Discussion

The unicellular eukaryote Trypanosoma cruzi, parasitic agent of Chagas disease, was once held up as a paradigm for clonal evolution. In later years, limited evidence emerged of recombination in the field and laboratory. The mechanisms and extent of genetic exchange in T. cruzi, however, remain very little understood. Here, we present evidence from 83 sequenced T. cruzi genomes that coincident meiotic and para-sexual mating cycles drive genetic structure among sympatric populations. In one section of the 100 km²-study region, host and vector-isolated strains carry single-nucleotide-polymorphisms at Hardy-Weinberg frequencies and under linkage decay consistent with widespread meiosis-like genetic exchange.  At adjacent sites, populations exhibit near-maximal excess-heterozygosity throughout the genome. Haplotype structure, mitochondrial and ploidy analyses suggest that these heterozygous groups originate from a para-sexual genome fusion event. Based on measurements of shared segment similarity, distribution and length, we give frequency estimates for these recombination processes and discuss their epidemiological and evolutionary implications.