WhyMahonia? Molecular recircumscription ofBerberiss.l., with the description of two new genera,AlloberberisandMoranothamnus

Abstract Whether Mahonia should be recognized as a distinct genus or subsumed under Berberis has long been debated since its publication in 1818. Although recent molecular phylogenetic studies showed the paraphyly of Mahonia and some advocated a broadly defined Berberis to include Mahonia , the acceptance of Berberis s.l. is far from universal. Due to insufficient sampling and analytical issues of outgroup rooting, taxon misidentification, and the inclusion of a problematic GenBank DNA sequence, we argue that the phylogenetic status of Mahonia and consequently the circumscription of Berberis s.l. remains problematic. In particular, Berberis claireae and Mahonia sect. Horridae , taxa both inhabiting xeric habitats and characterized by a transitional morphology between Berberis s.str. and typical Mahonia (core Mahonia ), have not been adequately sampled and well‐positioned phylogenetically. With the inclusion of these key species and an expanded sampling of core Mahonia , we re‐examine the phylogenetic relationships of Berberis s.l. using the internal transcribed spacer (ITS) of nrDNA, and three coding regions ( accD, ndhF, rbcL ) and one non‐coding region ( psbA‐trnH ) of the chloroplast genome. Our analyses reveal four clades within Berberis s.l., corresponding to Berberis s.str., B. claireae , core Mahonia , and Mahonia sect. Horridae , with the latter three (all compound‐leaved) forming a paraphyletic grade sister to simple‐leaved Berberis . Because of morphological and ecological distinctness of these four clades and their deep stem divergences equivalent to other genera of Berberidaceae, we propose a new classification of Berberis s.l. by applying a strict definition of Berberis (≡ Berberis s.str.), reinstating Mahonia (≡ core Mahonia ), and proposing the two new genera Alloberberis nom. & stat. nov. (≡ Mahonia sect. Horridae ) and Moranothamnus gen. nov. (≡ B. claireae ). This revised classification is consistent with the traditional perception of Berberis and results in a monophyletic Mahonia, maintaining the stable usage of these two household names in both academic and non‐academic communities.