Natural selection interacts with recombination to shape the evolution of hybrid genomes

TLDR

The study investigates how hybridization between two swordtail fish species shapes genome evolution by examining three naturally formed hybrid populations. The authors estimated fine‑scale genetic maps and inferred ancestry across 690 individuals in the hybrid populations. Ancestry from the minor parent is enriched in high‑recombination regions and where fewer deleterious epistatic targets exist, a pattern also seen in human‑archaic admixture, indicating that minor ancestry persists when rapidly uncoupled from deleterious interactions.

Abstract

To investigate the consequences of hybridization between species, we studied three replicate hybrid populations that formed naturally between two swordtail fish species, estimating their fine-scale genetic map and inferring ancestry along the genomes of 690 individuals. In all three populations, ancestry from the “minor” parental species is more common in regions of high recombination and where there is linkage to fewer putative targets of selection. The same patterns are apparent in a reanalysis of human and archaic admixture. These results support models in which ancestry from the minor parental species is more likely to persist when rapidly uncoupled from alleles that are deleterious in hybrids. Our analyses further indicate that selection on swordtail hybrids stems predominantly from deleterious combinations of epistatically interacting alleles.