Gene exchange between two divergent species of the fungal human pathogen,Coccidioides

Abstract

The fungal genus Coccidioides is composed of two species, Coccidioides immitis and Coccidioides posadasii. These two species are the causal agents of coccidioidomycosis, a pulmonary disease also known as valley fever. The two species are thought to have shared genetic material due to gene exchange in spite of their long divergence. To quantify the magnitude of shared ancestry between them, we analyzed the genomes of a population sample from each species. Next, we inferred what is the expected size of shared haplotypes that might be inherited from the last common ancestor of the two species and find a cutoff to find what haplotypes have conclusively been exchanged between species. Finally, we precisely identified the breakpoints of the haplotypes that have crossed the species boundary and measure the allele frequency of each introgression in this sample. We find that introgressions are not uniformly distributed across the genome. Most, but not all, of the introgressions segregate at low frequency. Our results show that divergent species can share alleles, that species boundaries can be porous, and highlight the need for a systematic exploration of gene exchange in fungal species.

Strong population structure in Venezuelan populations ofCoccidioides posadasii

“…As expected, PC1 (75.34% of the variance) separates the two Coccidioides species. Consistent with previous findings, we see no intermediate isolates suggesting that even though admixture between the two species of Coccidioides has occurred (28, 62), the amount of genetic exchange between species is small enough to not affect species delineations. Notably, PC2 (3.03% of the variance) differentiates between the Arizona + TX/MX/SA and Venezuela populations with the Caribbean (e.g., Guatemala, Florida) group appearing as intermediaries between these two populations.…”

“…Studying the magnitude of intraspecific gene exchange is not devoid of challenges. Species that have achieved genome-wide reciprocal monophyly will show fixed differences, which allows for detection of alleles that have crossed species boundaries after hybridization (e.g., (28, 82)). Populations from the same species, or even incipient species, are less likely to show these fixed differences, and analyses of introgression must be done based on differences of allele frequencies.…”

“…Previous studies have found that species of Coccidioides exchange alleles (55, 56). Our scope was different; we assessed whether populations within C. posadasii exchange genes.…”

“…In the case of C. immitis , genomic analyses have revealed the existence of two subdivided populations: Washington state (at the northernmost point of the known range of the species distribution) and the rest of the range (27). In the case of C. posadasii at least two distinct populations have been proposed: Arizona (AZ) and Texas/Mexico/South America (TX/MX/SA) (21, 28).…”

Structural characterization and evolutionary analyses of theCoccidioides immitisandCoccidioides posadasiimitochondrial genomes

“…Notably, nucDNA studies have found extensive differentiation between species of Coccidioides with some evidence for gene flow between species (17,18). The two species, C. immitis and C. posadasii, can be discriminated based on polymorphisms found at the first intron of the cox1 gene (19).…”