In Physalis, yellow flowers with darkly spotted throats give rise to berries which are completely enveloped by inflated, lantern-like calyces. Despite this distinctive morphology, taxonomists have had difficulty delimiting the genus, and little is known about the phylogenetic relationships of the 75+ species of Physalis. DNA sequence data from a segment of the nuclear gene waxy (600 bp) and the ITS region of the nrDNA (800 bp) was used to generate a phylogeny of Physalis. Taxon sampling included 30 species of Physalis plus related physaloid genera. The data sets were analyzed simultaneously using maximum parsimony as the optimality criterion. All characters had equal weights and gaps were treated as missing data. Trees were rooted using the outgroup Witheringia. As currently defined, Physalis is polyphyletic. While the morphologically typical species form a strongly supported clade, P. alkekengi (white flowers), P. carpenteri (clustered flowers) and P. microphysa (deeply lobed calyx) are separated from this clade by a grade of physaloid genera including Quincula, Physalis subgenus Physalodendron (P. melanocystis and P. arborescens), Oryctes and Chamaesaracha. P. alkekengi, the type of Physalis and its only Eurasian member, is not included in the main Physalis clade. That clade consists of Margaranthus (in fruit, indistinguishable from Physalis) and Physalis species with solitary yellow flowers and highly inflated calyces. Other than section Viscosa (predominantly North American), the sections of Physalis do not appear to be monophyletic, though a rhizomatous perennial clade is formed by section Viscosa and the U.S. species of section Lanceolatae. In general, the phylogeny supports the physaloid genera as being distinct from Physalis, but does not support the monophyly of sections within the genus. However, further sampling within Physalis may suggest ways in which the infrageneric classification can be adjusted to recognize both monophyletic and morphologically distinctive units.

Key words: ITS, phylogeny, Physalis, physaloid, Solanaceae, waxy