Incomplete lineage sorting and hybridization as sources of gene tree discordance among species of the Geminata clade of <i>Solanum</i> (Solanaceae)

Abstract Discordance among gene trees, including discrepancies with the species tree, is increasingly reported in analyses of phylogenomic data. Such discordance can result from technical issues such as misalignment, paralogy, or model misfit, or from biological processes such as incomplete lineage sorting (ILS), hybridization with introgression, or horizontal gene transfer. Here, we explore the utility of the Angiosperms353 bait set in resolving evolutionary relationships within the Geminata clade of Solanum and discuss potential sources of gene tree discordance. Our results identify four main lineages within Geminata and suggest a niche specialization to wet ecosystems along the backbone of the clade. We found ILS to be the primary source of discordance, while hybridization likely played a secondary role in the diversification of the clade.