Raw Genotyping-by-Sequencing reads of a population of Petunia that displays variation in the color of the corolla, as well as other species used in the project: Petunia secreta, Petunia exserta, and Petunia integrifolia subspecies integrifolia.

Petunia presents a unique opportunity to study speciation in a diverse region with various pollinator syndromes. Recently, we discovered a population near a biodiversity hotspot displaying an extensive range of flower colors, from light to dark purple, suggesting a hybrid origin. We conducted Genotyping-by-Sequencing on multiple individuals to understand the population's origin and Petunia speciation patterns. Structure analysis revealed distinct genetic components in this population, and hybridization detection methods yielded conflicting results. Such conflict suggests high levels of incomplete lineage sorting due to rapid speciation in the region. Additionally, we tested 12 demographic models to understand divergence patterns among Petunia lineages and found that most species diverged in the presence of gene flow. The population shares the transcription factor AN2 haplotype with a purple-flowered species. Thus, the observed color variation within the group arises due to the influences of a different gene in the pathway or other extrinsic factors. In conclusion, we demonstrate that the high diversity of Petunia in this region results from complex interactions between rapid speciation and speciation with gene flow and that the evolution of different flower colors in this area probably occurred multiple times through distinct genetic mechanisms.