Phylogenetic relationships among 48 species of Prunus were investigated by means of maximum parsimony analysis of sequence polymorphism from nuclear ITS and chloroplast trnL-trnF spacer DNA. Several genera that have been implicated as close relatives of Prunus in previous studies were utilized as outgroups. The objective of this study was to reconstruct the phylogeny of Prunus with the purpose of reviewing previously described taxonomic relationships and providing a basis for studies of morphological evolution in the genus. Variability and homoplasy are higher in ITS than in trnL-trnF. Parsimony analysis of both markers, separately and in combination, supported a close relationship among Exochorda, Oemleria, and Prinsepia but did not support a sister relationship of this clade with Prunus. Prunus is monophyletic and divided into two groups. The first is a strongly supported clade composed of subgenera Padus, Laurocerasus, and Cerasus. None of these subgenera is monophyletic and the trait used to characterize Padus and Laurocerasus, flowers arranged in racemes, can be more broadly interpreted as a synapomorphy for the clade. The second group included the subgenera Amygdalus and Prunus, and sections Microcerasus (subgenus Cerasus), and Penarmeniaca, which has never been assigned to a subgenus. The exclusively North American subgenus Emplectocladus may be an early diverging taxon sister to the second group. Sections Prunus and Armeniaca are monophyletic with low bootstrap support. Section Penarmeniaca, from southwestern US, and P. besseyi (section Microcerasus) are sister taxa. A Eurasian origin of Prunus is supported.

Communicating Editor: Richard Jensen