Pervasive weak incompatibilities shape phenotypic variation and genome evolution in yeast hybrids

Species barriers limit gene flow and maintain co-adapted genomes. Interspecific hybridization can break down species barriers, generating phenotypic variation and altering evolutionary potential. Although the phenotypic and genomic consequences of hybridization have been extensively studied in many systems, far less is known about the longer-term evolutionary dynamics of highly divergent, mosaic genomes and the extent to which genetic incompatibilities shape their adaptation. By suppressing anti-recombination genes in meiosis, we generate 20 haploid recombinant hybrids from a cross between Saccharomyces cerevisiae and Saccharomyces paradoxus. Across conditions, these hybrids are, on average, less fit than either parent and show broad phenotypic variation. Patterns of protein-complex inheritance reveal no evidence of strong pairwise lethality but support pervasive weak negative genetic interactions. Using laboratory evolution, we show that each recombinant genome follows a distinct adaptive trajectory, and that a small subset of hybrid protein complexes and loci show hybrid-specific mutational targeting. Species-of-origin alleles also bias evolutionary outcomes by reshaping selection on interacting genes. Together, these results indicate that strong pairwise incompatibilities are rare, while weak, background-dependent interactions are widespread and shape both phenotypic variation and genome evolution in hybrid genomes.