Adaptation and constraint at Toll-like receptors in primates

Abstract

Frequent positive selection is a hallmark of genes involved in the adaptive immune system of vertebrates, but the incidence of positive selection for genes underlying innate immunity in vertebrates has not been well studied. The toll-like receptors (TLRs) of the innate immune system represent the first line of defense against pathogens. TLRs lie directly at the host-environment interface, and they target microbial molecules. Because of this, they might be subject to frequent positive selection due to coevolutionary dynamics with their microbial counterparts. However, they also recognize conserved molecular motifs, and this might constrain their evolution. Here, we investigate the evolution of the ten human TLRs in the framework of these competing ideas. We studied rates of protein evolution among primate species and we analyzed patterns of polymorphism in humans and chimpanzees. This provides a window into TLR evolution at both long and short timescales. We found a clear signature of positive selection in the rates of substitution across primates in most TLRs. Some of the implicated sites fall in structurally important protein domains, involve radical amino acid changes, or overlap with polymorphisms with known clinical associations in humans. However, within species, patterns of nucleotide variation were generally compatible with purifying selection, and these patterns differed between humans and chimpanzees and between viral and nonviral TLRs. Thus, adaptive evolution at TLRs does not appear to reflect a constant turnover of alleles and instead might be more episodic in nature. This pattern is consistent with more ephemeral pathogen-host associations rather than with long-term coevolution.

FIG. 1.

Positively selected sites in the three-dimensional structures of TLRs. In each case, areas important for ligand binding that contain a concentration of sites under selection are squared. Amino acid positions of positively selected sites are labeled in red. (A) TLR4–TLR4 dimer; (B) TLR1–TLR2 dimer.

FIG. 2.

Positive selection at TLR4. (A) Physicochemical properties of the amino acids at the positively selected sites at TLR4. SM, small; NP, nonpolar; P, polar; NEU, neutral; POS, positively charged; NEG, negatively charged. (B) Estimated lineage-specific dN/dS ratios from the branch-based analysis are shown above the branches of the TLR4 phylogeny. For the sites under selection from the codon-based analysis, the amino acid changes reconstructed by parsimony are mapped. Each red mark represents one amino acid substitution. Branch lengths are proportional to dS.

FIG. 3.

Summary statistics of the allele frequency spectrum in TLRs compared with the empirical distribution of Akey et al. (2004) for the same populations. AA, African Americans; EA, European Americans.