VCF filtered files from <i>P. guarapuavensis,</i> <i>P. scheideana,</i> <i>P. saxicola,</i> <i>P. reitzii,</i> <i>P. interior and P. axillaris </i>as outgroup.

The great diversity of species in nature arises through various processes, with rapid and recent diversification, or evolutionary radiations, playing a critical role in biodiversity evolution. In montane systems, plant radiations can result from various speciation modes, including ecological adaptation, progenitor-derivative speciation, pollinator isolation, and geographical isolation followed by local adaptation. This study uses Petunia species to investigate the main drivers of their rapid divergence and the colonization of highlands. Employing low coverage genome sequencing and a genomic population approach, we focused on detecting structuration, ecological inference, hybridization/introgression, and phylogenetic patterns. Our findings reveal an intricate and complex array of drivers of diversity. Evidence of ecological adaptation was observed without strong genetic diversification. We identified rapid differentiation in two lineages that did not undergo significant morphological changes. Crucially, ancestral polymorphism played a significant role in maintaining genetic diversity, facilitating the fast divergence of these species. During the Pleistocene, these Petunia species expanded into new areas, followed by fragmentation as forests expanded and contracted in response to climatic fluctuations. This period of environmental change was pivotal in promoting rapid speciation through geographic isolation and subsequent adaptation to varied habitats. This study highlights the multifaceted nature of species diversification, influenced by a confluence of geographic distribution, demographic history, hybridization, and climatic changes. The interplay of these factors emphasizes the diverse and dynamic pathways to speciation, contributing to a deeper understanding of plant diversification and the importance of both genetic and environmental factors in shaping biodiversity.