DOI: 10.5061/dryad.pk20h
title: Data from: Determining epistatic selection in admixed populations

description: When two diverging species begin hybridizing, selection against
 hybridization is likely driven not by single substitutions, but by
 interactions between incompatible mutations. To identify these
 incompatibilities in natural populations, researchers examine the extent
 of non-random associations between ancestry at physically unlinked loci in
 admixed populations. In this approach, which we call “AD scans”,
 locus-pairs with significantly positive “ancestry disequilibrium” (AD,
 i.e. locus-pairs that positively covary by ancestry) represent
 incompatible alleles. Past research has uniformly revealed an excess of
 locus-pairs with significantly positive AD, suggesting that dozens to
 hundreds of incompatibilities separate species. With forward simulations,
 we show that many realistic demographic scenarios, including recent and/or
 ongoing contact, generate a bias towards positive ancestry disequilibrium.
 We suggest steps that researchers can take to avoid pitfalls in
 interpreting AD scans, and present a novel measure of AD, which minimizes
 but does not fully eliminate bias in the AD distribution. We also show, by
 simulation, that the tail of the AD distribution is enriched for true
 incompatibilities. To illustrate the potential power and appropriate
 caution in interpretation of AD scans, we reanalyze previously published
 data from two admixed populations of Xiphophorus fishes. Our results imply
 that the prevalence of positive LD in admixed populations does not in
 itself support the idea that two-locus incompatibilities are widespread,
 but the co-enrichment of top AD hits across the two Xiphophorus
 populations supports the idea that AD scans can identify candidate
 interspecific incompatibilities.
description: configuration files and
 admix'em input file for neutral simulationsRequired files to run
 neutral simulations including three admix'em configuration files for
 neutral hybrid swarm (admixsimul.cfg), neutral bottleneck hybrid swarm
 (admixsimul_bottle.cfg), and neutral hybrid swarm with migration
 simulations (admixsimul_mig.cfg) and other input files to admix'em
 called by these configuration filesneutral_simulations.tarconfiguration files and admix'em input file for selection simulationsadmix'em configuration files for simulations with epistatic selection under a hybrid swarm (admixsimul.cfg), bottleneck (admixsimul_bottle.cfg) and continuing migration model (admixsimul_mig.cfg) as well as admix'em input files called by these configuration filesselection_simulations.tarsimulation shell scriptshell script to run admix'em simulations for a given configuration file, number of generations, and number of individuals. NOTE: assumes admixem is installed in the same directory and that the executable is called admixemp. Also assumes that perl and sh scripts provided with this submission are available in the same directory. Usage: perl simulated_ld_shell.pl cfg_file out_folder_name num_iterations focal_gen num_indiv_samplesimulated_ld_shell_YB_MS.plgenerate_msg_data_header_200locisim.plscript to convert admix'em output for the simulation parameters provided to genotype format. This script is called by the simulation shell script: simulated_ld_shell_YB_MS.plhybrid_index.plscript to calculate hybrid index from the genotype-format admix'em output for the 200 loci simulated. This script is called by the simulation shell script: simulated_ld_shell_YB_MS.plrandom_sample.shscript to subsample the simulated individuals from the genotypes file to the desired number of individuals. This script is called by the simulation shell script: simulated_ld_shell_YB_MS.plcompressed neutral simulation files for reproduction of results figure 2"neutral.zip" contains neutral simulation results files and scripts needed to reproduce figure 2 in the main textneutral.zipcompressed selection simulation files for reproduction of results figure 3"selection.zip" contains neutral simulation results files and scripts needed to reproduce figure 3 in the main textselection.zip