Dated phylogeny, phylogeography, and classification of Allium subgenus Amerallium (Amaryllidaceae) from the Old World, based on six DNA fragments

Abstract The present study aims to reveal phylogenetic and phylogeographical patterns of the Eurasian species of Allium subg. Amerallium , covering 75% of the species in the Mediterranean region and East Asia, as well as 12 North American species representing most sections of the monophyletic American part of the subgenus. We sampled 38 species of A. subg. Amerallium out of a total of 52 species from the Old World. A molecular phylogeny of A. subg. Amerallium was constructed based on predominantly non‐coding sequences from two nuclear ribosomal RNA regions (ITS, ETS), and four chloroplast (cp) regions ( trnL‐trnF , atpB‐rbcL , rpl32‐trnL , rps16 intron). Most clades are well supported in the analyses of the combined nuclear and chloroplast data. However, analyses of single chloroplast fragments produced different topologies, which can be explained by differences in the variability of the chloroplast regions studied. Analysis of all cpDNA fragments combined produced a similar topology compared to the tree based on nuclear data. Most sections in the Eurasian part of A. subg. Amerallium are monophyletic. Only the position of A. chamaemoly (monotypic A. sect. Chamaeprason ) nested in A. sect. Molium makes the latter paraphyletic. Different positions of A. chamaemoly within nuclear and plastid trees indicate an ancient hybridogenic origin. Monophyly of the American species of A. subg. Amerallium suggests an origin from extinct North Asian taxa. Currently, only one species from this ancient group, A. kingdonii , still exists in the eastern Himalayas.