Molecular systematics of Lilium and allied genera (Liliaceae): phylogenetic relationships among Lilium and related genera based on the rbcL and matK gene sequence data

Coding regions of the rbcL and matK genes of cpDNA were sequenced to analyze phylogenetic relationships of the family Liliaceae sensu stricto , including the major 16 genera of Medeoloideae and Lilioideae of the Liliaceae, in reference to several genera such as Scoliopus, Uvularia, Disporum , and Trillium used as outgoups. The results were congruent with the taxonomic concept of Liliaceae sensu stricto recently proposed by . The inter‐ and infrageneric relationships in the genus Lilium and allied taxa were then analyzed based upon the rbcL and matK gene sequencing data, using Medeola and Erythronium as outgroups. The rbcL gene has evolved more slowly than matK and its phylogenetic resolution has been poor as a result of the low base substitution rates; whereas the matK gene has shown a much higher base substitution: 104 variable sites (including 80 informative sites) out of 1641 base pairs were detected. In addition, a remarkably high number of indels, i.e. 19 insertion/deletion events, were detected in the matK gene, which provided us with new evidence for structural changes of this gene within the genus Lilium and allied taxa. Phylogenetic analyses based on the majority rule of the sequence data of matK gene revealed that the genus Lilium consists of three different major clades, including taxa that were placed into different sections by earlier taxonomic treatments, and thus the results of molecular systematic analysis was not congruent with sectional delimitations of the genus Lilium based on the morphological characters. Nomocharis pardanthina and Nomocharis saluenensis were ingroup taxa of Lilium . Notholirion, Cardiocrinum , and Fritillaria turned out to be sister groups to Lilium . An evaluation of the morphological and life‐history characteristics was also attempted in light of the molecular phylogeny.