DOI: 10.5061/dryad.qnk98sfq1
title: Swordtail fish hybrids reveal that genome evolution is surprisingly predictable after initial hybridization

description: Over the past two decades, biologists have come to appreciate that
 hybridization, or genetic exchange between distinct lineages, is
 remarkably common – not just in particular lineages but in taxonomic
 groups across the tree of life. As a result, the genomes of many modern
 species harbor regions inherited from related species. This observation
 has raised fundamental questions about the degree to which the genomic
 outcomes of hybridization are repeatable and the degree to which natural
 selection drives such repeatability. However, a lack of appropriate
 systems to answer these questions has limited empirical progress in this
 area. Here, we leverage independently formed hybrid populations between
 the swordtail fish Xiphophorus birchmanni and X. cortezi to address this
 fundamental question. We find that local ancestry in one hybrid population
 is remarkably predictive of local ancestry in another, demographically
 independent hybrid population. Applying newly developed methods, we can
 attribute much of this repeatability to strong selection in the earliest
 generations after initial hybridization. We complement these analyses with
 time-series data that demonstrates that ancestry at regions under
 selection has remained stable over the past ~40 generations of evolution.
 Finally, we compare our results to the well-studied X. birchmanni×X.
 malinche hybrid populations and conclude that deeper evolutionary
 divergence has resulted in stronger selection and higher repeatability in
 patterns of local ancestry in hybrids between X. birchmanni and X.
 cortezi.
description: # Genome evolution is surprisingly predictable after initial hybridization
 [https://doi.org/10.5061/dryad.qnk98sfq1](https://doi.org/10.5061/dryad.qnk98sfq1) This dataset contains ancestry posterior probability files, processed ancestry files, LD map files, data used in wavelet analysis, genome annotation files, and input data used to generate figures in the manuscript. ## Description of the data and file structure *Ancestry file format:* ancestry-probs-par1: posterior probability of homozygous X. birchmanni ancestry for different samples and populations output by ancestryhmm ancestry-probs-par2: posterior probability of homozygous X. cortezi ancestry for different samples and populations output by ancestryhmm Posterior probabilities range from 0-1 and are given for each ancestry informative marker in each individual. The probability that a site is heterozygous for X. birchmanni and X. cortezi ancestry is equal to 1-(ancestry-probs-par1+ancestry-probs-par2). The file name contains the chromosome analyzed (allchrs), the population and individuals analyzed (CHPL - Chapulhuacanito, STAC - Santa Cruz, HUEX - Huextetitla), the collection year (2003, 2006, 2017, 2019, 2020, or 2021). Additionally, if the data was analyzed using a thinned set of ancestry informative markers, this is noted in the file name as "thinned AIMs." *Recombination map files:* LD_map post.txt files: output of LDhelmet estimating 4Ner between SNP intervals in X. birchmanni and X. cortezi population samples Recombination maps are provided separately for each chromosome (noted in the file name, e.g. chr-01 or scaf_01). The species for which the map corresponds is also noted in the file name: xbir - X. birchmanni and xcor - X. cortezi. Details on the LDhelmet output file format can be found in the LDhelmet documentation: [https://github.com/popgenmethods/LDhelmet](https://github.com/popgenmethods/LDhelmet) *Genome annotation files:* Gene annotation: .gff .gff format files are provided for annotation of the X. birchmanni (xbir-COAC-16-VIII-22-M_v2023.1.gff) and X. cortezi (xcor-PTHC-08-XII-21-M_v2023.2.gff) genome assemblies. Annotation was conducted using GeneWise, Exonerate, and AUGUSTUS, as described in the main text. Repeat master annotation: fa.out Predicted coordinates of repetitive elements identified in the X. birchmanni (xbir-COAC-16-VIII-22-M_v2023.1.fa.out) and X. cortezi genome assemblies (xcor-PTHC-08-XII-21-M_v2023.2.fa.out) using RepeatModeler and RepeatMasker, and repeat libraries Repbase and FishTEDB, as described in the main text. Output format of RepeatMasker is described in detail on the program's source page: [https://www.repeatmasker.org/](https://www.repeatmasker.org/) *Processed files:* Files used in analysis summarizing average ancestry, coding and conserved basepair density, and recombination rate datasets. allContempPops_crossover_codes_0.5cM_windows - input data file for ancestry crossover principal component analysis. For each window and each individual, a 1 indicates that a crossover was observed in that window in that individual and a 0 indicates that it was not. allSNPs_allsamples_xcorMapped_allChrs.map/ped - files in plink format for PCA analysis of SNPs for all high coverage individuals. hybrids_only_sharedXcorSNPs_allsamples_xcorMapped_allChrs.map/ped - files in plink format for PCA analysis of SNPs for all hybrid individuals. Only SNPs that fall in X. cortezi ancestry tracts are represented in this file (see Methods). sharedXcorSNPs_allsamples_xcorMapped_allChrs.map/ped - files in plink format for PCA analysis of SNPs for all individuals. Only SNPs that fall in X. cortezi ancestry tracts are represented in this file (see Methods). sharedXcorSNPs_justXcorInds_xcorMapped_allChrs.map/ped - files in plink format for PCA analysis of SNPs for pure X. cortezi individuals. Only SNPs that fall in X. cortezi ancestry tracts are represented in this file (see Methods). xbir_pacbio2023_allChrs_*cM_windows_recRate_codingBP_conservedBP_everything_minPar.txt - text files summarizing average minor parent ancestry, number of coding and conserved basepairs, number of SNPs and ancestry informative markers, for each population in windows of 0.05, 0.1, 0.25, 0.5 and 1 cM. xbir_2023pacbio_genome_0.05cm_windows_recRate_codingBP_xcorxbir_minPar_deserts_island.txt - text file following the above format but with an additional column specifying whether a region was a desert or Island, and in which population it was determined to be a desert or island. xbir_pacbio2023_allChrs_*kb_windows_recRate_codingBP_conservedBP_everything_minPar.txt - text files summarizing average minor parent ancestry, number of coding and conserved basepairs, number of SNPs and ancestry informative markers, for each population in windows of 5, 10 , 50, 100, 250, 500, and 1000 kb. xbirXcor_hybridIndex.txt - text file containing hybrid index of individuals analyzed in this study *Wavelet analysis files* Wavelet analyses were run on interpolated estimates of ancestry (see above under *Ancestry file format *for raw ancestry calls). Interpolation windows were intersected with LD-based recombination map and gene features to give interpolated estimates of recombination and gene density. This was done at two resolutions, 32kb (main text), and 1kb (supplement). The following files contain interpolated ancestry and recombination estimates: interpolated_ancestry_recomb_32kb.txt interpolated_ancestry_recomb_1kb.txt Results of wavelet analyses (wavelet variances and wavelet correlations) are provided in data tables associated with the relevant figures under "Data used to produce manuscript figures". ## Data used to produce manuscript figures Each file is named matching the figure and panel used to produce it. For example: "Fig1C_pcaDF_stacChplHuex_noOut_dataframe.txt" is the data file used to produce Figure 1 panel C in the manuscript. ## Sharing/Access information Raw sequence data is available on NCBI BioProject PRJNA1106506 ## Code/Software Code used in this project is available at: [https://github.com/Schumerlab/](https://github.com/Schumerlab/)