In many species, individuals prefer mates that are genetically dissimilar at the major histocompatibility complex (MHC), likely because it improves offspring resistance to pathogens. Here, we provide the first characterization of the MHC class II peptide binding region in bluegill (Lepomis macrochirus) and examine its effect on mating patterns. We captured female and male bluegill during spawning and sequenced these fish at the MHC. We found strong evidence that positive selection promotes genetic diversity at the MHC in bluegill, with a 5:2 ratio of non-synonymous to synonymous mutations. However, we found no evidence that the MHC led to disassortative mating between females and parental males. Extra-pair mating and the presence of specialized cuckolder males may have an important, albeit still unresolved, role in shaping mating patterns at the MHC in bluegill.
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