Alternative splicing contributes to plasticity and regulatory divergence in locally adapted house mice from the Americas

Abstract Alternative splicing is a major driver of transcriptome and proteome variation, but the role of alternative splicing in regulatory evolution is often overlooked. Alternative splicing can also contribute to phenotypic plasticity, which may be critical when taxa colonize new environments. Here, we investigate variation in alternative splicing among new wild-derived strains of mice from different climates in the Americas on both a standard and high-fat diet. We show that alternative splicing is widespread and highly context-dependent, underscoring its potential as a substrate for adaptation and plasticity. Comparisons between strains on different diets revealed abundant gene-by-environment interactions affecting alternative splicing. Most genes showed strain- and sex-specific diet responses, highlighting the importance of incorporating sex, genetic diversity, and environmental variation in studies of gene regulation. More often than not, genes that were differentially spliced between strains were not differentially expressed, adding to evidence that the two regulatory mechanisms often act independently. Moreover, patterns of expression and network analyses suggest that the two mechanisms differ in pleiotropic constraint. Importantly, divergence in alternative splicing was predominantly driven by cis-regulatory changes. However, trans changes affecting splicing may be central to plasticity as they were impacted more by environmental variation. Finally, we performed scans for selection and found that, while genes with splicing divergence more often co-localized with genomic outliers associated with metabolic traits, they were not enriched for genomic outliers. Overall, our results provide evidence that alternative splicing plays an important role in gene regulation in house mice, contributing to divergence and plasticity.