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

Citation

Rafajlovic, Marina et al. (2021), Inversions and genomic differentiation after secondary contact: when drift contributes to maintenance, not loss, of differentiation, Dryad, Dataset, https://doi.org/10.5061/dryad.v41ns1rvr

Abstract

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 harbour loci involved in RI. However, previous computer simulations of infinite populations with 2-4 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 than the persistence time without inversions. Thus, despite gene flux, population differentiation may be maintained for up to 100,000 generations, during which time new incompatibilities and/or local adaptations might accumulate and facilitate progress towards speciation. How often these conditions are met in nature remains to be determined.

Methods

Custom-made codes in Matlab. 

Usage Notes

There are four versions of the main code, each version being reserved for a separate model version. The .m file called "Analyze_WeightedTime.m" serves to compute the average weighted time of differentiation based on multiple model realisations. 

Funding

Svenska Forskningsrådet Formas, Award: 2019-00882

Hasselblad Foundation, Award: Female Scientist 2019-2020

Swedish Research Council, Award: 2018-05973

European Regional Development Fund, Award: FCOMP-01-0124-FEDER-014272

Foundation for Science and Technology, Award: PTDC/BIA-EVF/113805/2009

Ministerio de Ciencia e Innovación, Award: BFU2015-68649-P, MINECO/FEDER, UE

Spanish National Institute of Bioinforma, Award: PT17/0009/0020

Foundation for Science and Technology, Award: SFRH/BPD/89313/2012

H2020 Marie Skłodowska-Curie Actions, Award: 706376

Ministerio de Ciencia e Innovación, Award: PGC2018-101927-B-I00

Hasselblad Foundation, Award: Female Scientist 2019-2020

Swedish Research Council, Award: 2018-05973

Spanish National Institute of Bioinforma, Award: PT17/0009/0020