DOI: 10.5061/dryad.44sv0
title: Data from: A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes

description: Hybridization is increasingly recognized as a significant evolutionary
 process, in particular because it can lead to introgression of genes from
 one species to another. A striking pattern of discordance in the amount of
 introgression between mitochondrial and nuclear markers exists such that
 substantial mitochondrial introgression is often found in combination with
 no or little nuclear introgression. Multiple mechanisms have been proposed
 to explain this discordance, including positive selection for
 introgressing mitochondrial variants, several types of sex-biases, drift,
 negative selection against introgression in the nuclear genome, and
 spatial expansion. Most of these hypotheses are verbal, and have not been
 quantitatively evaluated so far. We use individual-based, multi-locus,
 computer simulations of secondary contact under a wide range of
 demographic and genetic scenarios to evaluate the ability of the different
 mechanisms to produce discordant introgression. Sex-biases and spatial
 expansions fail to produce substantial mito-nuclear discordance. Drift and
 nuclear selection can produce strong discordance, but only under a limited
 range of conditions. In contrast, selection on the mitochondrial genome
 produces strong discordance, particularly when dispersal rates are low.
 However, commonly used statistical tests have little power to detect this
 selection. Altogether, these results dismiss several popular hypotheses,
 and provide support for adaptive mitochondrial introgression.
description: SourceCodeSource code for the simulation of multi-locus introgression during secondary contacts. After decompression, add the file present at https://github.com/timotheenivalis/CodeAllForward/blob/master/MersenneTwister.h to the directory. The program can then be compiled, for instance, with g++ -o AllForward -O2 *.cppAllForward executableExecutable binary of the simulation program.AllForward.exeAllForward option fileExample of an option file to give instructions to AllForward.exe. This file should be placed in the same folder as the program AllForward.exe for the options to be read. This file must be named "AllForward.txt", unless another name is specified in the command line when calling the program.AllForward.txtFunctionsSimulR Functions used to analyze the simulations. - mtfunc does the general analyzes for one scenario (unique combination of parameters) - WrapMtFunc is a wrapper for a series of scenarios - mtfuncInvasion is a special "mtfunc" for invasion scenarios - mtfuncInvasionAllGrid is similar but uses the full grid in cases of invasion (unlike what we presented in the publication)ExampleAnalysisExample of the use of mtfunc() on a series of scenarios. Once the analyses are run for all scenarios, the result files (for instance BDbresults.txt, BDbresultsnofix.txt, and BDbDistriMtMax.txt here) can all be loaded to create AllRData.RData.AllRDataR data of all the analyzed simulations.GraphesKnitr (R+Latex) code used to produce the graphes in the publication. (needs AllRData.RData)READMEThis package contains the code used to simulate and analyze the data used in the publication.