Mahonia vs. Berberis Unloaded: Generic Delimitation and Infrafamilial Classification of Berberidaceae Based on Plastid Phylogenomics

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.

A New and Expanded Phylogenetic Analysis of Hyptidinae (Ocimeae-Lamiaceae)

Abstract— Hyptidinae, ca. 400 species, is an important component of Neotropical vegetation formations. Members of the subtribe possess flowers arranged in variously modified bracteolate cymes and nutlets with an expanded areole and all share a unique explosive mechanism of pollen release, except for Asterohyptis. In a recent phylogenetic study, the group had its generic delimitations rearranged with the recognition of 19 genera in the subtribe. Although the previous phylogenetic analysis covered almost all the higher taxa in the subtribe, it lacked a broader sampling at the species level. Here we present a new expanded phylogenetic analysis for the subtribe comprising 153 accessions of Hyptidinae sequenced for the nuclear nrITS, nrETS, and waxy regions and the plastid markers trnL-F, trnS-G, trnD-T, and matK. Our results widely support the previous phylogenetic results with some changes in the support and relationship between genera. It also uncovers the need for a new combination of Eriope machrisae in Hypenia and the phylogenetic position of Hyptis sect. Rhytidea, which was demonstrated to be part of Mesosphaerum. The generic delimitation in Hyptidinae is discussed, and we recommend that further studies with more markers are needed to confirm the monophyly of Hyptidendron and Mesosphaerum, as well as to support taxonomic changes on the infrageneric delimitation within Hyptis s. s.

A Taxonomic Revision of the Genus Dracophyllum Labill. (Ericaceae)

<p>In recent years the New Zealand biogeographic paradigm has shifted from 'Moa's Ark' (Bellamy et al. 1990) to the view that most biota has dispersed here in the lastà à ± 10 My (Fleming 1975, Pole 1994, McGlone et al. 2001). Large and widely distributed genera on island archipelagos and oceanic islands are important elements for the investigation of evolutionary processes such as dispersal from continents to islands and back, adaptive radiation and in some cases extinction. The genus Dracophyllum (Ericaceae: Richeeae) occurs on the Australian continent and the New Zealand archipelago as well as on many oceanic islands in the region. With its wide distribution, ecological importance and apparent taxonomic complexity, a monograph and phylogenetic study of Dracophyllum will make a valuable contribution towards the understanding of the above- mentioned processes. There is still uncertainty about generic limits within tribe Richeeae (Dracophyllum Labill., Richea R. Br. and Sphenotoma R. Br. ex Sweet). Sphenotoma is geographically isolated (southwest Western Australia), monophyletic and forms a distinct evolutionary lineage that diverged early from Dracophyllum and Richea (Powell et al. 1996, Kron et al. 2002). The generic limits between Dracophyllum and Richea still need to be addressed, preferably by making use of DNA sequence data. There are two fundamental aims of systematics: a) to discover, describe and name all species and b) to document the changes on the branches that have occurred during evolution and to transform these into a predictive classification system that reflects evolution (Systematics 18 Agenda 2000). Systematics is therefore the study of the biological diversity that exists on earth today and its evolutionary history (Judd et al. 1999). Taxonomic revisions, especially of large groups, need to focus on groups that are monophyletic (i.e. comprising an ancestor and all of its descendents) and not constrained by geography. Generic delimitation can become problematic when the flora of a specific region is studied in isolation. Many important aspects of genotypic and phenotypic variation are then not taken into consideration, resulting in a skewed and unrealistic representation of the genus as a whole. The long list of synonyms in the southern hemisphere for the genus Veronica L. is a reflection of this situation: Paederota L., Hebe Comm. ex Juss., Derwentia Raf., Pygmaea Hook.f., Detzneria Schltr. ex Diels, Parahebe W.R.B.Oliv., Chionohebe B.G.Briggs & Ehrend., Leonohebe Heads, Heliohebe Garn.-Jones and Hebejeebie Heads.</p>

A Taxonomic Revision of the Genus Dracophyllum Labill. (Ericaceae)

<p>In recent years the New Zealand biogeographic paradigm has shifted from 'Moa's Ark' (Bellamy et al. 1990) to the view that most biota has dispersed here in the lastà à ± 10 My (Fleming 1975, Pole 1994, McGlone et al. 2001). Large and widely distributed genera on island archipelagos and oceanic islands are important elements for the investigation of evolutionary processes such as dispersal from continents to islands and back, adaptive radiation and in some cases extinction. The genus Dracophyllum (Ericaceae: Richeeae) occurs on the Australian continent and the New Zealand archipelago as well as on many oceanic islands in the region. With its wide distribution, ecological importance and apparent taxonomic complexity, a monograph and phylogenetic study of Dracophyllum will make a valuable contribution towards the understanding of the above- mentioned processes. There is still uncertainty about generic limits within tribe Richeeae (Dracophyllum Labill., Richea R. Br. and Sphenotoma R. Br. ex Sweet). Sphenotoma is geographically isolated (southwest Western Australia), monophyletic and forms a distinct evolutionary lineage that diverged early from Dracophyllum and Richea (Powell et al. 1996, Kron et al. 2002). The generic limits between Dracophyllum and Richea still need to be addressed, preferably by making use of DNA sequence data. There are two fundamental aims of systematics: a) to discover, describe and name all species and b) to document the changes on the branches that have occurred during evolution and to transform these into a predictive classification system that reflects evolution (Systematics 18 Agenda 2000). Systematics is therefore the study of the biological diversity that exists on earth today and its evolutionary history (Judd et al. 1999). Taxonomic revisions, especially of large groups, need to focus on groups that are monophyletic (i.e. comprising an ancestor and all of its descendents) and not constrained by geography. Generic delimitation can become problematic when the flora of a specific region is studied in isolation. Many important aspects of genotypic and phenotypic variation are then not taken into consideration, resulting in a skewed and unrealistic representation of the genus as a whole. The long list of synonyms in the southern hemisphere for the genus Veronica L. is a reflection of this situation: Paederota L., Hebe Comm. ex Juss., Derwentia Raf., Pygmaea Hook.f., Detzneria Schltr. ex Diels, Parahebe W.R.B.Oliv., Chionohebe B.G.Briggs & Ehrend., Leonohebe Heads, Heliohebe Garn.-Jones and Hebejeebie Heads.</p>

Polyozellus vs. Pseudotomentella: generic delimitation with a multi-gene dataset

Polyozellus and Pseudotomentella are two genera of closely related, ectomycorrhizal fungi in the order Thelephorales; the former stipitate and the latter corticioid. Both are widespread in the Northern Hemisphere and many species from both genera seem to be restricted to old growth forest. This study aimed to: a) identify genetic regions useful in inferring the phylogenetic relationship between Polyozellus and Pseudotomentella, b) infer this relationship with the regions identified and c) make any taxonomic changes warranted by the result. RPB2, mtSSU and nearly full-length portions of nrLSU and nrSSU were found to be comparatively easy to sequence and provide a strong phylogenetic signal. A STACEY species tree of these three regions revealed that Polyozellus makes Pseudotomentella paraphyletic. As a result, nearly all species currently placed in Pseudotomentella were recombined to Polyozellus. Pseudotomentella larsenii was found to be closer to Tomentellopsis than Polyozellus, but its placement needs further study and it was hence not recombined.

Tocoyena longilobata, a replacement name for Posoqueria speciosa (Gardenieae, Rubiaceae)

Aublet (1775) described Posoqueria Aublet (1775: 133, tab. 51) and differentiated it from Tocoyena Aublet (1775: 131, tab. 50) by the number of locules of the ovary (unilocular vs. bilocular, respectively) and seed shape (angulate vs. subspherical, respectively). However, in subsequent studies, L.C.M.Richard (1792) and Lamarck (1793) published under Tocoyena certain species that morphologically matched the generic concept of Posoqueria, causing an historical confusion concerning their generic delimitation. Achille Richard (1830), in his Mémoire sur la famille des Rubiacées, synonymized Posoqueria under Tocoyena, a generic delimitation not widely adopted by subsequent authors. For example, Schumann (1889) in Flora Brasiliensis treated Posoqueria and Tocoyena as distinct genera.

A cladistic approach for generic delimitation of Paracloeodes Day, Rivudiva Lugo-Ortiz & McCafferty, and Varipes Lugo-Ortiz & McCafferty (Ephemeroptera: Baetidae)

The taxonomic knowledge of Baetidae has been greatly improved in the last decades in South America. Despite the advances, there are problems that need to be addressed. One of these problems is doubt concerning the systematics of species assigned to the genera Paracloeodes Day, Rivudiva Lugo-Ortiz & McCafferty, and Varipes Lugo-Ortiz & McCafferty, and the evolution of long setae on femora. In the present paper, the monophyly of these three genera is tested using a cladistic approach. The matrix included 53 species and 151 morphological characters: 127 for nymphs and 24 for adults. The dataset was analyzed under equal and implied weights with nine values of k. Group support was estimated with relative Bremer and frequency differences. The results corroborate (i) the paraphyly of Paracloeodes and Varipes, which become monophyletic without P. caldensis + V. singuil, proposed as a new genus Rhopyscelis gen. n., (ii) the long setae on femora as an independent acquisition between Rhopyscelis gen. n. + Varipes and Rivudiva, (iii) the transversal rows of setae on femora as an independent acquisition between Rhopyscelis gen. n. + Varipes and Rivudiva, (iv) the spine on subgenital plate as an independent acquisition between Paracloeodes, Rivudiva and Gen. A.