Taxonomy of the traditional medicinal plant genus Ferula (Apiaceae) is confounded by incongruence between nuclear rDNA and plastid DNA

The aim of this study was to identify major clades in the economically important and taxonomically difficult genus Ferula (Apiaceae tribe Scandiceae subtribe Ferulinae) to provide a classification framework. Phylogenetic relationships among 126 of Ferula spp. and eight species of its sister genus Leutea were evaluated based on nuclear ribosomal (nr) DNA ITS and three plastid regions: the rps16 intron, the rpoC1 intron and the rpoB-trnC intergenic spacer. One hundred and fifty-three accessions were considered including type specimens of seven species. Congruence between nrDNA and plastid DNA data was assessed using a hierarchical likelihood ratio test. Phylogenetic trees were inferred using maximum likelihood and Bayesian methods. Terminals introducing topological conflict were ascertained using two approaches: identifying (1) these with significantly different positions between nrDNA and plastid DNA trees; and (2) a set of rogue taxa in combined trees that, when removed, increased tree resolution and bootstrap support. The results demonstrate significant incongruence between nrDNA and plastid DNA data that persisted after the removal of 41 terminals identified as having significantly different position in nrDNA and plastid DNA trees or after the removal of 13 terminals identified as rogue taxa. Comparison of nrDNA and plastid DNA trees suggest intensive reticulate evolution, particularly in the Irano-Turanian floristic region. Traditional classification systems of the genus are not supported by molecular data, whereas some lineages apparent in molecular trees, particularly Chinese and Mediterranean endemics, are congruent with morphological characters and/or biogeography. We select lectotypes for several infrageneric names and propose a new classification system of the genus with four subgenera and ten sections.