Toll-Like Receptor Evolution in Birds: Gene Duplication, Pseudogenization, and Diversifying Selection

Abstract

Toll-like receptors (TLRs) are key sensor molecules in vertebrates triggering initial phases of immune responses to pathogens. The avian TLR family typically consists of ten receptors, each adapted to distinct ligands. To understand the complex evolutionary history of each avian TLR, we analyzed all members of the TLR family in the whole genome assemblies and target sequence data of 63 bird species covering all major avian clades. Our results indicate that gene duplication events most probably occurred in TLR1 before synapsids diversified from sauropsids. Unlike mammals, ssRNA-recognizing TLR7 has duplicated independently in several avian taxa, while flagellin-sensing TLR5 has pseudogenized multiple times in bird phylogeny. Our analysis revealed stronger positive, diversifying selection acting in TLR5 and the three-domain TLRs (TLR10 [TLR1A], TLR1 [TLR1B], TLR2A, TLR2B, TLR4) that face the extracellular space and bind complex ligands than in single-domain TLR15 and endosomal TLRs (TLR3, TLR7, TLR21). In total, 84 out of 306 positively selected sites were predicted to harbor substitutions dramatically changing the amino acid physicochemical properties. Furthermore, 105 positively selected sites were located in the known functionally relevant TLR regions. We found evidence for convergent evolution acting between birds and mammals at 54 of these sites. Our comparative study provides a comprehensive insight into the evolution of avian TLR genetic variability. Besides describing the history of avian TLR gene gain and gene loss, we also identified candidate positions in the receptors that have been likely shaped by direct molecular host–pathogen coevolutionary interactions and most probably play key functional roles in birds.

DNA methylation predicts immune gene expression in introduced house sparrows Passer domesticus

“…Interestingly, phenotypic plasticity may enable individuals to cope with environmental challenges including those with which individuals have little or no evolutionary history (Ghalambor et al , Forsman ). Further, molecular epigenetic mechanisms, such as DNA methylation (Schrey et al , Kilvitis et al , 2017), may underlie the ability to generate plasticity to overcome genetic paradoxes.…”

“…House sparrows Passer domesticus are ideal for studying relationships between epigenetic mechanisms and traits that facilitate invasion success, as they are a near‐globally distributed species, having colonized much of the world in the last 150 years (Anderson ). Several studies conducted on house sparrows in Kenya – site of one of the most recent introductions (~1950s) – have suggested that both genetic and epigenetic forces mediate population spread and phenotypic differentiation (Schrey et al , 2012, Liebl et al a). For instance, Kenyan house sparrows have lower genetic diversity than native and introduced North American populations (Schrey et al ), but across their Kenyan range, genetic diversity is actually higher at the range edge than the site of introduction even though populations behave as independent units.…”

“…For instance, DNA methylation was higher in Kenyan sparrows than an older, but also introduced North American population (Schrey et al ). More intriguingly, epigenetic and genetic diversity were inversely correlated among Kenyan populations, suggesting that methylation might compensate for low genetic diversity at some Kenyan sites (Liebl et al a).…”

“…Although many forms of epigenetic variation exist, DNA methylation is prevalent and extensive among most species, being a major mechanism whereby cells achieve distinct functions with the same DNA sequence. Some such variation is environmentally‐induced and erased each generation; other variation appears transgenerationally heritable, some of which might be independent of DNA sequence (Ledón‐Rettig et al ). Already we know that variation in DNA methylation patterns are quite extensive across the geographic range of house sparrows.…”

“…Our interest in the present study is to explore more directly whether DNA methylation might facilitate plasticity and hence allow for rapid phenotypic matching to local conditions (Kilvitis et al , Hawes et al 2018). The phenotypes of Kenyan house sparrow populations are quite variable (Liebl and Martin , 2013, 2014, Martin and Liebl , Martin et al , 2015), despite the recency of the expansion and extensive admixture (Schrey et al ). For example, distance from Mombasa, the site of initial introduction (and hence a proxy for population age), was a significant predictor of variation in Toll‐like receptor 4 ( TLR4 ) expression (Liebl et al , Martin et al ).…”