Species without dimorphic secondary sex characteristics easily visible to humans, such as difference in size or morphology, are expected to experience low levels of sex-specific selection. However, monomorphism in classic visible traits could be a result of genetic or physiological constraints that prevent the sexes from reaching divergent fitness optima. Additionally, biochemical and molecular work has revealed a variety of less easily observed phenotypes that none-the-less exhibit profound dimorphism. Sex-specific selection could act on these more subtle, less visible, traits. We investigate sex-specific selection in the polygynandrous dusky pipefish (Syngnathus floridae), which lacks size, color, and morphological dimorphism. Using experimental breeding populations, we revealed that although males and females have similar opportunities for sexual selection, only males experience significant sexual selection pressures on body size. We also investigated patterns of sex-biased and sex-specific gene expression in gonads, livers, and gills, and tested whether genes with highly divergent expression patterns between the sexes are more likely to be tissue specific, and therefore relieved of genetic constraints. We. Sex-bias in gene expression was widespread, although the reproductive organs had the most sex-biased and sex-specific genes. Sex-specific selection on gene expression in gills was primarily related to immune response, whereas the liver and gonads had a wide variety of cellular processes, as well as reproductive proteins, showing sex-biased expression. These sex-biased genes are likely less constrained by pleiotropy, as they were more organ-specific in their expression patterns. Altogether, we find evidence for ongoing and historical sex-specific selection in the dusky pipefish.

Over the past 65 million years, fishes in the family Syngnathidae (seahorses, pipefishes, and seadragons) have diversified into over 300 species that are globally distributed in marine and brackish environments, as well as in a small number of freshwater habitats. This clade is noteworthy for unusual species possessing novel and highly derived phenotypes, such as male pregnancy, elongated faces, prehensile tails, and ornate dermal outgrowths. Many of these traits evolved convergently in multiple lineages against the backdrop of the characteristic pipefish elongated phenotype. Though this family offers a rich system to explore developmental evolution in a vertebrate lineage, analysis of the genetic underpinnings of these traits has been hampered by a lack of high-quality, annotated genome assemblies for most syngnathid species. Here, we begin filling this gap by presenting high-quality, chromosome-scale genome assemblies for ten species from the Order Syngnathiformes. These assemblies, which we produced using a common assembly and annotation workflow, encompass nine syngnathid fishes and one outgroup species. We assembled each genome using PacBio High Fidelity reads and Hi-C contact maps and annotated them using the NCBI Eukaryotic Genome Annotation Pipeline. All nine genome assemblies are highly contiguous (with N50 values between 14Mb and 75Mb) and nearly complete (with BUSCO scores ranging from 97.6% to 99.6%). Assembled genomes range in size from 428 million base pairs to 3.1 billion base pairs, a pattern that likely resulted from lineage-specific genome duplication and repetitive DNA expansion and contraction. These ten genome assemblies are available publicly as RefSeq genome resources, providing a significant foundation for comparative genomic and functional genetic research on the wealth of fascinating syngnathid phenotypes.