Superinfection leads to cotransmission and recombination of distinct lineages#
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Coloured bars represent parasite genomes within a host. Here we imagine that hosts 1 and 2 each carry a clonal population of parasites, and that the two clonal populations can be differentiated by genotyping, represented by blue and red respectively. Host 3 is superinfected and carries a mixture of the two genotypes. The two genotypes recombine when this mixture is cotransmitted from host 3 to host 4, and there is further recombination when the mixture is cotransmitted from host 4 to host 5. The circles marked A and B represent two different loci in a parasite genome carried by host 5: locus A is inherited from host 1 whereas locus B is inherited from host 2. Thus it is not possible to represent this parasite population by a single phlyogenetic tree - because the red/blue recombinant genomes cannot be mapped onto a single position on the tree.