Coccidioides whole population genome SNP analysis reveals local population structure and patterns of dispersal in the Western Hemisphere. Coccidioides

Coccidioides immitis and C. posadasii are pathogenic environmental fungi causing coccidioidomycosis primarily in the desert Southwest of the United States, with scattered endemic foci throughout the Western Hemisphere. The complexities of their recombining genomes has, until recently, limited the development of tools for molecular epidemiology and phylogeographic analysis at both the regional and local levels. Here we perform whole genome sequence analyses of 64 new and 28 previously published genomes to ascertain the population structure of Coccidioides, particularly within local subpopulations of C. posadasii. 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 and South and Central America. Although a smaller number of C. immitis strains were included in the analyses, some evidence of phylogeographic structure was detected in this species as well. Specifically, newly identified clinical and environmental strains from Washington State formed a distinct well-supported clade on C. immitis genomic phylogeny. Phylogenetic analyses indicated that C. posadasii is the most ancient of the two species, and Southern Arizona contains the most diverse subpopulations. A model for distribution of C. posadasii out of the Southern Arizona region is proposed.