Members of the family Suidae have evolved and diverged over extended evolutionary periods and diverse environments. Such an evolutionary history suggests adaptation to endemic infectious agents may have occurred. We hypothesized that infectious agent mediated positive selection has contributed to the evolution of Suidae Toll-like receptors (TLRs), a multigene family that acts as the first line of defense against infectious microbes, at the host-environment interface. Thus, we analyzed Sus scrofa, Sus barbatus, Sus verrucosus, Sus celebensis, Sus scebifrons, Babyrousa babyrussa, Potamochoerus larvatus, Potamochoerus porcus and Phacochoerus africanus genomes for signatures of selection.
Specifically, analyses were performed to identify evidence of positive selection using Maximum likelihood (ML) methods within a phylogenetic framework for bacterial and viral sensing Suidae TLR extracellular domains. We observed both persistent and episodic diversifying selection having shaped Suidae TLR evolution. ML methods identified amino acid sites, within functional domains, of the bacterial sensing TLR1, TLR2, TLR6 and the viral sensing TLR8 to be under persistent positive selection. The branch leading to Sus clade: Sus cebifrons,Sus scrofa, Sus celebensis and Sus barbatus showed evidence of episodic diversifying selection at amino acid site 434 within TLR1, indicating selection mediated by infectious agents encountered within the geographic origin of the Sus. These results indicate that Suid species have positively selected residues within functional domains of TLRs reflective of previous infections.