explored in vitro. When treated with a prototypic polycyclic aromatic hydrocarbon, CYP1A promoters from New Bedford Harbor individuals significantly induced transcription of the luciferase reporter gene at higher levels as compared to promoters from reference populations. These results indicate that the underlying mechanism for the in vivo transcriptional phenotype may lay further upstream or downstream of the CYP1A promoter region which was sequenced, or involve proteins (trans- acting factors) which were not present in the cell line in which the transfection assays were completed. Extrapolating across the genome, these data suggest that rapid evolutionary change in natural populations can involve hundreds of loci, a few of which will be shared in independent events and may be functionally important in the resistance phenotype.