This software simulates whole genomes of hybridizing species and offers high flexibility for specifying the genetic architecture of hybrid incompatibilities, including epistasis and/or ecological selection. I developed this program together with Alex Buerkle, and source code is available from his website. We used the software to study the genomic outcomes of hybridization with simple and complex Dobzhansky-Muller-type incompatibilities or intragenomic co-adaptation of species-specific alleles. Our results are published in Evolution.


This program can simulate the effects of divergent selection and assortative mating on patterns of genome differentiation and linkage disequilibrium. Some of the results are published in a commentary article in the Journal of Evolutionary Biology. Source code is available from GitHub.

Simulation example