Copy number variations in response to chronic pollution: Basilichthys microlepidotus in central Chile

Abstract Pollution, driven by land use, industrial operations, and urban growth, significantly affects biodiversity in freshwater ecosystems. Studies have shown how freshwater organisms adapt to pollution, observing mechanisms like directional selection, balancing selection, and introgression. They have focused on genetic changes in populations exposed to pollution, particularly single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) in DNA. CNVs have been linked to environmental disturbances. This study investigates CNVs in Basilichthys microlepidotus in Chile’s polluted Maipo River watershed. CNVs were associated with pollution in chronically exposed populations, though population structure was weak, making it difficult to distinguish between reference and contaminated sites. However, outliers related to pollution functions were consistently identified. Eleven CNV loci correlated with three historical physical variables electroconductivity, pH, and total dissolved solids accounting for 5% of all detected CNV loci. These markers revealed a subtle but significant population structure, linking CNVs to gene expression changes and SNPs potentially affected by pollution-driven selection. The effects of these CNVs are unknown, and further analysis is required to unveil them, but they could potentially help these organisms adapt to environmental contamination.