Natural selection on synonymous genetic variation in the major histocompatibility complex

Abstract

Protein coding DNA sequences harbor synonymous nucleotide variation that does not change amino acid sequences but influences phenotypes via multiple effects on the pathway from gene to protein. Synonymous variation has recently been shown to coevolve between viruses and their natural hosts, but its potential role in host immune defenses has not been explored. Here, I present evidence of natural selection on synonymous variation in the major histocompatibility complex (MHC), a highly polymorphic multigene locus that plays a crucial role in pathogen recognition by the adaptive immune system of vertebrate species. Using data from a wild population of Great Reed Warblers, I show that codon usage in exon 3 of MHC class I (MHC-I) genes is under strong purifying selection in 57 out of 87 codon sites. Scanning the Great Reed Warbler genome for tRNA genes revealed that, for most amino acids, bias towards preferred codons was associated with abundances of tRNA isotypes, indicating that the purifying selection is likely driven by selection for increased translational efficiency. However, spikes of synonymous variation appeared in 30 of the 87 sites in the MHC-I exon 3, and in those sites, codon usage bias and correlations with tRNA abundances were reduced. About half of these sites fall in CpG contexts, where cytosine deamination elevates the mutation rate; the other half do not, leaving the driver of much of the variation unexplained. The distribution of the spikes of synonymous variation showed no consistent association with structural domains of the MHC-I protein, nor with sites under positive selection for amino acid change, which are considered important for antigen binding properties. Intriguingly, the amount of synonymous variation in genotypes showed a positive correlation with Darwinian fitness, indicating that important evolutionary forces are at play that neutralize purifying selection in the 30 sites. From an ultimate perspective, the release of purifying selection among certain sites in MHC genes may indicate an arms race with pathogens, and I propose that the spikes of synonymous variation reveal a footprint of natural selection to escape inhibitory molecular interactions targeting MHC mRNA. I advance this RNA-level arms race as a novel axis of host-pathogen coevolution and a hypothesis to be tested directly. The fitness association is specific to synonymous variation, independent of amino-acid differences and the number of MHC alleles in genotypes, implicating selection on the synonymous variation itself rather than linked protein-level diversity. These results expose a previously unrecognized layer of selection in a key immune gene family and highlight the potential functional importance of synonymous variation in host-pathogen coevolution with direct implications for understanding susceptibility to infectious diseases.