In a recent phylogeny of Physalis, 11 U.S. perennial species in sections Viscosae and Lanceolatae form a monophyletic group. This species complex is an excellent study group for examining some of the assumptions made about ITS and its phylogenetic utility, as they are diploid, thus avoiding the complications of multiple genomes, and their biology is relatively well known. The purpose of this study was to examine interspecific patterns of ITS variation and their effects on phylogenetic reconstruction, as well as the interplay between secondary structure and levels of nucleotide variation. A waxy gene tree provided the phylogenetic hypothesis, and the results of phylogenetic analysis of ITS sequences were compared to this tree. A broad sampling of species within the complex, as well as multiple individuals from four closely related species, were sequenced for ITS. Artificial hybrids from crosses made between three of these species were also sequenced. Within the four heavily sampled species, the ITS sequences formed paraphyletic groups in three cases: one due to putative hybridization and possibly biased gene conversion, one due to polymorphism for two different ITS types and incomplete lineage sorting, and one due to the recent divergence of two taxa sharing similar ITS types. Including artificial hybrids in the phylogenetic analysis had little topological effect, and the hybrid sequences did not behave in a way which distinguished them from their parents. Structural analysis of the ITS sequences indicated that most large indel regions occurred at the single-stranded tips of stem regions, and may be subject to structural constraints, including constraints on size and maintenance of some base pairing within large insertions. These indels do provide some phylogenetic information, but are often homoplasious, so mapping indels onto a phylogeny may be a better approach than including them in the initial analysis.

Key words: ITS, phylogeny, Physalis, secondary structure, Solanaceae