Peaches and almonds: phylogeny of Prunus subg. Amygdalus (Rosaceae) based on DNA sequences and morphology

Almonds and peaches are among the most economically important fruit crops in subtropical and temperate regions. Questions regarding the origin and domestication of the crop species, interspecific relationships, and evolutionary patterns of fruits have remained unanswered due to the lack of phylogenetic data of Prunus subgenus Amygdalus, in which both almond and peach are classified. Twenty-two species of subg. Amygdalus were included in phylogenetic analyses of plastid ndhF-rpl32, rpL16, trnH-psbA, trnL-trnF, trnQ-5'rps16, and trnS-trnG and nuclear s6pdh genes to investigate the circumscription of subg. Amygdalus, phylogenetic relationships among the species, and implication for mesocarp and endocarp evolution. Prunus subg. Amygdalus is best circumscribed to include both almonds and peaches, comprising two sections, Amygdalus and Persica. Species traditionally placed close to almonds, such as P. tenella, P. petunnikowii, P. triloba, and P. pedunculata, should be excluded from subg. Amygdalus. Characteristics used to diagnose subg. Amygdalus, such as dry, splitting mesocarp and the ornamentation of endocarp evolved multiple times in Prunus; thus classification based solely on these morphological characters produces a taxonomic scheme that might not represent common ancestry. A dry, splitting mesocarp is likely to be ancestral for the common ancestor of subg. Amygdalus, and the fleshy, non-splitting mesocarp found in peaches was derived from the dry, splitting mesocarp, presumably by domestication and selection for a fleshy fruit in China. Very low genetic divergence among cultivated almond and its close relatives might be associated with gene flow and/or rapid speciation within the group.