Pairwise comparison of isolates reveal progeny of a natural cross. (A) Log₂ ratios of probe intensities plotted along chromosome 14 for the hybridization of genomic DNA from isolates IQE2924 and IQE3502 display polymorphisms, indicated by upward and downward spikes for the left half of the chromosome. The normal distribution of log₂ ratios around 0 for the right half of the chromosome indicate that these two isolates share the same DNA sequence for this half of the chromosome. (B) Log of P-value for polymorphism detection plotted on chromosome 14 shows polymorphisms predicted only for half of the chromosome. The blue lines indicate polymorphisms in IQE2924 using IQE3502 as the reference, and the green indicates polymorphisms in IQE3502 using IQE2924 as the reference. The horizontal dashed line indicates a P-value cutoff of 1 × 10⁻⁵. (C) Blocks of 100 kb of sequence that displayed no polymorphisms by pairwise comparison of isolates were drawn (colored blue or red in panels C–H), and chromosome 14 is displayed. (D,E) Essentially “clonal” parasites, IQE2924 and IQE3416 (D) and IQE3848 and IQE3785 (E) show very few polymorphisms for the core chromosomal region. (F,G) Other pairwise comparisons showed parasites that shared the same genotype blocks for approximately half of the core chromosomal regions. IQE2924 and IQE3502 shared ∼60%, while IQE3848 and IQE3502 shared ∼40%. (H) Overlaying the genotype blocks comparing IQE3502 to IQE2924 and IQE3848 revealed that the latter two genotypes could explain the genotype of IQE3502, indicating that it was the progeny of a natural cross between these two genotypes. Magenta regions did not contain any polymorphisms between the parental and progeny genotypes, and thus are of uncertain assignment. (I) Analysis of inheritance of organellar genomes revealed that IQE3502 inherited the IQE3848 genotype, suggesting that this was the maternal genotype, while IQE2924 was the paternal.