Scripts from: Inversions and genomic differentiation after secondary contact: When drift contributes to maintenance, not loss, of differentiation

Due to their effects on reducing recombination, chromosomal inversions may play an important role in speciation by establishing and/or maintaining linked blocks of genes causing reproductive isolation (RI) between populations. This view fits empirical data indicating that inversions typically harbor loci involved in RI. However, previous computer simulations of infinite populations with two to four loci involved in RI implied that, even with gene flux as low as 10–8 per gamete, per generation between alternative arrangements, inversions may not have large, qualitative advantages over collinear regions in maintaining population differentiation after secondary contact. Here, we report that finite population sizes can help counteract the homogenizing consequences of gene flux, especially when several fitness-related loci reside within the inversion. In these cases, the persistence time of differentiation after secondary contact can be similar to when gene flux is absent and notably longer ..., Custom-made codes in Matlab. , , # Scripts from: Inversions and genomic differentiation after secondary contact: When drift contributes to maintenance, not loss, of differentiation

by Rafajlovic et al. (2021; Evolution).

Data DOI link [https://doi.org/10.5061/dryad.v41ns1rvr](https://doi.org/10.5061/dryad.v41ns1rvr)

**Code File Names:**

There are four versions of the main code, each version being reserved for a separate model version.

“Model2_ConsecArray.m” simulates Model 2, consecutive array version.

“Model2_HalfHalfArray.m” simulates Model 2, half-half array version.

“Model4_ConsecArray.m” simulates Model 4, consecutive array version.

“Model4_HalfHalfArray.m” simulates Model 4, half-half array version.

Each code has preset parameter values, and they can easily be changed by the user. All parameters are explained in the form of comments in the code files.

**Output and data analysis**

The main output, as presented in the publication, is the average weighted time of differentiation. To perform this calculat..., , **Changes after Mar 17, 2021:** 

The README file has been updated according to the Dryad instructions.