Code for: Adaptive epigenetic divergence can facilitate ecological speciation

This archive contains the code for simulations and the generation of figures in the article 'Adaptive epigenetic divergence can facilitate ecological speciation'. Details of how to run the code are given in the README file. The abstract of the article is as follows:

Migration between populations homogenizes genetic divergence and can thus prevent speciation. However, environmentally induced epigenetic marks can remain divergent between populations despite migration. Thus, epigenetic variation might facilitate speciation under conditions where it is challenging for genetic barriers to gene flow to establish. Here, we develop a model to test this hypothesis, by quantifying reproductive isolation (RI) at a neutral genetic locus linked with an epigenetic locus under divergent selection. This also allows us to test how RI is influenced by: (i) the degree of induction of epigenetic state by the environment; and (ii) the transmission of epigenetic state between generations. With high migration rate, we find that an epigenetic locus which is highly inducible produces stronger RI than an equivalent genetic locus. Furthermore, at lower migration rates, the strength of RI produced by an epigenetic locus increases when epigenetic state is more transmissible between generations. Our findings suggest three regimes of speciation by divergent selection at an epigenetic locus, whereby highly inducible epigenetic marks could give way to more transmissible epigenetic marks and ultimately genetic differentiation, as ecological speciation progresses.