Raw Genotyping-by-sequencing reads of Petunia axillaris subsp. subandina, Petunia exserta, and Petunia sp3 (natural hybrid between P. exserta and P. secreta). Raw sequence reads
Delimiting species is a complex yet crucial task for understanding biodiversity. However, this challenge intensifies when species boundaries are blurred by hybridization, as most species delimitation methods do not directly account for gene flow. The plant genus Petunia offers a unique opportunity to investigate the impact of gene flow on species diversification and delimitation due to diverse hybrid classes found in nature, even between species with distinct pollination syndromes. This study aimed to reconstruct phylogenetic relationships among multiple Petunia lineages within the long corolla tube clade and assess the effect of sampling admixed individuals on species delimitation analyses. We used genotyping-by-sequencing (GBS) data from 315 individuals spanning different lineages and contact zones. Our findings unveil rapid diversification and substantial levels of incomplete lineage sorting among these taxa. Moreover, these species have undergone extensive ancient and recent hybridization, even between species with distinct pollination syndromes. Using BFD* to delimit species, we found that species count is overestimated regardless of the presence of admixed individuals. Our conclusion highlights the persistent challenge of delineating species boundaries, indicating that even with genomic advancements, integrative taxonomy remains essential for delimiting species, particularly in hybridization-prone taxa.