Signatures of diversifying selection and convergence acting on passerine Toll‐like receptor 4 in an evolutionary context

Abstract

Positive selection acting on Toll-like receptors (TLRs) has been recently investigated to reveal evolutionary mechanisms of host-pathogen molecular co-adaptation. Much of this research, however, has focused mainly on the identification of sites predicted to be under positive selection, bringing little insight into the functional differences and similarities among species and a limited understanding of convergent evolution in the innate immune molecules. In this study, we provide evidence of phenotypic variability in the avian TLR4 ligand-binding region (LBR), the direct interface between host and pathogen molecular structures. We show that 55 passerine species vary substantially in the distribution of electrostatic potential on the surface of the receptor, and based on these distinct patterns, we identified four species clusters. Seven of the 34 evolutionarily nonconservative and positively selected residues correspond topologically to sites previously identified as being important for lipopolysaccharide, lipid IVa or MD-2 binding. Five of these positions codetermine the identity of the charge clusters. Groups of species that host-related communities of pathogens were predicted to cluster based on their TLR4 LBR charge. Despite some evidence for convergence among taxa, there were no clear associations between the TLR4 LBR charge distribution and any of the general ecological characteristics compared (migration, latitudinal distribution and diet). Closely related species, however, mostly belonged to the same surface charge cluster indicating that phylogenetic constraints are key determinants shaping TLR4 adaptive evolution. Our results suggest that host innate immune evolution is consistent with Fahrenholz's rule on the cospeciation of hosts and their parasites.

Positive selection and convergent evolution shape molecular phenotypic traits of innate immunity receptors in tits (Paridae)

“…Consistent with previously published results (Králová et al., 2018; Vinkler et al., 2014), high variation was revealed in the TLR4 and TLR5 LBR surface charge patterns. This molecular trait reflects the high sequence variation of TLR4 and TLR5, unlike the shape of the tertiary structures (Fornuskova et al., 2014; Vinkler et al., 2014) or surface hydrophobicity.…”

“…Consistent with Králová et al. (2018), PSSs were considered in close topological proximity to the functionally relevant residues only if located <0.5 nm apart. This cutoff distance reflects the putative span of hydrogen bonds, salt bridges (Donald, Kulp, & Degrado, 2012) and longer‐range hydrophobic interactions (Onofrio et al., 2014).…”

“…Based on our criteria for adaptive convergence, three reliable convergent PSSs in TLR4 (270, 325, 397) and six PSSs in TLR5 (36, 56, 82, 104, 235, 377) were selected. Interestingly, all these PSSs except position 82 in TLR5 have been previously identified as positively selected in other bird and mammal species (Areal, Abrantes, & Esteves, 2011; Grueber, Wallis, & Jamieson, 2013; Grueber et al., 2014; Králová et al., 2018; Nakajima et al., 2008; Smith et al., 2012; Velová et al., 2018; Vinkler, Bryjova, Albrecht, & Bryja, 2009; Wlasiuk, Khan, Switzer, & Nachman, 2009), suggesting broader phylogenetic patterns of the convergence revealed. Importantly, several of these sites were also shown to be directly functionally relevant; for example, positions 36, 56, 104 and 377 are flagellin binding sites in TLR5 (Yoon et al., 2013) and the E325K variation in TLR4 is involved in determination of the major electrostatic surface charge clusters in tits.…”

“…Until recently, there has only been limited study of convergent evolution in immune genes (e.g., the Major Histocompatibility Complex [MHC] with convergence best documented for the peptide‐binding region [PBR]: Yeager & Hughes, 1999; Kriener, O'hUigin, Tichy, & Klein, 2000; Li, Zhou, & Chen, 2011; Klein et al., 2007; Kaesler et al., 2017; antimicrobial peptides: Unckless & Lazzaro, 2016; Toll‐like receptors: Králová et al., 2018; Świderská et al., 2018). However, due to their extreme variability, high copy number variation preventing identification of direct gene orthology and structural plasticity of the PBR, MHC genes may be problematic models to study molecular convergence (Koch et al., 2007).…”

Adaptive landscape genetics and malaria across divergent island bird populations

“…The TLR4 SNPs sequenced here are situated within the ligand‐binding region, which plays a key role in TLR pathogen recognition (Werling, Jann, Offord, Glass, & Coffey, ). Evidence of positive selection in birds or mammals has been detected at each of the codons identified as polymorphic in Berthelot's pipits (Areal, Abrantes, & Esteves, ; Králová et al, ; Wlasiuk & Nachman, ), suggesting that these sites may be important for the evolution of pathogen recognition. On Tenerife, the presence of the TLR4 protein haplotype TLR4_P1 was associated with decreased malaria infection prevalence in 2011, but not across all sampling years.…”