Supplementary Material for: Sex-biased gene expression in the northern pipefish (Syngnathus fuscus), a species with male pregnancy, is widespread and linked to tissue specificity

Introduction: Sexual conflict is pervasive and can favor the evolution of differential gene expression patterns between males and females. The evolution of such sex-biased expression patterns is constrained by pleiotropic functions of differentially expressed genes, such as widespread expression across tissues.
Methods: We investigated sex-biased gene expression and its relationship to tissue specificity in reproductive and somatic organs in the Northern pipefish, Syngnathus fuscus, a polygynandrous species with extreme paternal care and no evidence of sex chromosomes – conditions ripe for intra-locus sexual conflict.
Results: We found patterns of sex-biased expression in the gonads, liver, and gills of the Northern pipefish, with the largest number of sex-biased genes identified in the gonads. In general, sex-biased genes were only more tissue-specific in the reproductive tissues (gonads), but not in either of the somatic tissues (liver or gills). Sex-biased genes with evidence of branch-specific selection were also more tissue specific.
Discussion: We highlight the potential for different sex-specific selection pressures to be acting on each tissue type as there were widespread differences in the protein classes represented by sex-biased genes across both organs and sexes, although sex-biased genes did not experience stronger episodic selection than unbiased genes. Furthermore, our results support the hypothesis that broad expression can constrain the molecular evolution of a gene. The work presented here supports the potential for sex-biased gene expression to act as a mechanism for phenotypic differentiation between the sexes and increases our knowledge of patterns of gene expression in an unusual group of fishes.