title: Adaptive Evolution of Toll-Like Receptors (TLRs) in the Family Suidae.
abstract: 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.
authors.affiliation: Department of Animal Sciences, University of Illinois, Urbana-Champaign, Illinois, United States of America.
authors.forename: Kwame A
authors.initials: KA
authors.lastname: Darfour-Oduro
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands.
authors.forename: Hendrik-Jan
authors.initials: HJ
authors.lastname: Megens
authors.affiliation: Department of Animal Sciences, University of Illinois, Urbana-Champaign, Illinois, United States of America.
authors.forename: Alfred L
authors.initials: AL
authors.lastname: Roca
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands.
authors.forename: Martien A M
authors.initials: MA
authors.lastname: Groenen
authors.affiliation: Department of Animal Sciences, University of Illinois, Urbana-Champaign, Illinois, United States of America.
authors.forename: Lawrence B
authors.initials: LB
authors.lastname: Schook
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D000818:Animals; D003062:Codon; D019143:Evolution, Molecular; D005843:Geography; D016013:Likelihood Functions; D005810:Multigene Family; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D017422:Sequence Analysis, DNA; D034421:Sus scrofa / Q000235:genetics; D013552:Swine / Q000235:genetics*; D051193:Toll-Like Receptors / Q000235:genetics* / Q000378:metabolism
chemical_list: D000596:Amino Acids; D003062:Codon; D051193:Toll-Like Receptors