DOI: 10.5061/dryad.dbrv15f8v
title: Pervasive gene flow despite strong and varied reproductive barriers in swordtails

description: The evolution of reproductive barriers leads to the formation of new
 species. However, recent research has demonstrated that hybridization has
 been pervasive across the tree of life even in the presence of strong
 barriers. Using swordtail fishes (genus Xiphophorus), an emerging model
 system, we document overlapping mechanisms that act as barriers to gene
 flow between X. birchmanni and X. cortezi by combining genomic sequencing
 from natural hybrid populations, experimental laboratory crosses,
 behavioral assays, sperm performance, and developmental studies. We show
 that assortative mating plays a role in maintaining subpopulations with
 distinct ancestry within natural hybrid populations. Using F2 hybrids we
 identify several genomic regions that strongly impact hybrid viability.
 Strikingly, two of these regions underlie genetic incompatibilities in
 hybrids between X. birchmanni and its sister species X. malinche. Our
 results demonstrate that ancient hybridization has played a role in the
 origin of this shared genetic incompatibility. Moreover, ancestry mismatch
 at these incompatible regions has remarkably similar consequences for
 phenotypes and hybrid survival in X. cortezi  × X.
 birchmanni hybrids as in X. malinche × X. birchmanni hybrids. Our
 findings identify varied reproductive barriers that shape genetic exchange
 between naturally hybridizing species and highlight the complex
 evolutionary outcomes of hybridization.
description: # Pervasive gene flow despite strong and varied reproductive barriers in
 swordtails
 [https://doi.org/10.5061/dryad.dbrv15f8v](https://doi.org/10.5061/dryad.dbrv15f8v) ## Description of the data and file structure Please see the Main Text and Supplementary Information from Aguillon et al. for details on analyses using these data files. Note on abbreviations across data files: "CHPL" = Chapulhuacanito (the primary sampling location); "cor" or "xcor" = *X. cortezi*; "bir" or "xbir" = *X. birchmanni*; "corXbir" or "XcorXbir" = hybrid between *X. cortezi* and *X. birchmanni*; "NA" = indicates a missing value * **Files containing an estimate of overall genomic ancestry:** `CHPL-contemporary-ancestry.txt` (contemporary samples from Chapulhuacanito in years 2021-2022), `CHPL-historic-ancestry.txt` (historical samples from Chapulhuacanito in years 2003, 2006, 2017), `mother-embryo-ancestry.txt` (paired mother/embryo samples), `testing-priors-xbir.txt` (testing the use of a uniform versus cluster-specific admixture prior with the ancestry HMM in the Chapulhuacanito *X.* *birchmanni* cluster), `testing-priors-xcor.txt` (testing the use of a uniform versus cluster-specific admixture prior with the ancestry HMM in the Chapulhuacanito admixed cluster). These files contain columns on # of ancestry informative markers with *X. cortezi* (cor_count) or *X. birchmanni* (bir_count) ancestry, the calculated hybrid index, heterozygosity, # of sequencing reads (read_count), and mitochondrial haplotype (mtDNA; 0 = *X. birchmanni*, 2 = *X. cortezi*) for each sampled individual (sampleID). For the files testing uniform versus cluster-specific admixture priors, columns end in either \_U (uniform prior) or \_N (not uniform prior, e.g., cluster-specific prior) to indicate the difference between ancestry HMM runs. * **Files containing F2 genotypes:** `XcorXbir-PF2-genotypes-110623.txt``transposed`* *and `XcorXbir-PF2-I-24-S255-genotypes-021924.txt_transposed` contain hard genotype calls for all ancestry informative markers (AIMs) for *X. cortezi* x *X. birchmanni* F2 hybrids. These files are organized with individual F2s as columns and AIMs as rows. Included genotypes are 1 (homozygous *X. birchmanni*), 2 (heterozygous), or 3 (homozygous *X. cortezi*). Additionally, the file `XcorXbir-F2-fullgenotypes.txt_transposed_ancestry_by_site` has taken these genotype calls and used them to determine average ancestry (across all the F2s) at all sites along the genome. The files include columns for the chromosome (chr or group), position along the chromosome in basepairs (pos or position), hybrid index, and # of individuals with sufficient sequencing reads at that position (indivs_cov). * **Files related to sperm morphology and motility:** `sperm-morphology.xlsx` (data on sperm head length, sperm head width, and sperm mid-length) and `sperm-motilities.csv` (data on sperm VSL, VCL, VAP, STR, and progressive motility). Both files include data taken from four males each of *X. birchmanni, X. cortezi*, and their lab-produced F1 and F2 hybrids. Abbreviations: head_l = head length, head_w = head width, mid_l = midpiece length, VSL = straight-line velocity between the start and end of the sperm path, VCL = curvilinear velocity along the actual sperm path, VAP = the velocity over a smoothed sperm path, PM = progressive motility (a measure of the proportion of sperm swimming in a mostly straight line), STR = path straightness (VSL/VAP * 100).  * **Files related to behavioral assays:** Files with the name format `Raw_data-cor-bir-pheromone-tracking-Trial____##.xlsx` or `Raw_data-CHPL-pheromone-tracking-Trial____##.xlsx` are raw output files from the tracking program EthoVision from processing video recordings of mate choice trials. Starting at row 35, these raw data files include the X,Y position of the fish within the experimental tank at 0.2 or 0.4 s intervals, along with a 0 (absent) or 1 (present) value for if the tested individual was found within either of the two association zones at the time point. This data is preceded by header information (row 1-33) detailing settings used to process the raw video recordings in EthoVision. The useful variables from the header include Trial name (the # at the end of the file name, and matching the "file_name" column in the associated keyfile), Video file (with info matching the "trial_name" column in the associated keyfile), and Arena settings (which indicates if the processed file was for the A or B trial lane, and matching the "trial_lane" column in the associated keyfile). All associated analyses were conducted using the presence/absence data below the header using custom scripts. The two associated "keyfiles" (`pheromone-trial-keyfile.xlsx` and `CHPL-pheromone-trial-keyfile.xlsx`) contain columns on individual fish used in trials, date/time trials were conducted, and information connecting trials to EthoVision raw output. Note that the correct date/time of the conducted trials is included in the keyfiles, not the raw Ethovision output (as the header information in the latter reflects the processing of the trial, not the recording of the trial). The file `live-male-behavior-data.xlsx` includes results on behavioral trials that were conducted with live male as stimuli. The file `video-observations-summary.csv` includes results from video observations in the Chapulhuacanito population. * **Files containing output from ABC simulations:** `ABC_simulations_accepted_F2s_Feb2024_ch6.txt` (ABC simulation results for the genomic region containing the gene *ndufa13*) `ABC_simulations_accepted_F2s_Feb2024_ch13.txt` (ABC simulation results for the genomic region containing the gene *ndufs5*), `ABC_simulations_accepted_F2s_Feb2024_ch7.txt` (ABC simulation results for a genomic region with distorted ancestry proportions on chromosome 7), `ABC_simulations_accepted_F2s_ch14.txt` (ABC simulation results for a genomic region with distorted ancestry proportions on chromosome 14). These simulations were for selection and the relevant columns are s (selection) and h (dominance). Additionally, `ABC_mito_tdiv_simulations_accepted_November2024.txt`  includes ABC simulation results to estimate the divergence time between *X. cortezi* and *X. malinche* mitochondrial haplotypes. The relevant column is Generations. * **Files containing output from SLiM simulations:** `all_xmal_xcor_simulated_results_100sim_burnin.txt` (results from SLiM simulations comparing *X. malinche* with *X. cortezi*), `all_xmal_xmoz_simulated_results_100sim_burnin.txt` (results from SLiM simulations comparing *X. malinche* with *X. montezumae*), `all_xmal_xbir_simulated_results_100sim_burnin.txt` (results from SLiM simulations comparing *X. malinche* with *X. birchmanni*).  ## Genomic Data Availability New genomic data generated for this project is available through the NCBI BioProject [PRJNA1106506](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1106506). ## Code Availability Data processing scripts to work with all included files are available on GitHub ([https://github.com/stepfanie-aguillon/swordtail-reproductive-barriers-NatureEE2025](https://github.com/stepfanie-aguillon/swordtail-reproductive-barriers-NatureEE2025), [https://github.com/Schumerlab/Lab_shared_scripts](https://github.com/Schumerlab/Lab_shared_scripts)) or Zenodo ([https://doi.org/10.5281/zenodo.14736259](https://doi.org/10.5281/zenodo.14736259)). Note that data file names in the Dryad Repository are consistent with those used in the GitHub/Zenodo Repository code.