DOI: 10.5061/dryad.p8cz8wb3h
title: Data from: Admixture mapping reveals evidence for multiple mitonuclear incompatibilities in swordtail fish hybrids

description: How barriers to gene flow arise between closely related species is one of
 the oldest questions in evolutionary biology. Classic models in
 evolutionary biology predict that negative epistatic interactions between
 variants in the genomes of diverged lineages, known as hybrid
 incompatibilities, will reduce viability or fertility in hybrids. The
 genetic architecture of these interactions and the evolutionary paths
 through which they arise have profound implications for the efficacy of
 hybrid incompatibilities as barriers to gene flow between species. While
 these questions have been studied using theoretical approaches for several
 decades, only recently has it become possible to genetically map larger
 numbers of hybrid incompatibilities. Here, we use admixture mapping in
 natural hybrid populations of swordtail fish (Xiphophorus) to identify
 hybrid incompatibilities involving genetic interactions between the
 mitochondrial and nuclear genomes. We find that at least nine regions of
 the genome are involved in mitonuclear incompatibilities. These
 incompatibilities involve interactions between the nuclear genome and the
 X. malinche mitochondria, the X. birchmanni mitochondria, or both.
 Moreover, they vary in the strength of selection they experience and the
 degree to which they limit gene flow in natural hybrid populations. Our
 results build a deeper understanding of the complex architecture of
 selection against incompatibilities in naturally hybridizing species and
 highlight an important role of mitonuclear interactions in the evolution
 of reproductive barriers between closely related species.
description: # Data from: Admixture mapping reveals evidence for multiple mitonuclear
 incompatibilities in swordtail fish hybrids Dataset DOI:
 [10.5061/dryad.p8cz8wb3h](10.5061/dryad.p8cz8wb3h) ## Description of the
 data and file structure Data included here was used in the analysis for
 "Admixture mapping reveals evidence for multiple mitonuclear
 incompatibilities in swordtail fish hybrids" (Robles et al. 2025).
 Files are organized by general group of analyses. Additional files may be
 found here:
 [https://github.com/Schumerlab/mitonuc_DMI2](https://github.com/Schumerlab/mitonuc_DMI). The relevant input files can be found at [https://doi.org/10.5061/dryad.p8cz8wb3h](https://doi.org/10.5061/dryad.p8cz8wb3h), while raw sequencing files can be found under SRA BioProjects PRJNA744894, PRJNA746324, PRJNA610049, PRJNA361133, PRJNA745218, and PRJNA1305547.  This dataset includes a variety of data types, all of which aim to comprehensively explore putative mitonuclear incompatibilities in hybridizing swordtails of the genus *Xiphophorus*. This includes large amounts of local ancestry information from *Xiphophorus* hybrids, simulation input and output files, and miscellaneous tabular data from morphological measurements. In general, the local ancestry information is either presented as the raw output of the ancestryinfer pipeline ([https://doi.org/10.1111/1755-0998.13175](https://doi.org/10.1111/1755-0998.13175)), or a processed genotype file. The former is identified with the naming convention "ancestry-probs-par[1 or 2]*.txt", where 1 is birchmanni and 2 is malinche. The latter is identified by the convention "genotypes*" and include coordinates from the *X. birchmanni* reference genome as columns, individuals as rows, and genotypes as 0 (birchmanni), 1 (heterozygote), or 2 (malinche or cortezi, as applicable). 
 
 ### Files and variables #### File: CALL_NaturalHybrids_Data.zip
 **Description:** Data used for Natural Population Analysis from CALL and
 ACUA sites. Ancestry probabilities and genotype files from the Calnali Low
 (CALL) hybrid population and Acuapa (ACUA), referred to as the
 "admixture mapping population" in the manuscript. These data
 were used in partial correlation tests of mitonuclear associations, as
 well as the inference of selection and dominance coefficients of the
 identified incompatibilities. #### File: ClineAnalysis_Data.zip
 **Description:**  All data used for Cline Analysis. Ancestry probabilities
 and genotype files from natural hybrids at the following sites: CULH,
 TEXC, CSRL, POCH, PHLW, OCOT, ISLT, PICO, TULA, VCHO, ATMP, and AREN.
 Genotypes files are provided for each site, generated from the
 ancestry-tsv files output by ancestryinfer. Genotypes files were generated
 with the script
 [https://github.com/Schumerlab/Lab_shared_scripts/blob/master/parsetsv_to_genotypes_Dec2017_v2.pl](https://github.com/Schumerlab/Lab_shared_scripts/blob/master/parsetsv_to_genotypes_Dec2017_v2.pl) with a posterior probability threshold of 0.9. Tables include genotypes for each sampled individual at each ancestry informative site. 2 indicates homozygous X. malinche ancestry, 1 indicates heterozygous, and 0 indicates homozygous birchmanni ancestry. For sites without posterior probability 0.9 or greater for any ancestry state, NA is recorded. \ \ Data file formatted for input into the HZAR program (doi: 10.1111/1755-0998.12209): Cline_data_reformat_pochula_header_popinfo.csv\ Formatted data includes sampling sites (Loc.names), arbitrary locality id (Locality.ID), sampling elevation and sampling distance (Elevation_(Km) and Distance_(Km)), and then an entry of average ancestry per population and number of samples per population for each genomic marker. #### File: Simulations_Data.zip **Description:** Input files for null simulations using the program admixem ([https://doi.org/10.1093/bioinformatics/btv700](https://doi.org/10.1093/bioinformatics/btv700)) and simulation results. #### File: Lab_Generated_Hybrids_Data.zip **Description:** Ancestry data from second-generation (F2) *X. birchmanni* x *X. malinche* hybrids sequenced as part of the project. Note that other F2 hybrid genotypes included in this paper are available in another Dryad dataset: [https://doi.org/10.5061/dryad.z8w9ghx82](https://doi.org/10.5061/dryad.z8w9ghx82) and [https://doi.org/10.5061/dryad.j3tx95xmx](https://doi.org/10.5061/dryad.j3tx95xmx). #### File: Others_Data.zip **Description:** RNA-Seq metaData, raw expression data and other files used in the project that do not correspond to any of the previous sets of analysis. 1. Read count information used to test for allele-specific expression (ASE) of the genes ndufs5 and ndufa13 in liver samples of first-generation (F1) hybrids. 2. Normalized counts of four Complex I genes from RNAseq of pure *X. birchmanni* and *X. malinche,* plus F1 hybrids. ## Code/software Mac or Linux softwares are recommended to visualize the data. Data was created with a combination of R ( R/4.4.2),  Linux Bash, Python (python/3.9) and Perl (perl/5.26.0) code.  ## Access information Data was derived from the following code sources: * [https://github.com/Schumerlab/mitonuc_DMI2](https://github.com/Schumerlab/mitonuc_DMI2) * [https://github.com/Schumerlab/mitonuc_DMI](https://github.com/Schumerlab/mitonuc_DMI2) * [https://github.com/Schumerlab/Lab_shared_scripts](https://github.com/Schumerlab/Lab_shared_scripts)