Incomplete lineage sorting and hybridization underlie of tree discordance in Petunia and related genera (Petunieae, Solanaceae)

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Pedro Henrique Pezzi , Lucas C Wheeler, Loreta Brandão Freitas, Stacey D. Smith


Despite the overarching history of species divergence, phylogenetic studies often reveal distinct topologies across regions of the genome. The sources of these gene tree discordances are variable, but incomplete lineage sorting (ILS) and hybridization are among those with the most biological importance. Petunia serves as a classic system for studying hybridization in the wild. While field studies suggest that hybridization is frequent, the extent of reticulation within Petunia and its closely related genera has never been examined from a phylogenetic perspective. In this study, we used transcriptomic data from 11 Petunia, 16 Calibrachoa, and 10 Fabiana species to illuminate the relationships between these species and investigate whether hybridization played a significant role in the diversification of the clade. We inferred that gene tree discordance within genera is linked to hybridization events along with high levels of ILS due to their rapid diversification. Moreover, network analyses estimated deeper hybridization events between Petunia and Calibrachoa, genera that have different chromosome numbers. Although these genera cannot hybridize at the present time, ancestral hybridization could have played a role in their parallel radiations, as they share the same habitat and life history.



Biodiversity, Bioinformatics, Botany, Genomics


gene flow, Incomplete lineage sorting, Introgression, Solanaceae, Speciation., incomplete lineage sorting, introgression, Solanaceae, speciation


Published: 2024-03-29 04:09

Last Updated: 2024-06-25 06:33

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CC-BY Attribution-NonCommercial 4.0 International

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Conflict of interest statement:

Data and Code Availability Statement:
All scripts and processed data files are available at and The raw RNA-seq data files are available in SRA under the BioProject accession number PRJNA746328.