The Role of Alternative Splicing in Marine–Freshwater Divergence in Threespine Stickleback

Alternative splicing regulates which parts of a gene are kept in the messenger RNA and has long been appreciated as a mechanism to increase the diversity of the proteome within eukaryotic species. There is a growing body of evidence that alternative splicing might also play an important role in adaptive evolution. However, the relative contribution of differential alternative splicing (DS) to phenotypic evolution and adaptation is still unknown. In this study, we asked whether DS played a role in adaptation to divergent marine and freshwater habitats in threespine stickleback (Gasterosteus aculeatus). Using two published gill RNA-seq datasets, we identified differentially expressed and differentially spliced genes (DEGs and DSGs) between population pairs of marine–freshwater stickleback in the Northeast Pacific and tested whether they are preferentially found in regions of the genome involved in marine–freshwater divergence. We found over 100 DSGs, which were found more often than expected in peaks of genetic divergence and quantitative trait loci that underlie phenotypic divergence between ecotypes. DSGs and DEGs are similarly enriched in these regions. Among the different types of DS, mutually exclusive exon splicing is most strongly correlated with genetic divergence between ecotypes. Taken together, our results add support to the growing evidence that natural selection might have acted on DS and might have specifically played a role in the adaptive divergence of marine and freshwater sticklebacks. Our results also suggest that some types of DS events might contribute more than others to adaptation.