Fig. 6: Analysis of local ancestry using MOSAIC.

a Local ancestry of three F₂ isolates along chromosome 16 (top panel) expressed as the probability of copying (E[ancestry]) from the two parental isolates 4 A and 7 A (bottom panel). The bottom panel’s x-axis shows the copying probabilities of two ancestries from isolates 4 A and 7 A. The proportions of ancestry in the two-way admixture model in the sample of three isolates is shown on the top (0.608 and 0.392). b Copying matrix for the clades in the Pgt panel modeled as two-way admixture. Row names show clades used as target panels, and columns show reference panels. The proportions are scaled as % of the most copied within rows. The numbers listed on the left are the averaged copying proportions across the reference panels in a two-way admixture model. Based on the analysis of the local ancestry of individual Pgt isolates, we inferred whether the origin of a clade is linked with sexual recombination (SR), somatic hybridization (SH), or lack of admixture (non-admixed - NA). c The genome-wide estimates of local ancestry in the 83PAK03-2 isolate from clade UN2. d The genome-wide estimates of copying proportions in two-way admixture for clade VII, which is ancestral to isolate 13ETH18-1. e The genome-wide estimates of Ug99 ancestry in two groups of isolates from clades II and IX (includes Pgt21-0). f Genotype of Ug99 in comparison with the genotypes of isolates from two sources, a group isolates from clades II and IX. SNPs used in the analysis showed homozygous genotype calls (0|0 and 1|1) in the source isolates and heterozygosity (0|1 or 1|0) in Ug99.