{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T06:45:00Z","timestamp":1777531500641,"version":"3.51.4"},"reference-count":88,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2013,11,27]],"date-time":"2013-11-27T00:00:00Z","timestamp":1385510400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0081864","type":"journal-article","created":{"date-parts":[[2013,11,27]],"date-time":"2013-11-27T23:48:17Z","timestamp":1385596097000},"page":"e81864","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":30,"title":["Positive Evolutionary Selection On the RIG-I-Like Receptor Genes in Mammals"],"prefix":"10.1371","volume":"8","author":[{"given":"Ana","family":"Lemos de Matos","sequence":"first","affiliation":[]},{"given":"Grant","family":"McFadden","sequence":"additional","affiliation":[]},{"given":"Pedro J.","family":"Esteves","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2013,11,27]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1038\/nature02021","article-title":"The immune response of Drosophila","volume":"426","author":"JA Hoffmann","year":"2003","journal-title":"Nature"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1016\/j.cell.2006.02.015","article-title":"Pathogen recognition and innate immunity","volume":"124","author":"S Akira","year":"2006","journal-title":"Cell"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1093\/intimm\/dxp017","article-title":"The roles of TLRs, RLRs and NLRs in pathogen recognition","volume":"21","author":"T Kawai","year":"2009","journal-title":"Int Immunol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1101\/SQB.1989.054.01.003","article-title":"Approaching the asymptote? Evolution and revolution in immunology","volume":"54","author":"CA Janeway Jr.","year":"1989","journal-title":"Cold Spring Harb Symp Quant Biol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1056\/NEJM200008033430506","article-title":"Innate immunity","volume":"343","author":"R Medzhitov","year":"2000","journal-title":"N Engl J Med"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1038\/nature06246","article-title":"Recognition of microorganisms and activation of the immune response","volume":"449","author":"R Medzhitov","year":"2007","journal-title":"Nature"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1038\/icb.2008.55","article-title":"Dendritic cells and C-type lectin receptors: coupling innate to adaptive immune responses","volume":"86","author":"SJ van Vliet","year":"2008","journal-title":"Immunol Cell Biol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.ejcb.2011.01.011","article-title":"Regulation of RLR-mediated innate immune signaling--it is all about keeping the balance","volume":"91","author":"K Eisen\u00e4cher","year":"2012","journal-title":"Eur J Cell Biol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1038\/ni1303","article-title":"Innate immune recognition of viral infection","volume":"7","author":"T Kawai","year":"2006","journal-title":"Nat Immunol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"2851","DOI":"10.4049\/jimmunol.175.5.2851","article-title":"Shared and unique functions of the DExD\/H-box helicases RIG-I, MDA5, and LGP2 in antiviral innate immunity","volume":"175","author":"M Yoneyama","year":"2005","journal-title":"J Immunol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"9700","DOI":"10.1074\/jbc.M807365200","article-title":"Regulation of signal transduction by enzymatically inactive antiviral RNA helicase proteins MDA5, RIG-I, and LGP2","volume":"284","author":"D Bamming","year":"2009","journal-title":"J Biol Chem"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1111\/j.1600-065X.2011.01052.x","article-title":"RIG-I-like receptors: cytoplasmic sensors for non-self","volume":"243","author":"H Kato","year":"2011","journal-title":"RNA - Immunol Rev"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"680","DOI":"10.1016\/j.immuni.2011.05.003","article-title":"Immune signaling by RIG-I-like receptors","volume":"34","author":"YM Loo","year":"2011","journal-title":"Immunity"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/B978-0-12-410524-9.00004-9","article-title":"Intracellular Pathogen Detection by RIG-I-Like Receptors","volume":"117","author":"E Dixit","year":"2013","journal-title":"Adv Immunol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"194","DOI":"10.3109\/10409238.2011.630974","article-title":"Activation of RIG-I-like receptor signal transduction","volume":"47","author":"AM Bruns","year":"2012","journal-title":"Crit Rev Biochem Mol Biol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.ejcb.2011.01.015","article-title":"Sensing of viral nucleic acids by RIG-I: from translocation to translation","volume":"91","author":"A Schmidt","year":"2012","journal-title":"Eur J Cell Biol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1038\/ni1087","article-title":"The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses","volume":"5","author":"M Yoneyama","year":"2004","journal-title":"Nat Immunol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1073\/pnas.0606699104","article-title":"Regulation of innate antiviral defenses through a shared repressor domain in RIG-I and LGP2","volume":"104","author":"T Saito","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"5260","DOI":"10.4049\/jimmunol.175.8.5260","article-title":"The RNA helicase Lgp2 inhibits TLR-independent sensing of viral replication by retinoic acid-inducible gene-I","volume":"175","author":"S Rothenfusser","year":"2005","journal-title":"J Immunol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"6444","DOI":"10.4049\/jimmunol.178.10.6444","article-title":"Loss of DExD\/H box RNA helicase LGP2 manifests disparate antiviral responses","volume":"178","author":"T Venkataraman","year":"2007","journal-title":"J Immunol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1512","DOI":"10.1073\/pnas.0912986107","article-title":"LGP2 is a positive regulator of RIG-I- and MDA5-mediated antiviral responses","volume":"107","author":"T Satoh","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nature04734","article-title":"Differential roles of MDA5 and RIG-I helicases in the recognition of RNA viruses","volume":"441","author":"H Kato","year":"2006","journal-title":"Nature"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1126\/science.1132505","article-title":"5'-Triphosphate RNA is the ligand for RIG-I","volume":"314","author":"V Hornung","year":"2006","journal-title":"Science"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1126\/science.1132998","article-title":"RIG-I-mediated antiviral responses to single-stranded RNA bearing 5'-phosphates","volume":"314","author":"A Pichlmair","year":"2006","journal-title":"Science"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/j.immuni.2009.05.008","article-title":"Recognition of 5' triphosphate by RIG-I helicase requires short blunt double-stranded RNA as contained in panhandle of negative-strand virus","volume":"31","author":"M Schlee","year":"2009","journal-title":"Immunity"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"16303","DOI":"10.1073\/pnas.1005077107","article-title":"Preference of RIG-I for short viral RNA molecules in infected cells revealed by next-generation sequencing","volume":"107","author":"A Baum","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1111\/cmi.12061","article-title":"Structural basis of innate immune recognition of viral","volume":"15","author":"IC Berke","year":"2013","journal-title":"RNA - Cell Microbiol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"e2032","DOI":"10.1371\/journal.pone.0002032","article-title":"Processing of genome 5' termini as a strategy of negative-strand RNA viruses to avoid RIG-I-dependent interferon induction","volume":"3","author":"M Habjan","year":"2008","journal-title":"PLOS ONE"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"2689","DOI":"10.1128\/JVI.79.5.2689-2699.2005","article-title":"Regulating intracellular antiviral defense and permissiveness to hepatitis C virus RNA replication through a cellular RNA helicase, RIG-I","volume":"79","author":"R Sumpter Jr.","year":"2005","journal-title":"J Virol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1128\/JVI.01080-07","article-title":"Distinct RIG-I and MDA5 signaling by RNA viruses in innate immunity","volume":"82","author":"YM Loo","year":"2008","journal-title":"J Virol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"e279","DOI":"10.1371\/journal.pone.0000279","article-title":"Cytosolic 5'-triphosphate ended viral leader transcript of measles virus as activator of the RIG I-mediated interferon response","volume":"2","author":"S Plumet","year":"2007","journal-title":"PLOS ONE"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"8459","DOI":"10.1073\/pnas.0603082103","article-title":"Essential role of mda-5 in type I IFN responses to polyriboinosinic:polyribocytidylic acid and encephalomyocarditis picornavirus","volume":"103","author":"L Gitlin","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"e1000108","DOI":"10.1371\/journal.ppat.1000108","article-title":"MDA-5 recognition of a murine norovirus","volume":"4","author":"SA McCartney","year":"2008","journal-title":"PLoS Pathog"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"9829","DOI":"10.1128\/JVI.01199-08","article-title":"Murine coronavirus mouse hepatitis virus is recognized by MDA5 and induces type I interferon in brain macrophages\/microglia","volume":"82","author":"JK Roth-Cross","year":"2008","journal-title":"J Virol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1128\/JVI.01305-07","article-title":"Establishment and maintenance of the innate antiviral response to West Nile Virus involves both RIG-I and MDA5 signaling through IPS-1","volume":"82","author":"BL Fredericksen","year":"2008","journal-title":"J Virol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1038\/ni.1779","article-title":"RIG-I-dependent sensing of poly(dA:dT) through the induction of an RNA polymerase III-transcribed RNA intermediate","volume":"10","author":"A Ablasser","year":"2009","journal-title":"Nat Immunol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.cell.2009.06.015","article-title":"RNA polymerase III detects cytosolic DNA and induces type I interferons through the RIG-I pathway","volume":"138","author":"YH Chiu","year":"2009","journal-title":"Cell"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"4207","DOI":"10.1038\/sj.emboj.7601314","article-title":"EB virus-encoded RNAs are recognized by RIG-I and activate signaling to induce type I IFN","volume":"25","author":"M Samanta","year":"2006","journal-title":"EMBO J"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"e1000099","DOI":"10.1371\/journal.ppat.1000099","article-title":"RIG-I mediates the co-induction of tumor necrosis factor and type I interferon elicited by myxoma virus in primary human macrophages","volume":"4","author":"F Wang","year":"2008","journal-title":"PLoS Pathog"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"10761","DOI":"10.1128\/JVI.00770-09","article-title":"Activation of MDA5 requires higher-order RNA structures generated during virus infection","volume":"83","author":"A Pichlmair","year":"2009","journal-title":"J Virol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1007\/s00239-003-2506-6","article-title":"The evolution of parasite recognition genes in the innate immune system: purifying selection on Drosophila melanogaster peptidoglycan recognition proteins","volume":"57","author":"FM Jiggins","year":"2003","journal-title":"J Mol Evol"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1016\/j.tim.2011.03.006","article-title":"Two-stepping through time: mammals and viruses","volume":"19","author":"NR Meyerson","year":"2011","journal-title":"Trends Microbiol"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1186\/1471-2148-11-368","article-title":"Signatures of positive selection in Toll-like receptor (TLR) genes in mammals","volume":"11","author":"H Areal","year":"2011","journal-title":"BMC Evol Biol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1101\/gr.085951.108","article-title":"Adaptive evolution of young gene duplicates in mammals","volume":"19","author":"MV Han","year":"2009","journal-title":"Genome Res"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1186\/1471-2148-11-342","article-title":"Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals","volume":"11","author":"JP Machado","year":"2011","journal-title":"BMC Evol Biol"},{"key":"ref46","first-page":"958164","article-title":"Positive Selection and the Evolution of izumo Genes in Mammals","volume":"7","author":"P Grayson","year":"2012","journal-title":"International - Journal of Evolutionary Biology"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1186\/1471-2148-13-121","article-title":"Evolution and divergence of the mammalian SAMD9\/SAMD9L gene family","volume":"13","author":"A Lemos de Matos","year":"2013","journal-title":"BMC Evol Biol"},{"key":"ref48","article-title":"Maximum-likelihood approaches reveal signatures of positive selection in IL genes in mammals. Innate","author":"F Neves","year":"2013","journal-title":"Immun"},{"key":"ref49","article-title":"Computational analyses of an evolutionary arms race between mammalian immunity mediated by immunoglobulin A and its subversion by bacterial pathogens","author":"A Pinheiro","year":"2013","journal-title":"PLOS ONE"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"1891","DOI":"10.1093\/molbev\/msl051","article-title":"Automated phylogenetic detection of recombination using a genetic algorithm","volume":"23","author":"SL Kosakovsky Pond","year":"2006","journal-title":"Mol Biol Evol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"3096","DOI":"10.1093\/bioinformatics\/btl474","article-title":"GARD: a genetic algorithm for recombination detection","volume":"22","author":"SL Kosakovsky Pond","year":"2006","journal-title":"Bioinformatics"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"2531","DOI":"10.1093\/bioinformatics\/bti320","article-title":"Datamonkey: rapid detection of selective pressure on individual sites of codon alignments","volume":"21","author":"SL Pond","year":"2005","journal-title":"Bioinformatics"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"2455","DOI":"10.1093\/bioinformatics\/btq429","article-title":"Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology","volume":"26","author":"W Delport","year":"2010","journal-title":"Bioinformatics"},{"key":"ref54","first-page":"555","article-title":"PAML: a program package for phylogenetic analysis by maximum likelihood","volume":"13","author":"Z Yang","year":"1997","journal-title":"Comput Appl Biosci"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: phylogenetic analysis by maximum likelihood","volume":"24","author":"Z Yang","year":"2007","journal-title":"Mol Biol Evol"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1093\/oxfordjournals.molbev.a025957","article-title":"Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution","volume":"15","author":"Z Yang","year":"1998","journal-title":"Mol Biol Evol"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"2493","DOI":"10.1093\/bioinformatics\/btl427","article-title":"Robust inference of positive selection from recombining coding sequences","volume":"22","author":"K Scheffler","year":"2006","journal-title":"Bioinformatics"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"1585","DOI":"10.1093\/oxfordjournals.molbev.a003945","article-title":"Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution","volume":"18","author":"M Anisimova","year":"2001","journal-title":"Mol Biol Evol"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"1675","DOI":"10.1093\/molbev\/mst062","article-title":"The Branch-Site Test of Positive Selection Is Surprisingly Robust but Lacks Power under Synonymous Substitution Saturation and Variation in GC","volume":"30","author":"WH Gharib","year":"2013","journal-title":"Mol Biol Evol"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"2531","DOI":"10.1093\/molbev\/msi250","article-title":"A Bayesian model comparison approach to inferring positive selection","volume":"22","author":"K Scheffler","year":"2005","journal-title":"Mol Biol Evol"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"1208","DOI":"10.1093\/molbev\/msi105","article-title":"Not so different after all: a comparison of methods for detecting amino acid sites under selection","volume":"22","author":"SL Kosakovsky Pond","year":"2005","journal-title":"Mol Biol Evol"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"e1002764","DOI":"10.1371\/journal.pgen.1002764","article-title":"Detecting individual sites subject to episodic diversifying selection","volume":"8","author":"B Murrell","year":"2012","journal-title":"PLoS Genet"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1093\/molbev\/mst030","article-title":"FUBAR: a fast, unconstrained bayesian approximation for inferring selection","volume":"30","author":"B Murrell","year":"2013","journal-title":"Mol Biol Evol"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"2172","DOI":"10.1093\/molbev\/msq104","article-title":"Adaptation and constraint at Toll-like receptors in primates","volume":"27","author":"G Wlasiuk","year":"2010","journal-title":"Mol Biol Evol"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1093\/molbev\/msm042","article-title":"Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites","volume":"24","author":"M Anisimova","year":"2007","journal-title":"Mol Biol Evol"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"2472","DOI":"10.1093\/molbev\/msi237","article-title":"Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level","volume":"22","author":"J Zhang","year":"2005","journal-title":"Mol Biol Evol"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"3033","DOI":"10.1093\/molbev\/msr125","article-title":"A random effects branch-site model for detecting episodic diversifying selection","volume":"28","author":"SL Kosakovsky Pond","year":"2011","journal-title":"Mol Biol Evol"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"4462","DOI":"10.1093\/hmg\/ddr377","article-title":"The selective footprints of viral pressures at the human RIG-I-like receptor family","volume":"20","author":"E Vasseur","year":"2011","journal-title":"Hum Mol Genet"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"136","DOI":"10.3389\/fimmu.2012.00136","article-title":"Dynamic evolution of toll-like receptor multigene families in echinoderms","volume":"3","author":"KM Buckley","year":"2012","journal-title":"Front Immunol"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"1703","DOI":"10.1093\/molbev\/msq351","article-title":"Molecular evolution of the toll-like receptor multigene family in birds","volume":"28","author":"M Alcaide","year":"2011","journal-title":"Mol Biol Evol"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"e1000562","DOI":"10.1371\/journal.pgen.1000562","article-title":"Evolutionary dynamics of human Toll-like receptors and their different contributions to host defense","volume":"5","author":"LB Barreiro","year":"2009","journal-title":"PLoS Genet"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1186\/1471-2148-8-288","article-title":"Molecular evolution of bovine Toll-like receptor 2 suggests substitutions of functional relevance","volume":"8","author":"OC Jann","year":"2008","journal-title":"BMC Evol Biol"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1007\/s00251-008-0332-0","article-title":"Natural selection in the TLR-related genes in the course of primate evolution","volume":"60","author":"T Nakajima","year":"2008","journal-title":"Immunogenetics"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1093\/molbev\/msp018","article-title":"A history of recurrent positive selection at the toll-like receptor 5 in primates","volume":"26","author":"G Wlasiuk","year":"2009","journal-title":"Mol Biol Evol"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1093\/genetics\/142.3.1033","article-title":"Synonymous nucleotide divergence: what is "saturation"?","volume":"142","author":"JM Smith","year":"1996","journal-title":"Genetics"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1080\/10635150802158670","article-title":"Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins","volume":"57","author":"TK Seo","year":"2008","journal-title":"Syst Biol"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1038\/ni1243","article-title":"IPS-1, an adaptor triggering RIG-I- and Mda5-mediated type I interferon induction","volume":"6","author":"T Kawai","year":"2005","journal-title":"Nat Immunol"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1016\/j.molcel.2007.11.028","article-title":"Nonself RNA-sensing mechanism of RIG-I helicase and activation of antiviral immune responses","volume":"29","author":"K Takahasi","year":"2008","journal-title":"Mol Cell"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1016\/j.sbi.2010.03.011","article-title":"SF1 and SF2 helicases: family matters","volume":"20","author":"ME Fairman-Williams","year":"2010","journal-title":"Curr Opin Struct Biol"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1016\/j.molcel.2007.10.032","article-title":"The C-terminal regulatory domain is the RNA 5'-triphosphate sensor of RIG-I","volume":"29","author":"S Cui","year":"2008","journal-title":"Mol Cell"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"JD Thompson","year":"1994","journal-title":"Nucleic Acids Res"},{"key":"ref82","first-page":"95","article-title":"BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95\/98\/NT","volume":"41","author":"T Hall","year":"1999","journal-title":"Nucleic Acids Symp Ser"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1007\/s00239-001-0034-9","article-title":"The effect of recombination on the accuracy of phylogeny estimation","volume":"54","author":"D Posada","year":"2002","journal-title":"J Mol Evol"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"1253","DOI":"10.1093\/molbev\/msn083","article-title":"jModelTest: phylogenetic model averaging","volume":"25","author":"D Posada","year":"2008","journal-title":"Mol Biol Evol"},{"key":"ref85","article-title":"Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion","author":"DJ Zwickl","year":"2006"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1093\/genetics\/148.3.929","article-title":"Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene","volume":"148","author":"R Nielsen","year":"1998","journal-title":"Genetics"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1093\/genetics\/155.1.431","article-title":"Codon-substitution models for heterogeneous selection pressure at amino acid sites","volume":"155","author":"Z Yang","year":"2000","journal-title":"Genetics"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1093\/molbev\/msi097","article-title":"Bayes empirical bayes inference of amino acid sites under positive selection","volume":"22","author":"Z Yang","year":"2005","journal-title":"Mol Biol Evol"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0081864","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,17]],"date-time":"2022-03-17T21:59:41Z","timestamp":1647554381000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0081864"}},"subtitle":[],"editor":[{"given":"Welkin\u00a0E.","family":"Johnson","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2013,11,27]]},"references-count":88,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2013,11,27]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0081864","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,11,27]]}}}