Fig. 1: Population structure of Aspergillus flavus reveals genetic isolation reflecting five populations, including a new population, D.

Analyses are based on 1,941,481 biallelic single nucleotide variants. A Estimates of individual ancestry, with K = 5, conducted using the software package LEA⁶⁷, which estimates individual admixture coefficients from a genotypic matrix⁹⁸. We estimated admixture for K = 2 through 10, with K = 5 providing the best fit for our data according to the cross-entropy criterion^68,69. B Discriminant analysis of principal components shows admixture among populations A, C, and D as well as clear separation of populations B and S-type. Dots represent individuals and ellipses indicate group clustering of individuals. Populations are color coded as indicated in the top right. The discriminant analysis eigenvalues are shown on the bottom left, with the darker bars showing eigenvalues retained. C A principal coordinates analysis displaying relative genetic distances of individual isolates, here represented by dots, using Nei’s genetic distance matrix. Axes indicate the two principal coordinates retained and the percentage of variance explained by each coordinate. Populations A, C, and D varied primarily along PC2 rather than PC1; population B showed genetic differentiation from other populations and varied primarily along PC1. Single nucleotide polymorphisms can be inferred from the alignment provided as our Source Data file.