Sexually dimorphic alternative splicing and its erosion following the loss of sex in stick insects

Abstract

Sexually dimorphic traits emerge from divergent selective pressures acting on males and females and are facilitated by gene regulatory mechanisms. While gene expression differences have been the subject of considerable focus in the evolution of sexual dimorphism, other regulatory processes remain comparatively understudied. One such mechanism is alternative splicing, whereby a single gene can encode multiple distinct transcripts, leading to functional diversification of the proteome. Leveraging long-read PacBio Iso-sequencing, we examine patterns of sex differences in gene expression and alternative splicing in three tissues of related Timema stick insect species, including five sexual and four asexual lineages. Alternative splicing is widespread in Timema, with the greatest isoform complexity found in the male gonad tissue. We observe similar levels of sex differences in gene expression and splicing, and a core set of genes involved in sexual differentiation and germline development that have conserved differential splicing patterns across the Timema phylogeny. However, patterns of sex-biased alternative splicing undergo faster lineage-specific turnover than sex-biased gene expression, and differentially spliced genes are subject to strong pleiotropic and purifying constraints. Following the transition from sexual reproduction to asexuality, there is a systematic reduction in isoform diversity and erosion of sex-biased splicing variation. Taken together, our findings suggest a role for sexual selection in maintaining splicing complexity in sexual Timema species.