Phase relation between the two epidemics in the simulation of the model.

Level contours plot the fraction of time epidemics are in-phase [Left], and anti-phase [Right]. Phase difference is calculated by considering 5000 years of simulation (100 years of transients are excluded), computing the fraction of the time series during which strains are in-phase and anti-phase and averaging these fractions over 40 stochastic replicates. Strains are categorized as in phase if the phase difference is less than an eighth of the period, and anti-phase if the difference is of a period. The three points marked (I), (II) and (III) are distinct scenarios examined in our inference tests. Model parameters are as in Table 1, with .