Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset.

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data. We found cytonuclear discordance between the two, which is likely a result of rampant hybridization among closely and more distantly related lineages. To evaluate the impact of such hybridization on the nuclear phylogeny reconstruction, we performed five different gene sampling routines, which increasingly removed putatively paralog genes. Our cleaned subset of 297 genes revealed high support for the tribes, whereas support for the main lineages (supertribes) was moderate. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene origin of the family. Finally, our results strongly support a recently published new family classification, dividing the family into two subfamilies (one with five supertribes), together representing 58 tribes. This includes five recently described or re-established tribes, including Arabidopsideae, a monogeneric tribe accommodating Arabidopsis without any close relatives. With a worldwide community of thousands of researchers working on Brassicaceae and its diverse members, our new genus-level family phylogeny will be an indispensable tool for studies on biodiversity and plant biology.

A New Classification of the Dictyostelids.

Traditional morphology-based taxonomy of dictyostelids is rejected by molecular phylogeny. A new classification is presented based on monophyletic entities with consistent and strong molecular phylogenetic support and that are, as far as possible, morphologically recognizable. All newly named clades are diagnosed with small subunit ribosomal RNA (18S rRNA) sequence signatures plus morphological synapomorphies where possible. The two major molecular clades are given the rank of order, as Acytosteliales ord. nov. and Dictyosteliales. The two major clades within each of these orders are recognized and given the rank of family as, respectively, Acytosteliaceae and Cavenderiaceae fam. nov. in Acytosteliales, and Dictyosteliaceae and Raperosteliaceae fam. nov. in Dictyosteliales. Twelve genera are recognized: Cavenderia gen. nov. in Cavenderiaceae, Acytostelium, Rostrostelium gen. nov. and Heterostelium gen. nov. in Acytosteliaceae, Tieghemostelium gen. nov., Hagiwaraea gen. nov., Raperostelium gen. nov. and Speleostelium gen. nov. in Raperosteliaceae, and Dictyostelium and Polysphondylium in Dictyosteliaceae. The "polycephalum" complex is treated as Coremiostelium gen. nov. (not assigned to family) and the "polycarpum" complex as Synstelium gen. nov. (not assigned to order and family). Coenonia, which may not be a dictyostelid, is treated as a genus incertae sedis. Eighty-eight new combinations are made at species and variety level, and Dictyostelium ammophilum is validated.

Evolution and loss of long-fringed petals: a case study using a dated phylogeny of the snake gourds, Trichosanthes (Cucurbitaceae).

BACKGROUND: The Cucurbitaceae genus Trichosanthes comprises 90-100 species that occur from India to Japan and southeast to Australia and Fiji. Most species have large white or pale yellow petals with conspicuously fringed margins, the fringes sometimes several cm long. Pollination is usually by hawkmoths. Previous molecular data for a small number of species suggested that a monophyletic Trichosanthes might include the Asian genera Gymnopetalum (four species, lacking long petal fringes) and Hodgsonia (two species with petals fringed). Here we test these groups' relationships using a species sampling of c. 60% and 4759 nucleotides of nuclear and plastid DNA. To infer the time and direction of the geographic expansion of the Trichosanthes clade we employ molecular clock dating and statistical biogeographic reconstruction, and we also address the gain or loss of petal fringes. RESULTS: Trichosanthes is monophyletic as long as it includes Gymnopetalum, which itself is polyphyletic. The closest relative of Trichosanthes appears to be the sponge gourds, Luffa, while Hodgsonia is more distantly related. Of six morphology-based sections in Trichosanthes with more than one species, three are supported by the molecular results; two new sections appear warranted. Molecular dating and biogeographic analyses suggest an Oligocene origin of Trichosanthes in Eurasia or East Asia, followed by diversification and spread throughout the Malesian biogeographic region and into the Australian continent. CONCLUSIONS: Long-fringed corollas evolved independently in Hodgsonia and Trichosanthes, followed by two losses in the latter coincident with shifts to other pollinators but not with long-distance dispersal events. Together with the Caribbean Linnaeosicyos, the Madagascan Ampelosicyos and the tropical African Telfairia, these cucurbit lineages represent an ideal system for more detailed studies of the evolution and function of petal fringes in plant-pollinator mutualisms.

Synopsis of Trichosanthes (Cucurbitaceae) based on recent molecular phylogenetic data.

The snake gourd genus, Trichosanthes, is the largest genus in the Cucurbitaceae family, with over 90 species. Recent molecular phylogenetic data have indicated that the genus Gymnopetalum is to be merged with Trichosanthes to maintain monophyly. A revised infrageneric classification of Trichosanthes including Gymnopetalum is proposed with two subgenera, (I) subg. Scotanthus comb. nov. and (II) subg. Trichosanthes, eleven sections, (i) sect. Asterospermae, (ii) sect. Cucumeroides, (iii) sect. Edulis, (iv) sect. Foliobracteola, (v) sect. Gymnopetalum, (vi) sect. Involucraria, (vii) sect. Pseudovariifera sect. nov., (viii) sect. Villosae stat. nov., (ix) sect. Trichosanthes, (x) sect. Tripodanthera, and (xi) sect. Truncata. A synopsis of Trichosanthes with the 91 species recognized here is presented, including four new combinations, Trichosanthes orientalis, Trichosanthes tubiflora, Trichosanthes scabra var. pectinata, Trichosanthes scabra var. penicaudii, and a clarified nomenclature of Trichosanthes costata and Trichosanthes scabra.

Vigna (Leguminosae) sensu lato: the names and identities of the American segregate genera.

PREMISE OF STUDY: The legume genus Vigna and close relatives have highly elaborated floral morphologies that involve the coiling, bending, and intricate connection of flower parts. Banners, levers, platforms, and pumps have evolved that attract pollinators and then manipulate their movement. Given this three-dimensional floral complexity, the taxonomy of Vigna and relatives has been confounded by the study of mostly two-dimensional museum specimens. A molecular phylogenetic analysis was undertaken in the effort to resolve long-standing taxonomic questions centered on floral morphology. METHODS: The phylogenetic analysis included cpDNA trnK and nuclear ribosomal ITS/5.8S (ITS) sequence variation. The American species were comprehensively sampled and outgroups included Old World relatives. KEY RESULTS: The trnK and ITS data analyses concurred in resolving six well-supported clades of American Vigna that are most closely related to other American genera: Dolichopsis, Macroptilium, Mysanthus, Oryxis, Oxyrhynchus, Phaseolus, Ramirezella, and Strophostyles. These 14 American clades ranked here as genera are resolved as sister to a clade comprising the mainly Old World species of Vigna. CONCLUSIONS: American Vigna clades were reassigned to the genera Ancistrotropis, Cochliasanthus, Condylostylis, Leptospron, Sigmoidotropis, and the newly described Helicotropis. Vigna sensu stricto in the Americas now includes relatively few and mostly pantropical species. Elaborate floral asymmetries are readily used to apomorphically diagnose nearly all of the American genera. The age estimates of the extant diversification of the American and its Old World sister clade are approximately coeval at ca. 6-7 million yr, which belies much greater floral variation in the Americas.

Old-New World and trans-African disjunctions of Thamnosma (Rutaceae): intercontinental long-distance dispersal and local differentiation in the succulent biome.

PREMISE OF THE STUDY: The succulent biome is highly fragmented throughout the Old and New World. The resulting disjunctions on global and regional scales have been explained by various hypotheses. To evaluate these, we used Thamnosma, which is restricted to the succulent biome and has trans-Atlantic and trans-African disjunctions. Its three main distribution centers are in southern North America, southern and eastern Africa including Socotra. METHODS: We conducted parsimony, maximum likelihood, and Bayesian phylogenetic analyses based on chloroplast and nuclear sequence data. We applied molecular clock calculations using the programs BEAST and MULTIDIVTIME and biogeographic reconstructions using S-DIVA and Lagrange. KEY RESULTS: Our data indicate a weakly supported paraphyly of the New World species with respect to a palaeotropical lineage, which is further subdivided into a southern African and a Horn of Africa group. The disjunctions in Thamnosma are mostly dated to the Miocene. CONCLUSIONS: We conclude that the Old-New World disjunction of Thamnosma is likely the result of long-distance dispersal. The Miocene closure of the arid corridor between southern and eastern Africa may have caused the split within the Old World lineage, thus making a vicariance explanation feasible. The colonization of Socotra is also due to long-distance dispersal. All recent Thamnosma species are part of the succulent biome, and the North American species may have been members of the arid Neogene Madro-Tertiary Geoflora. Phylogenetic niche conservatism, rare long-distance dispersal, and local differentiation account for the diversity among species of Thamnosma.

Evidence for a vicariant origin of Macaronesian-Eritreo/Arabian disjunctions in Campylanthus Roth (Plantaginaceae).

The numerous disjunct plant distributions between Macaronesia and eastern Africa-Arabia suggest that these could be the relicts of a once continuous vegetation belt along the southern Tethys, which has been fragmented by Upper Miocene-Pliocene aridification. We tested this vicariance hypothesis with a phylogenetic analysis of Campylanthus (Plantaginaceae), based on nuclear and plastid DNA sequence data. Our results indicate a basal split within Campylanthus giving rise to Macaronesian and Eritreo-Arabian lineages in the Pliocene/Upper Miocene. This is consistent with the vicariance hypothesis, thus obviating the need to postulate trans-Saharan long-distance dispersal. The biogeography of Campylanthus may parallel patterns in other plant groups and the implications for our understanding of the biogeography of northern and eastern Africa, and Arabia are discussed.

Relationships of cucumbers and melons unraveled: molecular phylogenetics of Cucumis and related genera (Benincaseae, Cucurbitaceae).

Cucumis (Cucurbitaceae) comprises 33 species of annuals and perennials with a major native center of diversity in tropical and southern Africa. The genus includes some economically important and widely grown vegetables such as cucumbers and melons. Monophyly of the genus has been disputed in previous studies, but with only limited sampling. Relationships within Cucumis are thus poorly understood; moreover, the validity of the closely related genera has not been thoroughly tested. The present study was undertaken to test the monophyly of Cucumis and several closely related genera, to test sectional circumscriptions within Cucumis, and to understand the biogeographical history of the genus. We sequenced the nuclear ITS and plastid trnS-trnG regions for 40 ingroup and three outgroup taxa, representing all recognized subgenera and sections. Parsimony, maximum likelihood, and Bayesian analyses found Cucumella, Oreosyce, Mukia, Myrmecosicyos, and Dicaelospermum nested within Cucumis. The clades recovered within the Cucumis complex in some instances represent the first phylogenetically derived hypothesis of relationships, whereas others correspond to previous subgeneric and sectional classifications. At least four introductions from Africa to Asia, as well as one reintroduction to Africa, are suggested within the Cucumis complex. Cucumis sativus (cucumber) is strongly supported as sister to the eastern Asian C. hystrix, whereas C. melo (melon) is strongly supported as sister to C. sagittatus in southern Africa.

Botanical nomenclature in pharmacovigilance and a recommendation for standardisation.

Nomenclature of plants in pharmacology can be presented by pharmaceutical names or scientific names in the form of Linnaean binomials. In this paper, positive and negative aspects of both systems are discussed in the context of the scientific nomenclatural framework and the systems' practical applicability. The Uppsala Monitoring Centre (UMC) runs the WHO Programme for International Drug Monitoring and is responsible for the WHO Adverse Drug Reaction (ADR) database that currently contains 3.6 million records. In order for the UMC to monitor pharmacovigilance through ADRs to herbal medicine products the following nomenclatural criteria are important: (i) the name should indicate only one species of plant; (ii) the source for this name must be authoritative; (iii) the name should indicate which part of the plant is used. Based on these criteria, the UMC investigated four options: (i) adopt main names used in recognised (inter-) national pharmacopoeias or authoritative publications; (ii) adopt option 1, but cite the publication for all names in abbreviated form; (iii) three-part pharmaceutical names consisting of Latinised part name plus Latinised genus name, plus Latinised specific epithet; (iv) scientific binomial names, optionally with author and plant part used. The UMC has chosen the latter option and will at its adoption utilise the scientific botanical nomenclature as defined by the International Code of Botanical Nomenclature. This decision satisfies all criteria set by the UMC and renders the necessity of creating a new system or upgrading an old inconsistent system obsolete. The UMC has also issued an extensive synonymy checklist of vernacular, pharmaceutical and scientific names for the herbals in the WHO ADR database. We strongly recommend the adoption of scientific names to denote plant ingredients in medicine.

Botanical Nomenclature in Pharmacovigilance and a Recommendation for Standardisation.

Nomenclature of plants in pharmacology can be presented by pharmaceutical names or scientific names in the form of Linnaean binomials. In this paper, positive and negative aspects of both systems are discussed in the context of the scientific nomenclatural framework and the systems' practical applicability. The Uppsala Monitoring Centre (UMC) runs the WHO Programme for International Drug Monitoring and is responsible for the WHO Adverse Drug Reaction (ADR) database that currently contains 3.6 million records. In order for the UMC to monitor pharmacovigilance through ADRs to herbal medicine products the following nomenclatural criteria are important: (i) the name should indicate only one species of plant; (ii) the source for this name must be authoritative; (iii) the name should indicate which part of the plant is used. Based on these criteria, the UMC investigated four options: (i) adopt main names used in recognised (inter-) national pharmacopoeias or authoritative publications; (ii) adopt option 1, but cite the publication for all names in abbreviated form; (iii) three-part pharmaceutical names consisting of Latinised part name plus Latinised genus name, plus Latinised specific epithet; (iv) scientific binomial names, optionally with author and plant part used. The UMC has chosen the latter option and will at its adoption utilise the scientific botanical nomenclature as defined by the International Code of Botanical Nomenclature. This decision satisfies all criteria set by the UMC and renders the necessity of creating a new system or upgrading an old inconsistent system obsolete. The UMC has also issued an extensive synonymy checklist of vernacular, pharmaceutical and scientific names for the herbals in the WHO ADR database. We strongly recommend the adoption of scientific names to denote plant ingredients in medicine.

Metacommunity process rather than continental tectonic history better explains geographically structured phylogenies in legumes.

Penalized likelihood estimated ages of both densely sampled intracontinental and sparsely sampled transcontinental crown clades in the legume family show a mostly Quaternary to Neogene age distribution. The mode ages of the intracontinental crown clades range from 4-6 Myr ago, whereas those of the transcontinental crown clades range from 8-16 Myr ago. Both of these young age estimates are detected despite methodological approaches that bias results toward older ages. Hypotheses that resort to vicariance or continental history to explain continental disjunct distributions are dismissed because they require mostly Palaeogene and older tectonic events. An alternative explanation centring on dispersal that may well explain the geographical as well as the ecological phylogenetic structure of legume phylogenies is Hubbell's unified neutral theory of biodiversity and biogeography. This is the only dispersalist theory that encompasses evolutionary time and makes predictions about phylogenetic structure.