How many species are there? Lineage diversification and hidden speciation in Solanaceae from highland grasslands in southern South America

Species delimitation remains challenging, especially in recently diverged line-ages like P. guarapuavensis and P. scheideana, which exhibit morphological similarity despite independent species status. Diversification rates and morphological evolution are not strongly correlated, further complicating delimitation. Using RAD-seq employing a population genomic approach, we delimitated species and populations between P. guarapuavensis and P. scheideana. Despite slight morphological variation and unresolved phylogenetic relationships, we identified distinct lineages. Our analysis of 16,064 SNPs revealed P. scheideana (Psch1) and P. guarapuavensis as independent species. P. guarapuavensis splits into two lineages (Pgua1-6 and Pgua7-8), with a potential new lineage (Psch2-3) undergoing genetic and morphological speciation. While no evidence of hybridization was found, gene flow within P. guarapuavensis populations was observed. The Iguacu River likely contributes to the observed structuration between Pgua1-6 and Pgua7-8 + Psch2-3 populations by acting as a barrier, limiting gene flow. Fast divergence in Petunia may explain the morphological similarities despite species differentiation.