Host and parasite characterization
Following the model proposed by Higgs & Derrida (1991), parasite
individuals are explicitly modeled by biallelic sequences of infinite
sites, a simplified form to represent their genomes and heritable trait.
Individuals are monoic and engage in sexual reproduction, with
non-overlapping generations. The empirical data have evolutionary times
in the order of millions of years, and to maintain this time scale in
the model would demand a higher computational cost. As proposed by Costa
et al. (2019), in our approach we adopted a higher value of mutation
rate in order to decrease the number of iterations necessary for
speciation (time steps or generations) to happen. Furthermore, we
assumed that, due to the shorter life cycle of parasites, they have a
faster speciation rate (Dowton & Austin 1995; Light & Hafner 2007). To
satisfy these conditions, we rescaled the whole host phylogeny assuming
that the smaller branch length consists of the minimal time for
parasites to speciate in allopatry (𝞃agenerations - see the details in supplemental information I). The
simulation starts with a clonal parasite population using a unique host
species. The first host speciation occurs only after𝞃a generations, accumulating genetic variation
before the first host speciation (the root of the host phylogeny). Each
host species imposes a carrying capacity of K parasite
individuals. Thus, the overall carrying capacity increases by Kindividuals at each new host speciation.