RT Journal Article SR Electronic T1 Local population structure and patterns of Western Hemisphere dispersal for Coccidioides spp., the fungal cause of Valley Fever JF bioRxiv FD Cold Spring Harbor Laboratory SP 024778 DO 10.1101/024778 A1 David M. Engelthaler A1 Chandler C. Roe A1 Crystal M. Hepp A1 Marcus Teixeira A1 Elizabeth M. Driebe A1 James M. Schupp A1 Lalitha Gade A1 Victor Waddell A1 Kenneth Komatsu A1 Eduardo Arathoon A1 Heidi Logemann A1 George R. Thompson III A1 Tom Chiller A1 Bridget Barker A1 Paul Keim A1 Anastastia P. Litvintseva YR 2016 UL http://biorxiv.org/content/early/2016/03/30/024778.abstract AB Coccidioidomycosis (or Valley Fever) is a fungal disease with high morbidity and mortality that affects tens of thousands of people each year. This infection is caused by two sibling species, Coccidioides immitis and C. posadasii, 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 of 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 perform multiple phylogenetic inference and population genomics analyses of 68 new and 18 previously published genomes. The results provide evidence of substantial population structure in C. posadasii and demonstrate 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 C. immitis 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 C. posadasii 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 C. posadasii and describe a pathway for dispersal and distribution out of this region.