Molecular phylogeny of the genus Amygdalus (Rosaceae) based on nrDNA ITS and cpDNA trnS-trnG sequences

With over 40 species, almonds (Amygdalus L.) are among the most economically important Rosaceae fruit crops distributed in the Irano-Turanian region of southwestern and Central Asia and southeastern Europe. While Amygdalus is considered a separate genus in floristic treatments of Asian countries it is a subgenus or a section of Prunus L. s.l. in other treatments. Phylogenetic relationships of the Iranian wild almonds based on data from 2 nuclear and chloroplast spacers (nrDNA ITS and cpDNA trnS-trnG) were constructed using the maximum parsimony and maximum likelihood, Bayesian inference, and NeighborNet methods. Data from 2 nuclear and chloroplast spacers were congruent. All of the Iranian almonds formed a well-established monophyletic clade, and the subgenus Cerasus was recovered as sister to Amygdalus. Amygdalus spinosissima Bge. was sister to all other Amygdalus species included in this study. Most of the Amygdalus species were grouped in a monophyletic clade that consisted of 2 subclades. The taxonomic status of 2 traditional subgenera of Amygdalus, Amygdalus and Dodecandra (Spach) Browicz, did not agree with the phylogenetic relationships revealed here. Among the studied species of Amygdalus, species of the section Spartioides Spach form a monophyletic clade (BV = 83%). Amygdalus mira Koehne, Amygdalus davidiana (Carriere) Franch., Amygdalus triloba Ltdl., and Amygdalus nana L. were recovered outside the main clade Amygdalus, indicating that these species should be excluded from Amygdalus. Similar to the previous phylogenetic studies in Prunus s.l., phylogenetic analysis did not fully resolve relationships of the studied Amygdalus. NeighborNet analysis of the nrDNA ITS dataset of Iranian almonds supported reticulate relationships for all Amygdalus hybrids as previously reported.