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These fungi are highly host specific and uncultivable\n            <jats:italic>in vitro<\/jats:italic>\n            . Human\n            <jats:italic>Pneumocystis<\/jats:italic>\n            infections present major challenges because of a limited therapeutic arsenal and the rise of drug resistance. To investigate the diversity and demographic history of natural populations of\n            <jats:italic>Pneumocystis<\/jats:italic>\n            infecting humans, rats, and mice, we performed whole-genome and large-scale multilocus sequencing of infected tissues collected in various geographic locations. Here, we detected reduced levels of recombination and variations in historical demography, which shape the global population structures. We report estimates of evolutionary rates, levels of genetic diversity, and population sizes. Molecular clock estimates indicate that\n            <jats:italic>Pneumocystis<\/jats:italic>\n            species diverged before their hosts, while the asynchronous timing of population declines suggests host shifts. Our results have uncovered complex patterns of genetic variation influenced by multiple factors that shaped the adaptation of\n            <jats:italic>Pneumocystis<\/jats:italic>\n            populations during their spread across mammals.\n          <\/jats:p>\n          <jats:p>\n            <jats:bold>IMPORTANCE<\/jats:bold>\n            Understanding how natural pathogen populations evolve and identifying the determinants of genetic variation are central issues in evolutionary biology.\n            <jats:italic>Pneumocystis<\/jats:italic>\n            , a fungal pathogen which infects mammals exclusively, provides opportunities to explore these issues. In humans,\n            <jats:italic>Pneumocystis<\/jats:italic>\n            can cause a life-threatening pneumonia in immunosuppressed individuals. In analysis of different\n            <jats:italic>Pneumocystis<\/jats:italic>\n            species infecting humans, rats, and mice, we found that there are high infection rates and that natural populations maintain a high level of genetic variation despite low levels of recombination. We found no evidence of population structuring by geography. Our comparisons of the times of divergence of these species to their respective hosts suggest that\n            <jats:italic>Pneumocystis<\/jats:italic>\n            may have undergone recent host shifts. The results demonstrate that\n            <jats:italic>Pneumocystis<\/jats:italic>\n            strains are widely disseminated geographically and provide a new understanding of the evolution of these pathogens.\n          <\/jats:p>","DOI":"10.1128\/mbio.00381-18","type":"journal-article","created":{"date-parts":[[2018,5,7]],"date-time":"2018-05-07T09:36:45Z","timestamp":1525685805000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":38,"title":["Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen\n            <i>Pneumocystis<\/i>"],"prefix":"10.1128","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2990-2185","authenticated-orcid":false,"given":"Ousmane H.","family":"Ciss\u00e9","sequence":"first","affiliation":[{"name":"Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, 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Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2834-7922","authenticated-orcid":false,"given":"Philippe M.","family":"Hauser","sequence":"additional","affiliation":[{"name":"Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Pagni","sequence":"additional","affiliation":[{"name":"Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vanessa","family":"Hirsch","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard A.","family":"Lempicki","sequence":"additional","affiliation":[{"name":"Leidos Biomedical Research, 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