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We present SimHyb, a Java-based software for the simulation of mixed hybridizing populations. The software incorporates user-defined initial parameters and input files to account for the initial census size of two species in a closed population, the number of intermediate specific classes, the directional fertility among specific classes, the fitness coefficients for each specific class, the inheritance of fitness, and the degree of ageing and self-incompatibility of the individuals. All these demographic and adaptive parameters can be modified by the user to analyze their effect on the evolution of the mixed population. SimHyb allows the traceability of each individual, whose pedigree is also recorded. For each simulated generation the software yields an output file that is easily convertible to an input for Structure, one of the most popular softwares for the Bayesian analysis of populations. Application of SimHyb to simulate Quercus ilex and Q. suber hybridizing populations, and further analysis with Structure, reveals that advanced introgressed individuals are very often misclassified with the currently available set of nuclear microsatellite markers, so that introgression between these two species could have been underestimated in previous studies. However, we provide a simple parameter based on Structure results to identify the directionality of pollination in the progeny of a known mother tree.

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SimHyb: a simulation software for the study of the evolution of hybridizing populations. Application to Quercus ilex and Q. suber suggests hybridization could be underestimated