(A) Chromosomal levels of nucleotide variation (Θ) in A. oryzae (blue) and A. flavus (green). (B) Left panel: Parsimony-inferred phylogeny of the 16 A. oryzae (blue) and A. flavus (green) isolates from the 100,084 high quality genome-wide variant sites. Values near internodes indicate bootstrap support, generated by 1,000 replicates. The scale bar represents the number of changes. Right panel: structure-based membership coefficient for each isolate (population number K = 2). The A. oryzae and A. flavus genetic backgrounds are shown in blue and green, respectively. (C) Relative nucleotide diversity scores (ΘOF) for 5-kb windows (65,894 windows) with a 500 bp step size scanning the eight chromosomes. Points below the dotted line represent genomic regions below the empirical 0.25% quantile (164 windows) and comprise the candidate Putative Selective Sweep Regions (PSSRs). The right panel shows the distribution of ΘOF scores. (D) Close-ups of representative PSSRs and flanking regions.