# Local population structure and patterns of Western Hemisphere dispersal for Coccidioides spp., the fungal cause of Valley Fever

## TL;DR

This study explores the population structure and dispersal patterns of Coccidioides fungi, which cause Valley Fever, revealing new insights into their geographic spread and evolutionary history.

## Contribution

The study provides new evidence of genetic population structure and dispersal pathways for Coccidioides spp. using whole genome SNP analyses.

## Key findings

- C. posadasii shows substantial population structure with distinct geographic clades in Arizona, Texas, Mexico, and South America.
- C. immitis exhibits some phylogeographic structure despite being historically limited to California and Baja Mexico.
- C. posadasii is the more ancient species, with southern Arizona and northern Mexico as its likely origin.

## Abstract

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.