Phylogenetic and phylogenomic studies of wild onions (Allium, Amaryllidaceae) at three taxonomic scales

In North America north of Mexico, wild onions (Allium, Amaryllidaceae) are represented by 84 native species, 81 of which belong to subgenus Amerallium. Based on morphology, these species have been divided into eight informal taxonomic ‘alliances’ hypothesized to represent shared evolutionary history among species. The main aim of this research was to test the monophyly of the alliances with molecular phylogenetic methods. We sampled 74 Amerallium species north of Mexico and two Mexican endemics and constructed a molecular phylogeny of subgenus Amerallium in North America based on predominantly non-coding sequences from two nuclear ribosomal RNA regions (ITS and ETS) and two chloroplast regions (trnL–F and rpL32– trnL). Most clades are well supported in analyses of nuclear data and when nuclear and chloroplast data are combined. However the chloroplast data alone did not produce a wellresolved or well-supported tree. The alliances are largely supported by the molecular phylogenetic data, although strict monophyly was observed in only three of eight alliances. Morphological characters used to delimit groups are generally well-founded although there is some evidence of character reversal in bulb-coat structure. There is considerable geographic structure to the distribution of the two main clades, which are largely separated by the Rocky Mountains.