Expression diversity of cichlid MHC alleles

Abstract Background Diversification driven by natural selection is a major source of biodiversity. Parasites and pathogens impose important selective pressures on their hosts, contributing to high levels of polymorphism at immunologically relevant genes within and among populations. The antigen-recognizing class IIB genes of the major histocompatibility complex (MHC) are major targets of parasite-mediated selection and frequently show genetic differentiation and local adaptation among populations. Accumulating evidence suggests that, besides allele sequence, variation in MHC expression may contribute to functional differences among alleles and loci. Here, we studied allele-specific MHC IIB expression in wild cichlid populations and evaluated patterns of expression variation in relation to allele frequency, functional supertypes, and population structure. Results Building on previous knowledge of MHC class IIB diversity associated with ecological divergence in cichlid fish, we examined MHC expression patterns, their relationship with allele frequency, and their variability among populations and species. In Midas cichlids, a few highly abundant alleles showed consistently low expression, while many less common alleles showed high expression and were restricted to particular host populations. MHC alleles belonging to the same functional supertypes showed similar expression patterns. Lowly expressed supertypes showed relatively consistent expression across populations, while highly expressed supertypes exhibited substantially greater among-population variation. In the African cichlid dataset, putative MHC class IIB loci also showed marked variation in expression. Interestingly, lowly expressed Midas cichlid alleles clustered phylogenetically with lowly expressed putative African loci, while most highly expressed variants formed separate clusters. Conclusions Our findings reveal a strong relationship between MHC allele frequency and expression, with the most common alleles tending to show low expression and many less common alleles showing high expression. The phylogenetic association between lowly expressed Midas cichlid alleles and African putative loci suggests that low expression might be associated with distinct MHC lineages, although its functional significance remains unresolved. MHC expression also varied substantially among populations, particularly for highly expressed supertypes. Together, these results show that allele- and locus-specific expression provides an additional dimension of MHC diversity beyond sequence variation alone. Whether these expression patterns influence parasite recognition or are shaped by parasite-mediated selection remains to be tested using direct parasite and infection data.