The frequency of sex: population genomics reveals differences in recombination and population structure of the aflatoxin-producing fungus Aspergillus flavus

The apparent rarity of sex in many fungal species has raised questions about how much sex is needed to purge deleterious mutations and how differences in the frequency of sex impact fungal evolution. We sought to determine how differences in the extent of recombination between populations of Aspergillus flavus impact the evolution of genes associated with the synthesis of aflatoxin, a notoriously potent carcinogen. We sequenced the genomes of, and quantified aflatoxin production in, 94 isolates of A. flavus sampled from seven states in eastern and central latitudinal transects of the United States. The overall population is subdivided into three genetically differentiated populations (A, B, and C) that differ greatly in their extent of recombination, diversity, and aflatoxin-producing ability. Estimates of the number of recombination events and linkage disequilibrium decay suggest relatively frequent sex only in population A. Population B is sympatric with population A but produces significantly less aflatoxin and is the only population where the inability of non-aflatoxigenic isolates to produce aflatoxin was explained by multiple gene deletions. Population expansion evident in B suggests a recent introduction or range expansion. Population C is largely non-aflatoxigenic and restricted mainly to northern sampling locations through restricted migration and/or selection. Despite differences in the number and types of mutations in the aflatoxin gene cluster, codon optimization and site-frequency differences in synonymous and nonsynonymous mutations suggest that low levels of recombination in some A. flavus populations are sufficient to purge deleterious mutations.