Genetic diversity of secondary metabolic gene clusters within a fungal species. The phylogeny was constructed using 15,274 biallelic SNPs with no missing data.

The tree is midpoint rooted and all branches with bootstrap support less than 80% are collapsed. This phylogeny does not include strains Af10, Af210, Z5, or RP-2014, as short-read data were not available. Superfixes following strain names indicate publications associated with DNA sequencing. * indicates strains sequenced in this study, † indicates strains sequenced at JCVI with no associated publication, and ‡ indicates strains sequenced by Rikenwith no associated publication. Heat maps show presence, absence, and polymorphisms in SM gene clusters. Black indicates the cluster is present in a strain with no polymorphisms, aside from missense variants, light gray indicates 1 or more genes in the cluster are pseudogenized, and dark gray indicates the cluster is partially or entirely absent (see Fig 2). Colors for cluster 4 indicate which pseudogenizing variants are present (see Fig 3) and colors for cluster 10 indicate which allele of the cluster is present (see Fig 4). Chromosomal location of clusters 1 and 33 are indicated. If more than one type of polymorphism is present within a cluster in a strain, only 1 is depicted. Types of polymorphisms found in each cluster are summarized below the cluster heat map. DHN, dihydroxynaphthalene; JCVI, J. Craig Venter Institute; NRPS, nonribosomal peptide synthase; PKS, polyketide synthase; SM, secondary metabolite; SNP, single nucleotide polymorphism.