Analyses of recombination and gene flow between Cryptosporidium hominis hominis (clade 1) and Cryptosporidium hominis aquapotentis (clade 2). (A) LD decay plot showing rapid decay of linkage between SNPs in C. h. hominis (clade 1) compared with C. h. aquapotentis (clade 2). (B) Graphical representation of recombinant breakpoint positions detected by RDP4 program between C. h. hominis (clade 1) and C. h. aquapotentis (clade 2). (C,D) HybridCheck plots representing genomic signature of introgression in chromosomes 2 and 6, respectively. Analysis for chromosome 1 was excluded due to unknown parental sequences. The plots were generated for random set of triplets that includes recombinant (hybrid), minor (donor) and major (recipient) parental sequence, as detected by RDP4 program. Introgressed blocks (recombinant breakpoints) were illustrated with dashed boxes, showing high similarity between the recombinant (C. h. hominis hybrid isolates) and minor parent (C. h. aquapotentis isolates). The top panel illustrates the visualization of sequence similarity between sequences within the triplet, using RBG color triangle. The two sequences are colored same (yellow, purple, or turquoise) if they share polymorphism. (E) Gene flow analyses with ABBA–BABA test, representing D statistics for the random sets of triplets (as used in c,d) along with Cryptosporidium parvum as an outgroup. D statistic values close to −1 at all three recombinant events, suggesting gene flow between H1 and H3. (f,g) Pairwise LD of SNPs in chromosomes 2 and 6 of C. h. hominis showing red blocks of high linkage between SNPs in introgressed events 2–4.