Abstract
Anthropogenic salinisation of freshwater ecosystems represents a major threat to biodiversity. While the ecological consequences of freshwater salinisation have received extensive investigation, our knowledge of the evolutionary responses to projected salinisation is more limited. Phenotypic plasticity can be an important first step to facilitate population persistence in stressful environments. Here, we combined high‐resolution environmental data with a laboratory‐based experiment to investigate the time‐course of gene expression plasticity in response to projected salinisation in two populations of the western mosquitofish ( Gambusia affinis ) with different histories of salt exposure. We found significant differences in transcriptional plasticity between populations as well as a general tendency for non‐parallel expression change in salinity‐responsive genes identified in both populations. Despite this pattern, we identified a core set of genes that showed parallel responses to salinity in both populations across all time points. However, these parallel responses in gene expression were putatively regulated by largely non‐overlapping sets of microRNAs in each population. Finally, we found that genes expressed in parallel showed greater nucleotide diversity than genes with non‐parallel responses, possibly providing standing genetic variation to facilitate population persistence under changing salinity conditions. Our results provide insights into the evolutionary consequences of freshwater salinisation and demonstrate the potential of freshwater fish to cope with projected salinisation.