Parasite reproduction
Reproduction is sexual and occurs between parasite individuals that are in the same host and that have a minimum genetic similarity, qmin, measured based on the Hamming distance between genomes. In each host species, K offspring are born, replacing the parental population. We establish a maximum of K random trials with reposition to find one compatible partner. The offspring is generated by locus recombination of the parents and eachlocus has a probability μ of mutation. We set\(q_{\min\ }={0.5q}_{0}\), where \(q_{0\ }\)is the expected mean similarity within one population in equilibrium, because it avoids the occurrence of parasite speciation within the same host species. Consequently, parasite speciation only happens when more than one host species is used. For a more detailed description of the method, see the supplemental information I.