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In this study, we investigated the genetic diversity and host specificity of<jats:italic>Pneumocystis<\/jats:italic>organisms infecting Southeast Asian murid rodents through PCR amplification of two mitochondrial genes and tested the co-phylogeny hypothesis among these fungi and their rodent hosts.<jats:italic>Pneumocystis<\/jats:italic>DNA was detected in 215 of 445 wild rodents belonging to 18 Southeast Asian murid species. Three of the<jats:italic>Pneumocystis<\/jats:italic>lineages retrieved in our phylogenetic trees correspond to known<jats:italic>Pneumocystis<\/jats:italic>species, but some of the remaining lineages may correspond to new undescribed species. Most of these<jats:italic>Pneumocystis<\/jats:italic>species infect several rodent species or genera and some sequence types are shared among several host species and genera. These results indicated a weaker host specificity of<jats:italic>Pneumocystis<\/jats:italic>species infecting rodents than previously thought. Our co-phylogenetic analyses revealed a complex evolutionary history among<jats:italic>Pneumocystis<\/jats:italic>and their rodent hosts. Even if a significant global signal of co-speciation has been detected, co-speciation alone is not sufficient to explain the observed co-phylogenetic pattern and several host switches are inferred. These findings conflict with the traditional view of a prolonged process of co-evolution and co-speciation of<jats:italic>Pneumocystis<\/jats:italic>and their hosts.<\/jats:p>","DOI":"10.1017\/s0031182017001883","type":"journal-article","created":{"date-parts":[[2017,11,9]],"date-time":"2017-11-09T06:13:54Z","timestamp":1510208034000},"page":"885-900","update-policy":"https:\/\/doi.org\/10.1017\/policypage","source":"Crossref","is-referenced-by-count":25,"title":["Genetic diversity and evolution of<i>Pneumocystis<\/i>fungi infecting wild Southeast Asian murid rodents"],"prefix":"10.1017","volume":"145","author":[{"given":"Alice","family":"Latinne","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fran\u00e7ois","family":"Bez\u00e9","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurence","family":"Delhaes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muriel","family":"Pottier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nausicaa","family":"Gantois","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julien","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kim","family":"Blasdell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eduardo","family":"Dei-Cas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Serge","family":"Morand","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Magali","family":"Chab\u00e9","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"56","published-online":{"date-parts":[[2017,11,9]]},"reference":[{"key":"S0031182017001883_ref25","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0120839"},{"key":"S0031182017001883_ref40","doi-asserted-by":"publisher","DOI":"10.1017\/S0031182002001841"},{"key":"S0031182017001883_ref35","doi-asserted-by":"publisher","DOI":"10.1111\/j.1550-7408.2001.tb00475.x"},{"key":"S0031182017001883_ref41","doi-asserted-by":"publisher","DOI":"10.1080\/10635150390250893"},{"key":"S0031182017001883_ref16","doi-asserted-by":"publisher","DOI":"10.1186\/1748-7188-5-16"},{"key":"S0031182017001883_ref73","doi-asserted-by":"publisher","DOI":"10.1016\/0140-6736(90)92008-6"},{"key":"S0031182017001883_ref71","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1128\/JCM.36.1.90-93.1998","article-title":"Pre-AIDS era isolates of Pneumocystis carinii f. sp. hominis: high genotypic similarity with contemporary isolates","volume":"36","author":"Tsolaki","year":"1998","journal-title":"Journal of Clinical Microbiology"},{"key":"S0031182017001883_ref8","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0061048"},{"key":"S0031182017001883_ref68","volume-title":"PAUP*. 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