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Members of the family Suidae have diverged over extended evolutionary periods in diverse environments, suggesting that adaptation in response to endemic infectious agents may have occurred. Toll-like receptors (TLRs) comprise a multigene family that acts as the first line of defense against infectious microbes at the host-environment interface. We hypothesized that across the Suidae, positive selection mediated by infectious agents has contributed to the evolution of TLR diversity. Thus, we analyzed  Sus scrofa ,  Sus barbatus ,  Sus verrucosus ,  Sus celebensis ,  Sus scebifrons ,  Babyrousa babyrussa ,  Potamochoerus larvatus ,  Potamochoerus porcus  and  Phacochoerus africanus  genomes. 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. Our analyses did not reveal evidence of positive selection for  TLR3  and  TLR7 , suggesting strong functional conservation among these two genes for members of the Suidae. Positive selection was inferred for Suidae  TLR1 ,  TLR2 ,  TLR6  and  TLR8  evolution. ML methods identified amino acid sites of the bacterial sensing  TLR1 ,  TLR2 ,  TLR6  and the viral sensing  TLR8  to be under persistent positive selection. Some of these sites are in close proximity to functionally relevant sites, further strengthening the case for pathogen mediated selection for these sites. The branch leading to the genus  Sus  demonstrated evidence of episodic positive selection for  TLR1 , indicating selection mediated by infectious agents encountered within the specific geographic origin of the  Sus . These results indicate that species of the Suidae have positively selected residues within functional domains of TLRs reflective of prior infections. Thus, TLR genes represent candidates for experimental validation to determine their functional role in antibacterial and antiviral activity within members of the Suidae.

Adaptive Evolution of Toll-Like Receptors (TLRs) in the Family Suidae