Evolution requires processes that both generate novel (heritable) variation and processes that filter this variation through random genetic drift or natural selection. The revolution of modern sequencing techniques shed light on the importance of major genetic rearrangements, such as hybridization (Abbott et al. 2013; Runemark et al. 2019) and whole genome duplication (polyploidization; Van de Peer et al. 2017) for the origin of novel variation. The rapidly increasing genomic approaches has provided an opportunity for investigations into the adaptive potential and evolutionary constraints of the process of hybrid genome formation (Runemark et al. 2018a,b; Runemark et al. 2019). One major challenge is to understand how selection interacts with hybrid and polyploid genomes in shaping genomic architecture and generating novel adaptation and adaptive radiation. One fruitful way forward is to focus our genomic efforts and apply cutting-edge genomic techniques to model systems with solid data on ecological selection, through the formation of strategic collaborations between researchers in evolutionary ecology and evolutionary genomics. Here, I will make full use of such a collaboration with Dr. Magne Friberg to address four key questions on the origins of novel variation in the ploidy-variable plant-insect interaction model system Lithophragma bolanderi (Friberg et al. 2019). Together, we address four main questions: 1. What is the genomic origins and composition of different ploidy levels and is this genomic composition predictive of phenotypes? 2. How repeatable is the genomic composition across different ploidy levels? 3. Are the patterns of gene expression, sub-genome dominance and diploidization consistent among ploidy levels, populations and/or polyploid origins? 4. How does pollinator-mediated natural selection interact with and shape the genomes?