Adaptation and Cryptic Pseudogenization in Penguin Toll-Like Receptors

Abstract

Penguins (Sphenisciformes) are an iconic order of flightless, diving seabirds distributed across a large latitudinal range in the Southern Hemisphere. The extensive area over which penguins are endemic is likely to have fostered variation in pathogen pressure, which in turn will have imposed differential selective pressures on the penguin immune system. At the front line of pathogen detection and response, the Toll-like receptors (TLRs) provide insight into host evolution in the face of microbial challenge. TLRs respond to conserved pathogen-associated molecular patterns and are frequently found to be under positive selection, despite retaining specificity for defined agonist classes. We undertook a comparative immunogenetics analysis of TLRs for all penguin species, and found evidence of adaptive evolution that was largely restricted to the cell surface expressed TLRs, with evidence of positive selection at, or near, key agonist-binding sites in TLR1B, TLR4 and TLR5. Intriguingly, TLR15, which is activated by fungal products, appeared to have been pseudogenized multiple times in the Eudyptes spp., but a full-length form was present as a rare haplotype at the population level. However, in vitro analysis revealed that even the full-length form of Eudyptes TLR15 was non-functional, indicating an ancestral cryptic pseudogenization prior to its eventual disruption multiple times in the Eudyptes lineage. This unusual pseudogenization event could provide an insight into immune adaptation to fungal pathogens such as Aspergillus, which is responsible for significant mortality in wild and captive bird populations.

Genomic insights into the secondary aquatic transition of penguins

“…Several of these genes might be under positive selection corresponding to host-pathogen coevolution. For instance, we confirm previous reports 53,54 that the bacterial-recognizing Toll-like receptors TLR4 and TLR5 (Figs. 4a and 5b) are positively selected in penguins.…”

Birth and death in terminal complement pathway

“…Sharma et al, 2020). Other lineage-specific gene loss events within specific clades of birds have also been identified (Fiddaman et al, 2022;Friocourt et al, 2017;Haimson et al, 2021;Huang et al, 2022;Wicher and Fries, 2006).…”

Comparative Genomics of the Waterfowl Innate Immune System

“…However, a study in chicken has shown that activation of TLR15 involves proteolytic cleavage of the LRR ectodomain ( de Zoete et al 2011 ), suggesting that genetic variation in this domain could be functionally neutral. In addition, TLR15 has been revealed to cryptically pseudogenize in some birds ( Fiddaman et al 2021 ) which could partially explain the high sequence variation detected in this gene. We did, however, not detect any signs of pseudogenization of TLR15 in the mallard genome, and a test for relaxation of selection pressure (implemented in Datamonkey) on TLR15 in the mallard versus all other investigated taxa was not significant ( K = 0.62, P = 0.67, LR = 0.18).…”