DOI: 10.5061/dryad.rn8pk0p75
title: R script: Species coexist more easily if reinforcement is based on habitat preferences than on species recognition

description: 1. Maladaptive hybridization selects for prezygotic isolation, a process
 known as reinforcement. Reinforcement reduces gene flow and contributes to
 the final stage of speciation. Ecologically, however, coexistence of the
 incipient species is difficult if they initially use identical resources.
 2. Habitat segregation offers an alternative to species discrimination as
 a way to reduce gene flow: production of unfit hybrids is reduced if mate
 encounters become rare due to differing habitat choice. Using a modelling
 approach, we show that hybridization avoidance alone can select for
 habitat specialization, even if neither of the species is intrinsically
 better at using a specific niche. 3. While habitat segregation and species
 discrimination both reduce the risk of producing unfit hybrids, these two
 isolation mechanisms differ from each other with respect to their effects
 on resource competition. Our model shows that, as a consequence of such
 differences, reinforcement evolves much more easily if hybridization is
 avoided based on habitat segregation than if the mechanism involves
 species recognition (mate choice traits). 4. We also examine the outcomes
 when both isolation mechanisms evolve jointly. The establishment of one
 isolation mechanism a priori weakens selection for the other. However, an
 asymmetry persists here too. The net effect of habitat segregation on
 species discrimination was typically facilitative, but not vice versa.
 This asymmetry arises because habitat segregation, by enhancing
 coexistence, secures time for the subsequent evolution of species
 discrimination in a mate choice context (still relevant if habitat use is
 not perfectly segregated). Species discrimination does not have such a
 stabilizing effect on coexistence. 5. Our results emphasize the importance
 of habitat segregation in reinforcement, and offer a way to interpret
 findings where closely related taxa show similar performance on different
 resources or in different habitats. Studies of ecological generalization
 and specialization should therefore take into account that niche
 differences can be initiated and/or maintained by hybridization avoidance.
description: An R script for individual based simulation models of
 reinforcement. There can be two incipient species. Maladaptive
 hybridization can occur between them. Either species recognition (based on
 male signal and female mate preference) or habitat segregation (based on
 habitat preference) or both can evolve. Demographic dynamics is also
 explicitly modelled. The two parental species (and matured hybrids) are
 ecologically identical.
description: Simulation runs for the publication were made using Windows
 computers. The simulation with the default settings (preferences
 [habitat.pref, mate.pref.1, mate.pref.2] ranged from 1, 2, 4, 8, ...,
 1024, and hybrid survival [s.hybrid] ranged from 0.00, 0.05, 0.10, 0.15,
 ..., 0.95, and each parameter combination replicated for 100 times) takes
 a few days with 64-cored computeres. When you try this code with fewer
 CPUs, you are advised to start with smaller replications and fewer
 parameter combinations.