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Genomics has changed the way that we think about the sources of genetic variation in fungi and will change the way that we think about species and populations.Phylogenomics has uncovered the role of gene family expansion and contraction in generating fungal genetic variation.Population genomics has uncovered the role that hybridization and introgression play in generating fungal genetic variation.An application of population genomics, genome wide association, is allowing mycologists to discover genes associated with complex phenotypes and even to assign function to hypothetical genes.