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This infection is caused by two sibling species,\n                    <jats:italic>Coccidioides immitis<\/jats:italic>\n                    and\n                    <jats:italic>C.\u00a0posadasii<\/jats:italic>\n                    , which are endemic to specific arid locales throughout the Western Hemisphere, particularly the desert southwest of the United States. Recent epidemiological and population genetic data suggest that the geographic range of coccidioidomycosis is expanding, as new endemic clusters have been identified in the state of Washington, well outside the established endemic range. The genetic mechanisms and epidemiological consequences of this expansion are unknown and require better understanding of the population structure and evolutionary history of these pathogens. Here we performed multiple phylogenetic inference and population genomics analyses of 68 new and 18 previously published genomes. The results provide evidence of substantial population structure in\n                    <jats:italic>C.\u00a0posadasii<\/jats:italic>\n                    and demonstrate the presence of distinct geographic clades in central and southern Arizona as well as dispersed populations in Texas, Mexico, South America, and Central America. Although a smaller number of\n                    <jats:italic>C.\u00a0immitis<\/jats:italic>\n                    strains were included in the analyses, some evidence of phylogeographic structure was also detected in this species, which has been historically limited to California and Baja, Mexico. Bayesian analyses indicated that\n                    <jats:italic>C.\u00a0posadasii<\/jats:italic>\n                    is the more ancient of the two species and that Arizona contains the most diverse subpopulations. We propose a southern Arizona-northern Mexico origin for\n                    <jats:italic>C.\u00a0posadasii<\/jats:italic>\n                    and describe a pathway for dispersal and distribution out of this region.\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>IMPORTANCE<\/jats:bold>\n                    Coccidioidomycosis, or valley fever, is caused by the pathogenic fungi\n                    <jats:italic>Coccidioides posadasii<\/jats:italic>\n                    and\n                    <jats:italic>C.\u00a0immitis<\/jats:italic>\n                    . The fungal species and disease are primarily found in the American desert southwest, with spotted distribution throughout the Western Hemisphere. Initial molecular studies suggested a likely anthropogenic movement of\n                    <jats:italic>C.\u00a0posadasii<\/jats:italic>\n                    from North America to South America. Here we comparatively analyze eighty-six genomes of the two\n                    <jats:italic>Coccidioides<\/jats:italic>\n                    species and establish local and species-wide population structures to not only clarify the earlier dispersal hypothesis but also provide evidence of likely ancestral populations and patterns of dispersal for the known subpopulations of\n                    <jats:italic>C.\u00a0posadasii<\/jats:italic>\n                    .\n                  <\/jats:p>","DOI":"10.1128\/mbio.00550-16","type":"journal-article","created":{"date-parts":[[2016,4,26]],"date-time":"2016-04-26T21:43:09Z","timestamp":1461706989000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":89,"title":["Local Population Structure and Patterns of Western Hemisphere Dispersal for\n                    <i>Coccidioides<\/i>\n                    spp., the Fungal Cause of Valley Fever"],"prefix":"10.1128","volume":"7","author":[{"given":"David M.","family":"Engelthaler","sequence":"first","affiliation":[{"name":"TGen North, Translational Genomics Research Institute, Flagstaff, Arizona, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chandler C.","family":"Roe","sequence":"additional","affiliation":[{"name":"TGen North, Translational Genomics Research Institute, Flagstaff, Arizona, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Crystal M.","family":"Hepp","sequence":"additional","affiliation":[{"name":"Informatics and Computing Center, Northern Arizona University, Flagstaff, Arizona, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcus","family":"Teixeira","sequence":"additional","affiliation":[{"name":"TGen North, Translational Genomics Research Institute, Flagstaff, Arizona, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth M.","family":"Driebe","sequence":"additional","affiliation":[{"name":"TGen North, Translational Genomics Research Institute, Flagstaff, Arizona, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James M.","family":"Schupp","sequence":"additional","affiliation":[{"name":"TGen North, Translational Genomics Research Institute, Flagstaff, Arizona, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lalitha","family":"Gade","sequence":"additional","affiliation":[{"name":"Mycotic Diseases Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victor","family":"Waddell","sequence":"additional","affiliation":[{"name":"Division of Public Health Services, Arizona Department of Health Services, Phoenix, Arizona, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenneth","family":"Komatsu","sequence":"additional","affiliation":[{"name":"Division of Public Health Services, Arizona Department of Health Services, Phoenix, Arizona, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eduardo","family":"Arathoon","sequence":"additional","affiliation":[{"name":"Asociaci\u00f3n de Salud Integral, Guatemala City, Guatemala"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heidi","family":"Logemann","sequence":"additional","affiliation":[{"name":"Universidad de San Carlos, Ciudad Universitaria, Guatemala City, Guatemala"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"III","given":"George R.","family":"Thompson","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Department of Medicine, University of California, Davis, Davis, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tom","family":"Chiller","sequence":"additional","affiliation":[{"name":"Mycotic Diseases Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3439-4517","authenticated-orcid":false,"given":"Bridget","family":"Barker","sequence":"additional","affiliation":[{"name":"TGen North, Translational Genomics Research Institute, Flagstaff, Arizona, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Keim","sequence":"additional","affiliation":[{"name":"TGen North, Translational Genomics Research Institute, Flagstaff, Arizona, USA"},{"name":"Microbial Genetics and Genomics Center, Northern Arizona University, Flagstaff, Arizona, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anastasia 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Coccidioides immitis identified in soil outside of its known range\u2014Washington 2013. MMWR Morb Mortal Wkly Rep 63:450."},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1196\/annals.1406.040"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.17.4.804-839.2004"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/br.31.1.25-34.1967"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.funeco.2011.07.010"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.087551.108"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.071406098"},{"key":"e_1_3_2_11_2","first-page":"297","volume-title":"Microbial forensics","author":"Engelthaler DM","year":"2010","unstructured":"Engelthaler DM, Balajee SA. 2010. Forensics and epidemiology of fungal pathogens, p 297\u2013313. In Budowle B, Schutzer SE, Breeze RG, Keim PS, Morse SA (ed), Microbial forensics. 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