Swordtail fish hybrids reveal that genome evolution is surprisingly predictable after initial hybridization

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 attribut..., , , # 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 contai...