{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T09:13:53Z","timestamp":1774689233233,"version":"3.50.1"},"reference-count":106,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2009,7,17]],"date-time":"2009-07-17T00:00:00Z","timestamp":1247788800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"DOI":"10.1371\/journal.pgen.1000562","type":"journal-article","created":{"date-parts":[[2009,7,16]],"date-time":"2009-07-16T22:04:52Z","timestamp":1247781892000},"page":"e1000562","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":348,"title":["Evolutionary Dynamics of Human Toll-Like Receptors and Their Different Contributions to Host Defense"],"prefix":"10.1371","volume":"5","author":[{"given":"Luis B.","family":"Barreiro","sequence":"first","affiliation":[]},{"given":"Meriem","family":"Ben-Ali","sequence":"additional","affiliation":[]},{"given":"H\u00e9l\u00e8ne","family":"Quach","sequence":"additional","affiliation":[]},{"given":"Guillaume","family":"Laval","sequence":"additional","affiliation":[]},{"given":"Etienne","family":"Patin","sequence":"additional","affiliation":[]},{"given":"Joseph K.","family":"Pickrell","sequence":"additional","affiliation":[]},{"given":"Christiane","family":"Bouchier","sequence":"additional","affiliation":[]},{"given":"Magali","family":"Tichit","sequence":"additional","affiliation":[]},{"given":"Olivier","family":"Neyrolles","sequence":"additional","affiliation":[]},{"given":"Brigitte","family":"Gicquel","sequence":"additional","affiliation":[]},{"given":"Judith R.","family":"Kidd","sequence":"additional","affiliation":[]},{"given":"Kenneth K.","family":"Kidd","sequence":"additional","affiliation":[]},{"given":"Alexandre","family":"Alca\u00efs","sequence":"additional","affiliation":[]},{"given":"Josiane","family":"Ragimbeau","sequence":"additional","affiliation":[]},{"given":"Sandra","family":"Pellegrini","sequence":"additional","affiliation":[]},{"given":"Laurent","family":"Abel","sequence":"additional","affiliation":[]},{"given":"Jean-Laurent","family":"Casanova","sequence":"additional","affiliation":[]},{"given":"Llu\u00eds","family":"Quintana-Murci","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2009,7,17]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1146\/annurev.immunol.25.022106.141615","article-title":"The host defense of Drosophila melanogaster.","volume":"25","author":"B Lemaitre","year":"2007","journal-title":"Annu Rev Immunol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1146\/annurev.immunol.20.083001.084359","article-title":"Innate immune recognition.","volume":"20","author":"CA Janeway Jr.","year":"2002","journal-title":"Annu Rev Immunol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/S0092-8674(00)80412-2","article-title":"Innate immunity: the virtues of a nonclonal system of recognition.","volume":"91","author":"R Medzhitov","year":"1997","journal-title":"Cell"},{"key":"ref4","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":"ref5","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1038\/nri1004","article-title":"Innate immune sensing and its roots: the story of endotoxin.","volume":"3","author":"B Beutler","year":"2003","journal-title":"Nat Rev Immunol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1038\/35066006","article-title":"The evolution and genetics of innate immunity.","volume":"2","author":"DA Kimbrell","year":"2001","journal-title":"Nat Rev Genet"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1038\/90609","article-title":"Toll-like receptors: critical proteins linking innate and acquired immunity.","volume":"2","author":"S Akira","year":"2001","journal-title":"Nat Immunol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.smim.2006.12.004","article-title":"TLR signaling.","volume":"19","author":"T Kawai","year":"2007","journal-title":"Semin Immunol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1038\/35100529","article-title":"Toll-like receptors and innate immunity.","volume":"1","author":"R Medzhitov","year":"2001","journal-title":"Nat Rev Immunol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1016\/0092-8674(85)90275-2","article-title":"Establishment of dorsal-ventral polarity in the Drosophila embryo: the induction of polarity by the Toll gene product.","volume":"42","author":"KV Anderson","year":"1985","journal-title":"Cell"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1038\/nri1390","article-title":"The road to Toll.","volume":"4","author":"B Lemaitre","year":"2004","journal-title":"Nat Rev Immunol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1016\/S0092-8674(00)80172-5","article-title":"The dorsoventral regulatory gene cassette spatzle\/Toll\/cactus controls the potent antifungal response in Drosophila adults.","volume":"86","author":"B Lemaitre","year":"1996","journal-title":"Cell"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"9577","DOI":"10.1073\/pnas.0502272102","article-title":"The evolution of vertebrate Toll-like receptors.","volume":"102","author":"JC Roach","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1038\/nrg2303","article-title":"Toll-like receptors\u2013taking an evolutionary approach.","volume":"9","author":"F Leulier","year":"2008","journal-title":"Nat Rev Genet"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1038\/sj.gene.6363937","article-title":"Toll-like receptors and their role in experimental models of microbial infection.","volume":"4","author":"ST Qureshi","year":"2003","journal-title":"Genes Immun"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"2085","DOI":"10.1126\/science.282.5396.2085","article-title":"Defective LPS signaling in C3H\/HeJ and C57BL\/10ScCr mice: mutations in Tlr4 gene.","volume":"282","author":"A Poltorak","year":"1998","journal-title":"Science"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"1366","DOI":"10.1038\/nm1140","article-title":"Toll-like receptor 3 mediates West Nile virus entry into the brain causing lethal encephalitis.","volume":"10","author":"T Wang","year":"2004","journal-title":"Nat Med"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1146\/annurev.immunol.24.021605.090552","article-title":"Genetic analysis of host resistance: Toll-like receptor signaling and immunity at large.","volume":"24","author":"B Beutler","year":"2006","journal-title":"Annu Rev Immunol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1038\/nature02761","article-title":"Inferences, questions and possibilities in Toll-like receptor signalling.","volume":"430","author":"B Beutler","year":"2004","journal-title":"Nature"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1146\/annurev.cellbio.21.122303.115827","article-title":"Recognition and signaling by toll-like receptors.","volume":"22","author":"AP West","year":"2006","journal-title":"Annu Rev Cell Dev Biol"},{"key":"ref21","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":"ref22","doi-asserted-by":"crossref","first-page":"2076","DOI":"10.1126\/science.1081902","article-title":"Pyogenic bacterial infections in humans with IRAK-4 deficiency.","volume":"299","author":"C Picard","year":"2003","journal-title":"Science"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1126\/science.1158298","article-title":"Pyogenic bacterial infections in humans with MyD88 deficiency.","volume":"321","author":"H von Bernuth","year":"2008","journal-title":"Science"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"2407","DOI":"10.1084\/jem.20070628","article-title":"Selective predisposition to bacterial infections in IRAK-4 deficient children: IRAK-4 dependent TLRs are otherwise redundant in protective immunity.","volume":"204","author":"CL Ku","year":"2007","journal-title":"J Exp Med"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1126\/science.1128346","article-title":"Herpes simplex virus encephalitis in human UNC-93B deficiency.","volume":"314","author":"A Casrouge","year":"2006","journal-title":"Science"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1522","DOI":"10.1126\/science.1139522","article-title":"TLR3 deficiency in patients with herpes simplex encephalitis.","volume":"317","author":"SY Zhang","year":"2007","journal-title":"Science"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1016\/S1473-3099(07)70185-8","article-title":"Innate immunogenetics: a tool for exploring new frontiers of host defence.","volume":"7","author":"PY Bochud","year":"2007","journal-title":"Lancet Infect Dis"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1146\/annurev.genet.39.073003.112420","article-title":"Molecular signatures of natural selection.","volume":"39","author":"R Nielsen","year":"2005","journal-title":"Annu Rev Genet"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1038\/nrg2187","article-title":"Recent and ongoing selection in the human genome.","volume":"8","author":"R Nielsen","year":"2007","journal-title":"Nat Rev Genet"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1614","DOI":"10.1126\/science.1124309","article-title":"Positive natural selection in the human lineage.","volume":"312","author":"PC Sabeti","year":"2006","journal-title":"Science"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1126\/science.1142963","article-title":"Primary immunodeficiencies: a field in its infancy.","volume":"317","author":"JL Casanova","year":"2007","journal-title":"Science"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.1038\/ni1535","article-title":"Immunology in natura: clinical, epidemiological and evolutionary genetics of infectious diseases.","volume":"8","author":"L Quintana-Murci","year":"2007","journal-title":"Nat Immunol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"952","DOI":"10.1016\/S0140-6736(04)15824-8","article-title":"Ancient footsteps in our genes: evolution and human disease. Gene variants selected during evolution may underlie many common diseases.","volume":"363","author":"J Bradbury","year":"2004","journal-title":"Lancet"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1146\/annurev.genom.3.022502.103149","article-title":"Balanced polymorphism selected by genetic versus infectious human disease.","volume":"3","author":"M Dean","year":"2002","journal-title":"Annu Rev Genomics Hum Genet"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"5897","DOI":"10.1073\/pnas.88.13.5897","article-title":"Heterozygosity at individual amino acid sites: extremely high levels for HLA-A and -B genes.","volume":"88","author":"PW Hedrick","year":"1991","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1038\/335167a0","article-title":"Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection.","volume":"335","author":"AL Hughes","year":"1988","journal-title":"Nature"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1093\/genetics\/130.4.925","article-title":"Polymorphism and balancing selection at major histocompatibility complex loci.","volume":"130","author":"N Takahata","year":"1992","journal-title":"Genetics"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1084\/jem.20051884","article-title":"Roles for HLA and KIR polymorphisms in natural killer cell repertoire selection and modulation of effector function.","volume":"203","author":"M Yawata","year":"2006","journal-title":"J Exp Med"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1136\/bmj.1.4857.290","article-title":"Protection afforded by sickle-cell trait against subtertian malareal infection.","volume":"1","author":"AC Allison","year":"1954","journal-title":"Br Med J"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"1591","DOI":"10.1534\/genetics.166.4.1591","article-title":"Two lessons from the interface of genetics and medicine.","volume":"166","author":"AC Allison","year":"2004","journal-title":"Genetics"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0950-3536(98)80069-3","article-title":"The population genetics of the haemoglobinopathies.","volume":"11","author":"J Flint","year":"1998","journal-title":"Baillieres Clin Haematol"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1084\/jem.180.2.497","article-title":"Identification of the erythrocyte binding domains of Plasmodium vivax and Plasmodium knowlesi proteins involved in erythrocyte invasion.","volume":"180","author":"CE Chitnis","year":"1994","journal-title":"J Exp Med"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1038\/ng0695-224","article-title":"Disruption of a GATA motif in the Duffy gene promoter abolishes erythroid gene expression in Duffy-negative individuals.","volume":"10","author":"C Tournamille","year":"1995","journal-title":"Nat Genet"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1111\/j.0105-2896.2005.00235.x","article-title":"Inherited disorders of human Toll-like receptor signaling: immunological implications.","volume":"203","author":"CL Ku","year":"2005","journal-title":"Immunol Rev"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1038\/ng1113","article-title":"The application of molecular genetic approaches to the study of human evolution.","volume":"33","author":"LL Cavalli-Sforza","year":"2003","journal-title":"Nat Genet"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1292","DOI":"10.1126\/science.3114877","article-title":"Africa: cradle of modern humans.","volume":"237","author":"R Lewin","year":"1987","journal-title":"Science"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"1161","DOI":"10.1093\/genetics\/132.4.1161","article-title":"Population genetics of polymorphism and divergence.","volume":"132","author":"SA Sawyer","year":"1992","journal-title":"Genetics"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1038\/416531a","article-title":"The cost of inbreeding in Arabidopsis.","volume":"416","author":"CD Bustamante","year":"2002","journal-title":"Nature"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"1153","DOI":"10.1038\/nature04240","article-title":"Natural selection on protein-coding genes in the human genome.","volume":"437","author":"CD Bustamante","year":"2005","journal-title":"Nature"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1086\/378132","article-title":"Natural selection on the olfactory receptor gene family in humans and chimpanzees.","volume":"73","author":"Y Gilad","year":"2003","journal-title":"Am J Hum Genet"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1016\/j.immuni.2007.08.012","article-title":"Innate recognition of viruses.","volume":"27","author":"A Pichlmair","year":"2007","journal-title":"Immunity"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"3894","DOI":"10.1093\/nar\/gkf493","article-title":"Human non-synonymous SNPs: server and survey.","volume":"30","author":"V Ramensky","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1017\/S0016672399003870","article-title":"Recombination and the power of statistical tests of neutrality.","volume":"74","author":"JD Wall","year":"1999","journal-title":"Genet Res Camb"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1146\/annurev.genom.1.1.539","article-title":"Methods to detect selection in populations with applications to the human.","volume":"1","author":"M Kreitman","year":"2000","journal-title":"Annu Rev Genomics Hum Genet"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"18508","DOI":"10.1073\/pnas.0507325102","article-title":"Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes.","volume":"102","author":"BF Voight","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1093\/genetics\/131.2.479","article-title":"Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data.","volume":"131","author":"L Excoffier","year":"1992","journal-title":"Genetics"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"1358","DOI":"10.2307\/2408641","article-title":"Estimating F-statistics for the analysis of population structure.","volume":"38","author":"CL Weir","year":"1984","journal-title":"Evolution"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1038\/ng.78","article-title":"Natural selection has driven population differentiation in modern humans.","volume":"40","author":"LB Barreiro","year":"2008","journal-title":"Nat Genet"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1038\/nature06258","article-title":"A second generation human haplotype map of over 3.1 million SNPs.","volume":"449","author":"KA Frazer","year":"2007","journal-title":"Nature"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"1299","DOI":"10.1038\/nature04226","article-title":"A haplotype map of the human genome.","volume":"437","year":"2005","journal-title":"Nature"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1038\/nature01140","article-title":"Detecting recent positive selection in the human genome from haplotype structure.","volume":"419","author":"PC Sabeti","year":"2002","journal-title":"Nature"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1038\/nri2038","article-title":"Cooperation of Toll-like receptor signals in innate immune defence.","volume":"7","author":"G Trinchieri","year":"2007","journal-title":"Nat Rev Immunol"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1046\/j.1462-5822.2003.00356.x","article-title":"Stimulation of human Toll-like receptor (TLR) 2 and TLR6 with membrane lipoproteins of Mycoplasma fermentans induces apoptotic cell death after NF-kappa B activation.","volume":"6","author":"T Into","year":"2004","journal-title":"Cell Microbiol"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"e1318","DOI":"10.1371\/journal.pone.0001318","article-title":"Full-exon resequencing reveals toll-like receptor variants contribute to human susceptibility to tuberculosis disease.","volume":"2","author":"X Ma","year":"2007","journal-title":"PLoS ONE"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"6387","DOI":"10.4049\/jimmunol.178.10.6387","article-title":"The polymorphism P315L of human toll-like receptor 1 impairs innate immune sensing of microbial cell wall components.","volume":"178","author":"KO Omueti","year":"2007","journal-title":"J Immunol"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"2280","DOI":"10.1002\/eji.200737034","article-title":"A common human TLR1 polymorphism regulates the innate immune response to lipopeptides.","volume":"37","author":"TR Hawn","year":"2007","journal-title":"Eur J Immunol"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"7520","DOI":"10.4049\/jimmunol.178.12.7520","article-title":"Cutting edge: A common polymorphism impairs cell surface trafficking and functional responses of TLR1 but protects against leprosy.","volume":"178","author":"CM Johnson","year":"2007","journal-title":"J Immunol"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"4580","DOI":"10.1046\/j.1432-1327.2001.02385.x","article-title":"Essential roles of CD14 and lipopolysaccharide-binding protein for activation of toll-like receptor (TLR)2 as well as TLR4 Reconstitution of TLR2- and TLR4-activation by distinguishable ligands in LPS preparations.","volume":"268","author":"T Muta","year":"2001","journal-title":"Eur J Biochem"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1016\/j.mib.2008.05.001","article-title":"Natural selection on the Drosophila antimicrobial immune system.","volume":"11","author":"BP Lazzaro","year":"2008","journal-title":"Curr Opin Microbiol"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1016\/j.tig.2007.04.004","article-title":"A call to arms: coevolution of animal viruses and host innate immune responses.","volume":"23","author":"JT Marques","year":"2007","journal-title":"Trends Genet"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1016\/j.tig.2006.09.011","article-title":"Molecular evolution of plant immune system genes.","volume":"22","author":"P Tiffin","year":"2006","journal-title":"Trends Genet"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"1803","DOI":"10.1105\/tpc.106.042614","article-title":"A genome-wide survey of R gene polymorphisms in Arabidopsis.","volume":"18","author":"EG Bakker","year":"2006","journal-title":"Plant Cell"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1126\/science.1138632","article-title":"Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana.","volume":"317","author":"RM Clark","year":"2007","journal-title":"Science"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"1461","DOI":"10.1038\/ng.2007.60","article-title":"Dynamic evolution of the innate immune system in Drosophila.","volume":"39","author":"TB Sackton","year":"2007","journal-title":"Nat Genet"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"1471","DOI":"10.1093\/genetics\/164.4.1471","article-title":"Natural selection drives Drosophila immune system evolution.","volume":"164","author":"TA Schlenke","year":"2003","journal-title":"Genetics"},{"key":"ref76","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":"ref77","doi-asserted-by":"crossref","first-page":"2023","DOI":"10.1534\/genetics.104.034249","article-title":"Elevated polymorphism and divergence in the class C scavenger receptors of Drosophila melanogaster and D. simulans.","volume":"169","author":"BP Lazzaro","year":"2005","journal-title":"Genetics"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"7073","DOI":"10.1073\/pnas.0811357106","article-title":"Signatures of natural selection are not uniform across genes of innate immune system, but purifying selection is the dominant signature.","volume":"106","author":"S Mukherjee","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"1315","DOI":"10.4049\/jimmunol.181.2.1315","article-title":"Balancing selection is the main force shaping the evolution of innate immunity genes.","volume":"181","author":"A Ferrer-Admetlla","year":"2008","journal-title":"J Immunol"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1016\/j.immuni.2005.09.016","article-title":"Human TLR-7-, -8-, and -9-mediated induction of IFN-alpha\/beta and -lambda Is IRAK-4 dependent and redundant for protective immunity to viruses.","volume":"23","author":"K Yang","year":"2005","journal-title":"Immunity"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"pe47","DOI":"10.1126\/stke.4022007pe47","article-title":"Toll-like receptors in brain development and homeostasis.","volume":"2007","author":"PH Larsen","year":"2007","journal-title":"Sci STKE"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1083\/jcb.200606016","article-title":"Toll-like receptor 8 functions as a negative regulator of neurite outgrowth and inducer of neuronal apoptosis.","volume":"175","author":"Y Ma","year":"2006","journal-title":"J Cell Biol"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1038\/nri1957","article-title":"Toll-like receptors in systemic autoimmune disease.","volume":"6","author":"A Marshak-Rothstein","year":"2006","journal-title":"Nat Rev Immunol"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"6573","DOI":"10.4049\/jimmunol.177.10.6573","article-title":"Nucleic acid-sensing TLRs as modifiers of autoimmunity.","volume":"177","author":"JA Deane","year":"2006","journal-title":"J Immunol"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"1669","DOI":"10.1126\/science.1124978","article-title":"Autoreactive B cell responses to RNA-related antigens due to TLR7 gene duplication.","volume":"312","author":"P Pisitkun","year":"2006","journal-title":"Science"},{"key":"ref86","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":"ref87","doi-asserted-by":"crossref","first-page":"e52","DOI":"10.1371\/journal.pbio.0040052","article-title":"Gene losses during human origins.","volume":"4","author":"X Wang","year":"2006","journal-title":"PLoS Biol"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1016\/j.ajhg.2009.01.008","article-title":"A genome-wide survey of the prevalence and evolutionary forces acting on human nonsense SNPs.","volume":"84","author":"B Yngvadottir","year":"2009","journal-title":"Am J Hum Genet"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1086\/503116","article-title":"Spread of an inactive form of caspase-12 in humans is due to recent positive selection.","volume":"78","author":"Y Xue","year":"2006","journal-title":"Am J Hum Genet"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"2650","DOI":"10.1093\/hmg\/ddl193","article-title":"Evolutionary insights into the high worldwide prevalence of MBL2 deficiency alleles.","volume":"15","author":"P Verdu","year":"2006","journal-title":"Hum Mol Genet"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1007\/s00281-007-0078-z","article-title":"TLR5 and Ipaf: dual sensors of bacterial flagellin in the innate immune system.","volume":"29","author":"EA Miao","year":"2007","journal-title":"Semin Immunopathol"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"1657","DOI":"10.1093\/genetics\/158.4.1657","article-title":"Excess of rare amino acid polymorphisms in the Toll-like receptor 4 in humans.","volume":"158","author":"I Smirnova","year":"2001","journal-title":"Genetics"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1093\/genetics\/160.3.1179","article-title":"The signature of positive selection at randomly chosen loci.","volume":"160","author":"M Przeworski","year":"2002","journal-title":"Genetics"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"e231","DOI":"10.1371\/journal.pntd.0000231","article-title":"Human TLR1 Deficiency Is Associated with Impaired Mycobacterial Signaling and Protection from Leprosy Reversal Reaction.","volume":"2","author":"EA Misch","year":"2008","journal-title":"PLoS Negl Trop Dis"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1142\/S021972000300006X","article-title":"Automated identification of single nucleotide polymorphisms from sequencing data.","volume":"1","author":"M Takahashi","year":"2003","journal-title":"J Bioinform Comput Biol"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"1162","DOI":"10.1086\/379378","article-title":"A comparison of bayesian methods for haplotype reconstruction from population genotype data.","volume":"73","author":"M Stephens","year":"2003","journal-title":"Am J Hum Genet"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"2496","DOI":"10.1093\/bioinformatics\/btg359","article-title":"DnaSP, DNA polymorphism analyses by the coalescent and other methods.","volume":"19","author":"J Rozas","year":"2003","journal-title":"Bioinformatics"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1038\/ng917","article-title":"A high-resolution recombination map of the human genome.","volume":"31","author":"A Kong","year":"2002","journal-title":"Nat Genet"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"2485","DOI":"10.1093\/bioinformatics\/bth264","article-title":"SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history.","volume":"20","author":"G Laval","year":"2004","journal-title":"Bioinformatics"},{"key":"ref100","doi-asserted-by":"crossref","first-page":"652","DOI":"10.1038\/351652a0","article-title":"Adaptive protein evolution at the Adh locus in Drosophila.","volume":"351","author":"JH McDonald","year":"1991","journal-title":"Nature"},{"key":"ref101","doi-asserted-by":"crossref","first-page":"7882","DOI":"10.1073\/pnas.0502300102","article-title":"Simultaneous inference of selection and population growth from patterns of variation in the human genome.","volume":"102","author":"SH Williamson","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref102","doi-asserted-by":"crossref","first-page":"2129","DOI":"10.1101\/gr.772403","article-title":"PANTHER: a library of protein families and subfamilies indexed by function.","volume":"13","author":"PD Thomas","year":"2003","journal-title":"Genome Res"},{"key":"ref103","doi-asserted-by":"crossref","first-page":"D257","DOI":"10.1093\/nar\/gkj079","article-title":"SMART 5: domains in the context of genomes and networks.","volume":"34","author":"I Letunic","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref104","doi-asserted-by":"crossref","first-page":"1496","DOI":"10.1101\/gr.4107905","article-title":"Ascertainment bias in studies of human genome-wide polymorphism.","volume":"15","author":"AG Clark","year":"2005","journal-title":"Genome Res"},{"key":"ref105","doi-asserted-by":"crossref","first-page":"3673","DOI":"10.1093\/bioinformatics\/bth417","article-title":"SelSim: a program to simulate population genetic data with natural selection and recombination.","volume":"20","author":"CC Spencer","year":"2004","journal-title":"Bioinformatics"},{"key":"ref106","doi-asserted-by":"crossref","first-page":"2225","DOI":"10.1126\/science.1069424","article-title":"The structure of haplotype blocks in the human genome.","volume":"296","author":"SB Gabriel","year":"2002","journal-title":"Science"}],"container-title":["PLoS Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pgen.1000562","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,10,8]],"date-time":"2021-10-08T19:25:45Z","timestamp":1633721145000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1000562"}},"subtitle":[],"editor":[{"given":"Gil","family":"McVean","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2009,7,17]]},"references-count":106,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2009,7,17]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1000562","relation":{},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,7,17]]}}}