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
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.