Polyploidy plays a prominent role in the speciation process in plants. Many species are known to be part of agamic complexes comprising sexual diploids and more or less exclusively asexual polyploids. However, polyploid formation has been studied in very few cases, primarily because of the challenges in examining these cases phylogenetically. In this study, we demonstrate the use of a variety of phylogenetic approaches to unravel origins and infer reticulation history in a diploid-polyploid complex of black-fruited Polyploidy, or the multiplication of entire genomes, has played an important role in the diversification of species lineages and has been found common in plants as well as, increasingly, in fish and amphibians (Ptacek et al.