Abstract
The classical class I HLA loci of humans show an excess of nonsynonymous with respect to synonymous substitutions at codons of the antigen recognition site (ARS), a hallmark of adaptive evolution. Additionally, high polymporphism, linkage disequilibrium, and disease associations suggest that one or more balancing selection regimes have acted upon these genes. However, several questions about these selective regimes remain open. First, it is unclear if stronger evidence for selection on deep timescales is due to changes in the intensity of selection over time or to a lack of power of most methods to detect selection on recent timescales. Another question concerns the functional entities which define the selected phenotype. While most analyses focus on selection acting on individual alleles, it is also plausible that phylogenetically defined groups of alleles (“lineages”) are targets of selection. To address these questions, we analyzed how \({\mathrm{d}}N/{\mathrm{d}}S\) (\(\omega\)) varies with respect to divergence times between alleles and phylogenetic placement (position of branches). We find that \(\omega\) for ARS codons of class I HLA genes increases with divergence time and is higher for inter-lineage branches. Throughout our analyses, we used non-selected codons to control for possible effects of inflation of \(\omega\) associated to intra-specific analysis, and showed that our results are not artifactual. Our findings indicate the importance of considering the timescale effect when analysing \(\omega\) over a wide spectrum of divergences. Finally, our results support the divergent allele advantage model, whereby heterozygotes with more divergent alleles have higher fitness than those carrying similar alleles.
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Acknowledgments
The authors thank Kelly Nunes for thoughtful comments on the manuscript, Richard Single for comments on the statistical aspects of this work, Aida M. Andrés for general comments and Débora Y.C.Brandt for help with the 1000 Genomes data sets. BDB was funded by grants #08/56502-6 and #11/12500-2, São Paulo Research Foundation (FAPESP), and #152676/2011-2, Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). RSF was funded by grant #142130/2009-5 (CNPq) and DM was funded by grants #09/09127-8 (FAPESP) and #308960/2009-2 (CNPq).
Author’s Contributions
BDB participated in the design of the study, performed analyses, discussed results and drafted the manuscript. RDF performed analyses to detect recombinants and contributed to discussions. DM conceived of the study, participated in its design and discussion and in the drafting of the manuscript. All authors read and approved the final manuscript.
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Bitarello, B.D., Francisco, R.d. & Meyer, D. Heterogeneity of \({\varvec{\rm d}}{\varvec{N}}/{\varvec{\rm d}}{\varvec{S}}\) Ratios at the Classical HLA Class I Genes over Divergence Time and Across the Allelic Phylogeny. J Mol Evol 82, 38–50 (2016). https://doi.org/10.1007/s00239-015-9713-9
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DOI: https://doi.org/10.1007/s00239-015-9713-9