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

Abstract

Despite widespread variability and redundancy abounding animal immunity, little is currently known about the rate of evolutionary convergence (functionally analogous traits not inherited from a common ancestor) in host molecular adaptations to parasite selective pressures. Toll‐like receptors (TLRs) provide the molecular interface allowing hosts to recognize pathogenic structures and trigger early danger signals initiating an immune response. Using a novel combination of bioinformatic approaches, here we explore genetic variation in ligand‐binding regions of bacteria‐sensing TLR4 and TLR5 in 29 species belonging to the tit family of passerine birds (Aves: Paridae). Three out of the four consensual positively selected sites in TLR4 and six out of 14 positively selected positions in TLR5 were located on the receptor surface near the functionally important sites, and based on the phylogenetic pattern evolved in a convergent (parallel) manner. This type of evolution was also seen at one N‐glycosylation site and two positively selected phosphorylation sites, providing the first evidence of convergence in post‐translational modifications in evolutionary immunology. Finally, the overall mismatch between phylogeny and the clustering of surface charge distribution demonstrates that convergence is common in overall TLR4 and TLR5 molecular phenotypes involved in ligand binding. Our analysis did not reveal any broad ecological traits explaining the convergence observed in electrostatic potentials, suggesting that information on microbial symbionts may be needed to explain TLR evolution. Adopting state‐of‐the‐art predictive structural bionformatics, we have outlined a new broadly applicable methodological approach to estimate the functional significance of positively selected variation and test for the adaptive molecular convergence in protein‐coding polymorphisms.

Adaptation and Cryptic Pseudogenization in Penguin Toll-Like Receptors

“…Despite this, TLRs in vertebrates frequently undergo diversifying selection through coevolution with pathogens ( Areal et al 2011 ; Velova et al 2018 ; Liu et al 2020 ). Even closely related taxa may show substantial variability in molecular phenotypes of individual TLRs ( Králová et al 2018 ; Levy et al 2020 ; Těšický et al 2020 ). Our findings are similar to those reported elsewhere in birds.…”

Selection Balancing at Innate Immune Genes: Adaptive Polymorphism Maintenance in Toll-Like Receptors

“…TLRs represent a valuable model for studying such evolutionary mechanisms as (1) they show strong positive selection signatures at the interspecific level ( Velová et al 2018 ) and (2) unlike MHC , they are single-copy genes, allowing more effective tracking of adaptive evolution. Furthermore, their general structural conservation allows positive selection to be linked with protein structure molecular adaptations ( Těšický et al 2020 ), allowing functional identification of the phenotypic effects of molecular variation ( Walsh et al 2008 ; Levy et al 2020 ; Fiddaman et al 2022 ).…”

“…Although only around 5% of TLR codons experience pathogen-mediated positive selection ( Grueber et al 2014 ; Velová et al 2018 ), this polymorphism may play a paramount role in pathogen recognition as it is mostly located in the ligand-binding regions of TLR exodomains, that is, at molecular surfaces crucial for pathogen recognition ( Downing et al 2010 ; Vinkler et al 2014 ; Velová et al 2018 ). TLR adaptations at these sites may affect the physicochemical properties of the receptor surface, including its electrostatic potential ( Králová et al 2018 ; Těšický et al 2020 ). In pathogens, and particularly those with simple genomes such as bacteria or (especially) viruses, convergent evolution is common, indicating functional limits in their structural evolution ( Wang et al 2015 ; Gutierrez et al 2019 ).…”

“…Given these limits to the number of structural variants of pathogen-derived ligands, diversifying selection can also be predicted to select for a finite (but possibly multiple) number of TLR variants. At the interspecific level, constraints in host and pathogen structure variation may lead to evolutionary convergence ( Walsh et al 2008 ; Świderská et al 2018 ; Těšický et al 2020 ), whereas TLR polymorphism at the intraspecific level may be maintained within populations via balancing selection. Though nonnegligible levels of functional, and potentially functional, variability at TLRs has recently been revealed across and within phylogenetically diverse vertebrate lineages, including humans ( Ferwerda et al 2007 ), domestic animals ( Leveque et al 2003 ; Świderská et al 2018 ), and wild species ( Alcaide and Edwards 2011 ; Quéméré et al 2015 ; Vinkler et al 2015 ; Minias et al 2021 ), the mechanisms of balancing selection actively maintaining this variation within populations are still debated.…”

Repeated MDA5 Gene Loss in Birds: An Evolutionary Perspective

“…The distances between PSSs and functionally relevant sites were measured using function iterate implemented in PyMol. Consistent with [39], given the putative span of hydrogen bonds, salt bridges [40], and longer-range hydrophobic interactions [41], PSSs were considered in close topological proximity to the functional residues only if located < 5 Å apart.…”