DOI: 10.5061/dryad.m63xsj495
title: Data from: Do genetic loci that cause reproductive isolation in the lab inhibit gene flow in nature?

description: The genetic dissection of reproductive barriers between diverging lineages
 provides enticing clues into the origin of species. One strategy uses
 linkage analysis in experimental crosses to identify genomic locations
 involved in phenotypes that mediate reproductive isolation. A second
 framework searches for genomic regions that show reduced rates of exchange
 across natural hybrid zones. It is often assumed that these approaches
 will point to the same loci, but this assumption is rarely tested. In this
 perspective, we discuss the factors that determine whether loci connected
 to postzygotic reproductive barriers in the laboratory are inferred to
 reduce gene flow in nature. We synthesize data on the genetics of
 postzygotic isolation in house mice, one of the most intensively studied
 systems in speciation genetics. In a rare empirical comparison, we measure
 the correspondence of loci tied to postzygotic barriers via genetic
 mapping in the laboratory and loci at which gene flow is inhibited across
 a natural hybrid zone. We find no evidence that the two sets of loci
 overlap beyond what is expected by chance. In light of these results, we
 recommend avenues for empirical and theoretical research to resolve the
 potential incongruence between the two predominant strategies for
 understanding the genetics of speciation.
description: # Data from: Do genetic loci that cause reproductive isolation in the lab
 inhibit gene flow in nature?
 [https://doi.org/10.5061/dryad.m63xsj495](https://doi.org/10.5061/dryad.m63xsj495) This dataset contains two types of data:  1\) Summary of genomic regions associated with reproductive isolation in house mice. This data was individually compiled from publically available datasets from 36 studies and remapped to the mm10 reference genome using LiftOver. The archived dataset contains both the original and the mapped coordinates.  2\) Results of permutation tests and rank sum tests looking for overlap within the house mouse data set. This was generated from tests comparing subsets of the house mouse dataset to each other. This data consists of CSV tables of p-values for overlap permutation tests, mean clines widths, and p-values for tests of cline width differences. ## Description of the data and file structure The data are in two folders. In "*house_mouse_data*", there are six files. These files contain our compilations of the publicly available datasets. Genes are described in one csv file (containing metadata on the source of the genes: "gene_list.csv") and one bed file (containing remapped genomic intervals: "remapped_gene_bed_081023.bed"). There are four versions of the interval loci dataset. These versions have the same list of intervals but differ in the way certain intervals are handled. For the main file ("lit_survey_candidate_loci.csv"), all intervals are reported as is for each dataset. For the subsequent files, QTL are reduced to 1Mb intervals around their peak value ("lit_survey_candidate_loci_1MbQTL.csv"), single marker loci are increased to 1Mb intervals around their values ("lit_survey_candidate_loci_1MbMarkers.csv"), or both ("lit_survey_candidate_loci_1MbQTL_1MbMarkers.csv"). A file labeled "annotation_glossary.csv" contains descriptions of the columns present in the other csv files. Columns that are actually required to complete the main analyses of the study are also indicated in this file. In "*comparison_data*", we have two csv files compiling the results of the comparisons described in our manuscript. One file ("permutation_summary.csv") includes the observed number of overlaps, p-values, and overlaps observed in permutations for all permutation tests measuring overlap between datasets. This file could be used to reconstruct the distributions of the permutation output. The second file ("cline_data.csv") contains mean cline widths and p-values for all comparisons of the data. ## Sharing/Access information The house mouse data provided here was compiled from the following studies: * Balcova, Maria, Barbora Faltusova, Vaclav Gergelits, Tanmoy Bhattacharyya, Ondrej Mihola, Zdenek Trachtulec, Corinna Knopf, et al. 2016. “Hybrid Sterility Locus on Chromosome X Controls Meiotic Recombination Rate in Mouse.” *PLOS Genetics* 12 (4): e1005906. https://doi.org/10.1371/journal.pgen.1005906. * Bímová, Barbora Vošlajerová, Miloš Macholán, Stuart J. E. 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