Global analysis of mutations driving microevolution of a heterozygous diploid fungal pathogen

Significance Evolution acts on mutations that naturally arise within the genome and are shaped both by intrinsic genomic features and by the cellular environment. We catalog the mutations arising in a heterozygous diploid yeast during passaging in vitro and in the mammalian host. We establish genome-wide mutation rates and reveal that “microscale” changes (base substitutions and short-track recombination events) are the primary drivers of microevolution, although chromosomal-level changes also occur in specific host environments. Our results define mutation hotspots, including those adjoining recombination tracts, and indicate that many mutations are purged from the population due to purifying selection. Together, these data provide a high-resolution picture of how the heterozygous diploid genome of a fungal pathogen undergoes evolution over short time scales.