Abstract
The analysis of the genomic architecture of selection can be insightful for the understanding of sexual conflict and sexual selection acting in wild populations. In general, there will be a wide range of possible targets of selection in the reproductive system of sexually promiscuous species. In the context of a dynamic conflict, selection is expected to be predominantly recurrent and it might be best investigated by combining population‐level and phylogenetic approaches on multiple species. First, we used population‐based methods to scan for recent selection in the socially polygynous pectoral sandpiper ( Calidris melanotos ). We assembled and annotated the pectoral sandpiper genome and re‐sequenced the genome of 20 random individuals of a single breeding population. We identified genes coding for axonemal constituents which are mostly expressed in the testis as selection targets. These genes most likely influence energy‐driven sperm motility, suggesting a role in sperm competition in this species. Second, we replicated the analysis and found similar results in another promiscuous shorebird, the ruff ( Calidris pugnax ), using publicly available data of 25 re‐sequenced individuals. Finally, a comparative genomics approach among six Calidris species with publicly available genome assemblies showed similar signals of selection, suggesting historical episodes of postcopulatory sexual selection or sexual conflict in genes related to sperm motility.