Reticulate History of Southern South American Wild Potatoes: Recurrent Hybridization, Cytonuclear Discordance, and Phylogenetic Placement of Solanum malmeanum

Hybridization is a powerful process in plant evolution generating reticulate patterns of speciation, introgression, and chloroplast capture. In the Petota clade of Solanum, which spans cultivated and wild potatoes, these processes cause much of the taxonomic complexity of the group. We examined the evolutionary history of the Commersoniana group (Solanum commersonii and S. malmeanum) relative to S. chacoense (Tuberosa Group) using an integrative framework of phylogenomics and morphology. With target-capture sequencing (Angiosperms353) of nuclear and plastid loci recovered from herbarium specimens, together with data mining we built nuclear and plastome phylogenies and ran symmetry tests, gene concordance analyses, and coalescent simulations to weigh incomplete lineage sorting against chloroplast capture. The data reveal cytonuclear discordance and events consistent with chloroplast capture from S. chacoense into Commersoniana lineages supported by both empirical and simulated results. Phylogenetic networks confirm repeated historical and recent reticulation, especially involving S. malmeanum. Non-metric Multidimensional Scaling (NMDS) of morphological traits did not recover clear species boundaries but was consistent with a hybrid origin for the group. These results indicate that recurrent hybridization and event consistent with chloroplast capture are strongly influencing evolution in the examined wild potatoes, complicating classical taxonomy and informing conservation and breeding. They also underscore the value of combining genomic and phenotypic data to resolve species boundaries in plant groups with tangled hybrid histories.