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.

The early-diverging eudicot family Berberidaceae is composed of a morphologically diverse assemblage of disjunctly distributed genera long praised for their great horticultural and medicinal values. However, despite century-long studies, generic delimitation of Berberidaceae remains controversial and its tribal classification has never been formally proposed under a rigorous phylogenetic context. Currently, the number of accepted genera in Berberidaceae ranges consecutively from 13 to 19, depending on whether to define Berberis, Jeffersonia, and Podophyllum broadly, or to segregate these three genera further and recognize Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Dysosma, Diphylleia, and Sinopodophyllum, respectively. To resolve Berberidaceae’s taxonomic disputes, we newly assembled 23 plastomes and, together with 85 plastomes from the GenBank, completed the generic sampling of the family. With 4 problematic and 14 redundant plastome sequences excluded, robust phylogenomic relationships were reconstructed based on 93 plastomes representing all 19 genera of Berberidaceae and three outgroups. Maximum likelihood phylogenomic relationships corroborated with divergence time estimation support the recognition of three subfamilies Berberidoideae, Nandinoideae, and Podophylloideae, with tribes Berberideae and Ranzanieae, Leonticeae and Nandineae, and Podophylleae, Achlydeae, Bongardieae tr. nov., Epimedieae, and Jeffersonieae tr. nov. in the former three subfamilies, respectively. By applying specifically stated criteria, our phylogenomic data also support the classification of 19 genera, recognizing Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Diphylleia, Dysosma, and Sinopodophyllum that are morphologically and evolutionarily distinct from Berberis, Jeffersonia, and Podophyllum, respectively. Comparison of plastome structures across Berberidaceae confirms inverted repeat expansion in the tribe Berberideae and reveals substantial length variation in accD gene caused by repeated sequences in Berberidoideae. Comparison of plastome tree with previous studies and nuclear ribosomal DNA (nrDNA) phylogeny also reveals considerable conflicts at different phylogenetic levels, suggesting that incomplete lineage sorting and/or hybridization had occurred throughout the evolutionary history of Berberidaceae and that Alloberberis and Moranothamnus could have resulted from reciprocal hybridization between Berberis and Mahonia in ancient times prior to the radiations of the latter two genera.

The Asian paleotropical flora is characterized by abundance of endemic species, high biodiversity, and complex geological and climatic histories. However, the main driving mechanism underlying such high tropical biodiversity remains unclear. Hence, the present study aimed to investigate the biogeographic origin of the Asian paleotropical flora by tracking the speciation and diversification history of a typical tropical perennial, Typhonium sensu stricto (s.s.) (Araceae), using a time‐calibrated whole‐plastome phylogeny. In particular, we tested whether the Asian paleotropic region is a macroevolutionary source or sink. We observed that Typhonium s.s. originated in Indochina during the early–middle Miocene epoch, ca. 17.24 Ma (95% highest posterior density [HPD]: 12.83 ̶ 21.99 Ma). Most of the in situ diversification within the genus Typhonium s.s. has been underway since 14.73 Ma, with an accelerated lineage diversification at ca. 15−17 Ma, which may have been triggered by the intensification of the Asian monsoon system around the middle Miocene. Furthermore, the underground tuberous stem of Typhonium s.s. might have played an essential role in the adaptation to the seasonality caused by the monsoon in Indochina. Our results also suggested that peripatric speciation may be important in the diversification of T. trilobatum and T. roxburghii. This study provides a framework for studies in biogeography and evolution of the Asian paleotropical flora.

Berberis sect. Wallichianae are species of evergreen shrubs that in Taiwan are found in subalpine and montane-temperate areas and which have a notoriously controversial taxonomic history. Based on multivariate statistical analyses of morphometric data and an explicitly stated species criterion, the taxonomy of the group in Taiwan and its close relative in Luzon (B. barandana) is revised and their endemicity is evaluated by molecular data. In addition to the six species recognized in the Flora of Taiwan (rbcL, ycf6-psbM, and psbA-trnH) place all Taiwanese species and B. barandana in a strongly supported clade derived from within the continental Asian species of sect. Wallichianae, indicating their independent evolutionary history and supporting their endemic status.