Bárbara D Bitarello, Rodrigo dos Santos Francisco, Diogo Meyer
Many HLA loci show an excess of nonsynonymous (dN) with respect to synonymous (dS) substitutions at codons of the antigen recognition site (ARS), a hallmark of adaptive evolution. However, it remains unclear how these changes are distributed over time and across branches of the HLA phylogeny. In particular, although HLA alleles can be assigned to functionally and phylogenetically defined groups (“lineages”), a test for differences in ω (ω = dN/dS) within and between lineages is lacking. We analysed variation of ω across divergence times and phylogenetic contexts (placement of branches in the phylogeny). We found a significant positive correlation between ω at ARS codons and divergence time, and that branches between lineages have higher ω than those within lineages. The excess of nonsynonymous hanges between lineages attained significance when we used non-ARS codons to account for the fact that, even under purifying selection, ω is inflated for recently diverged alleles. Although less intensely selected, within-lineage variation at ARS codons bears evidence of selection, in the form of higher ω than those of non-ARS codons. Our results show that ω ratios of class I HLA genes vary over time, and are higher in branches connecting alleles from distinct lineages. These results suggest that although within-lineage variation bears evidence of balancing selection, the between-lineage changes have been more intensely selected. Our findings indicate the importance of considering the effect of timescale when analysing ω values over a wide spectrum of divergences, and the value of using additional markers (in our case the tightly linked non-ARS codons) to account for the temporal dynamics of ω.