Understanding the genetic basis of ecological differences between two endangered hybridizing Arabis floodplain species

Hybridization between closely related species has been increasingly recognized as a major source of biodiversity. Yet, whether hybridization can create advantageous trait combinations while effectively removing harmful alleles remains poorly understood. We focused on two close relatives Arabis nemorensis and A. sagittata, two endangered floodplain species that currently hybridize in a single hotspot. We measured 22 phenotypic traits and mapped their genetic basis in an F2 population. In total, 58 QTLs were identified for 20 traits, with both additive and dominance effects fitting a gaussian distribution. Six large-effect QTLs were linked to significant hybrid fitness loss. Two genomic regions showed strong transmission bias favoring A. sagittata alleles, potentially promoting introgression. However, 48% of QTLs were not linked to reduced fitness or segregation distortion, suggesting that hybrids may generate transgressive genotypes that exceed parental performance. Notably, a major QTL affecting flowering time explained 23% of phenotypic variation and implicated TFL1 as a candidate gene for life history adaptation. Comparing these results with patterns of ancient introgression and selection showed that genetic variation was not shaped by past gene flow. Overall, our findings demonstrate that interspecific hybridization has the potential to fuel adaptation.