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A number of recent studies have shown that TLR genes (\n                    <jats:italic>Tlrs<\/jats:italic>\n                    ) often exhibit large polymorphism in natural populations. Yet, there is little knowledge on how this polymorphism is maintained and how it influences disease susceptibility in the wild. In previous work, we showed that some\n                    <jats:italic>Tlrs<\/jats:italic>\n                    exhibit similarly high levels of genetic diversity as genes of the Major Histocompatibility Complex (MHC), and signatures of contemporary balancing selection in roe deer (\n                    <jats:italic>Capreolus capreolus<\/jats:italic>\n                    ), the most abundant cervid species in Europe. Here, we investigated the evolutionary mechanisms by which pathogen\u2010mediated selection could shape this innate immunity genetic diversity by examining the relationships between\n                    <jats:italic>Tlr<\/jats:italic>\n                    (\n                    <jats:italic>Tlr2<\/jats:italic>\n                    ,\n                    <jats:italic>Tlr4<\/jats:italic>\n                    and\n                    <jats:italic>Tlr5<\/jats:italic>\n                    ) genotypes (heterozygosity status and presence of specific alleles) and infections with\n                    <jats:italic>Toxoplasma<\/jats:italic>\n                    and\n                    <jats:italic>Chlamydia<\/jats:italic>\n                    , two widespread intracellular pathogens known to cause reproductive failure in ungulates. We showed that\n                    <jats:italic>Toxoplasma<\/jats:italic>\n                    and\n                    <jats:italic>Chlamydia<\/jats:italic>\n                    exposures vary significantly across years and landscape features with few co\u2010infection events detected and that the two pathogens exert antagonistic selection on\n                    <jats:italic>Tlr2<\/jats:italic>\n                    polymorphism. By contrast, we found limited support for\n                    <jats:italic>Tlr<\/jats:italic>\n                    heterozygote advantage. Our study confirmed the importance of looking beyond\n                    <jats:italic>Mhc<\/jats:italic>\n                    genes in wildlife immunogenetic studies. It also emphasized the necessity to consider multiple pathogen challenges and their spatiotemporal variation to improve our understanding of vertebrate defence evolution against pathogens.\n                  <\/jats:p>","DOI":"10.1111\/jeb.13876","type":"journal-article","created":{"date-parts":[[2021,6,1]],"date-time":"2021-06-01T12:44:36Z","timestamp":1622551476000},"page":"1156-1166","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Pathogen\u2010mediated selection favours the maintenance of innate immunity gene polymorphism in a widespread wild ungulate"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3880-1933","authenticated-orcid":false,"given":"Erwan","family":"Qu\u00e9m\u00e9r\u00e9","sequence":"first","affiliation":[{"name":"Universit\u00e9 de Toulouse INRAE, CEFS Castanet\u2010Tolosan France"},{"name":"LTSER ZA PYR\u00e9n\u00e9es GARonne Auzeville\u2010Tolosane 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