Epistatic interactions drive biased gene retention in the face of massive nuclear introgression

Phylogenomic analyses are recovering previously hidden histories of hybridization, revealing the genomic consequences of these events on the architecture of extant genomes. We exploit a suite of genomic resources to show that introgressive hybridization occurred between close relatives of Arabidopsis, impacting our understanding of species relationships in the group. We show that cytonuclear discordance arose via massive nuclear, rather than cytoplasmic, introgression. We develop a divergence-based test to distinguish donor from recipient lineages and find that selection against epistatic incompatibilities acted to preserve alleles of the recipient lineage, while neutral processes also contributed to genome composition through the retention of ancient haplotype blocks.