bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cardamine maritima group (Brassicaceae) in the amphi‐Adriatic area: A hotspot of species diversity revealed by DNA sequences and morphological variation
Authors: Kučera Jaromír , Marhold Karol , Lihová Judita 
Published: February 2019

AbstractThe western Balkans, characterized by high rates of endemism, are recognized as one of the most diverse and species‐rich areas of Europe. The present study focuses on diploid speciation in a poorly explored ancestral group of the genus Cardamine that is distributed in the amphi‐Adriatic territory. Morphological data and DNA sequences (plastid trnL intron and trnL‐trnF spacer, ITS of nrDNA, and single‐copy nuclear gene CHS) were used to address taxonomic, phylogenetic and evolutionary questions. Recognition of several previously described, but recently not accepted narrow endemics is supported (C. fialae, C. rupestris, C. serbica). Cardamine maritima s.str. is segregated into three distinct entities, which were given species rank. A new taxonomic concept of the group is proposed, including identification key, synonymy, typifications, C. montenegrina sp. nov. and C. adriatica nom. nov. Chloroplast data indicate radiation of the ancestral lineage into a series of distinct endemic species; lack of resolution at internal nodes and incongruence with nuclear phylogenies suggest that this radiation occurred rapidly. Nuclear data indicate more recent hybridization events. It is assumed that glacial‐induced local‐scale and altitudinal migrations along the Balkan coastline and in adjacent massifs caused contacts between previously isolated populations, resulting in occasional interspecific gene‐flow. Trans‐Adriatic contacts and gene exchange are also suggested.
Floral formulae updated for routine inclusion in formal taxonomic descriptions
Authors: Prenner Gerhard , Bateman Richard M. , Rudall Paula J. 
Published: February 2019

AbstractBuilding on two centuries of history, we advocate an expanded and maximally informative format for floral formulae to describe angiosperm flowers in formal taxonomic descriptions. Using standard typeface and Unicode character codes, the format can summarise a wide range of features, including: acropetal sequence of organ initiation, number and symmetry of each whorl of floral organs (bracts, sepals, petals [or tepals], androecium, gynoecium, ovules), position of the organs relative to each other, partial and/or complete fusion of organs, resupination, organ loss and suppression, and deviations from standard bisexuality. We use several complex flowers to demonstrate our view that all known flower morphs can be accurately represented by the updated format, and show how use of floral formulae can outline some unanswered questions regarding the floral organisation of the model organism Arabidopsis. Possible uses of floral formulae extend beyond static description of mature morphology into the comparative realm. When combined with phylogenies, they help to elucidate generalised groundplans, plesiomorphic architecture, and the location and polarity of particular character‐state transitions. They can usefully be applied within as well as between species, to compare wildtype versus mutant morphs and different ontogenetic stages. Perhaps their greatest strengths are that they (1) require only a universally available typescript, and (2) bring a comprehensive uniformity to the description of flowers, acting as a checklist of features to be examined. We recommend that floral formulae become a routine component of diagnoses in protologues and other formal taxonomic (re)descriptions, functioning as a logical phenotypic counterpart to the DNA barcode.
DNA barcoding of African Podostemaceae (river‐weeds): A test of proposed barcode regions
Authors: Kelly Laura J. , Ameka Gabriel K. , Chase Mark W. 
Published: February 2019

AbstractDNA barcoding has the possibility for application in many fields, ranging from biological inventory and species discovery to forensics and quality control. Barcoding could have great utility within the aquatic angiosperm family Podostemaceae, as these plants can be extremely difficult to identify on the basis of morphological characters alone, but are important components of tropical rivers and face threats from increased water pollution. Several potential barcodes for land plants have been suggested, including two 3‐locus combinations proposed by the Plant Working Group of the Consortium for the Barcode of Life. These loci, matK, rpoB, rpoC1, and trnH‐psbA, were tested for their potential utility in African members of the Podostemaceae. Our results show that although the rpoC1 region performs best in terms of universality of amplification and sequencing, the superior resolving power of matK makes it the most promising of the regions for use in barcoding. In the light of these results, we discuss the potential to apply barcoding to Podostemaceae of Africa and make suggestions for the directions of future work to exploit the full potential of this new technology in this group of plants.
Back to types! Towards stability of names in Indian Curcuma L. (Zingiberaceae)
Authors: Leong-Škorničková Jana , Šída Otakar , Marhold Karol 
Published: February 2019

AbstractThe existence of the type material indicated in the protologues of all Indian Curcuma species names is confirmed or excluded following visits to numerous herbaria. Lectotypes, neotypes and epitypes are designated for previously untypified names or names for which the holotype is missing. Earlier ineffective or superfluous typifications are discussed, several new synonyms are recognised and notes on critical taxa are provided.
Report of the Nomenclature Committee for Fungi: 15
Authors: Norvell Lorelei L. 
Published: February 2019

AbstractThe following names are recommended for conservation: Pseudocercospora against Stigmina and Phaeoisariopsis; Boletus applanatus against B. lipsiensis; Lyophyllum with L. semitale as conserved type; Roccellina against Roccellaria; Psilocybe with P. semilanceata as conserved type; Calvatia nom. cons. against Lanopila; and Phaeographis against Cre‐ographa, Ectographis, Flegographa, Hymenodecton, Platygramma, and Pyrographa and with P. dendritica as conserved type. As a result of reference under Art. 32.4, the Committee recommends that the descriptive statement accompanying publication of Ascomycota Cavalier‐Smith be considered adequate for valid publication but recommends that that for Blasto‐cladiomycota Doweld should not.
Paraphyly and the origin and classification of angiosperms
Authors: Stuessy Tod F. 
Published: February 2019

AbstractThe recent classification of angiosperms by Chase and Reveal, based on APG III and emphasizing holophyletic concepts, results in a system of 16 coordinate superorders. Some of these contain very little diversity, such as Amborellanae or Ceratophyllanae, and others are extremely rich, such as Lilianae (monocots) or Rosanae. It is argued that the very diverse basal angiosperm group may represent ancient early lines of evolution (early evolutionary experiments) that have come from different seed fern ancestors. A reasonable approach to the classification of this mixed group is to regard them as a paraphyletic class of angiosperms (Archaeangiospermae). This allows the eudicots and monocots to be treated, as often in the past, as class Dicotyledonae and class Monocotyledonae.
The origins of Eleocharis (Cyperaceae) and the status of Websteria, Egleria, and Chillania
Authors: Hinchliff Cody E. , Lliully A. Ariel Ernesto , Carey Timothy , Roalson Eric H. 
Published: February 2019

AbstractEleocharis R. Br. is an ecologically and economically important genus that contains about 250 species of annual and perennial sedges, with centers of diversity in seasonally wet tropical to subtropical regions. Phylogenetic relationships in the genus are poorly understood, particularly in relation to three monotypic genera—Egleria L.T. Eiten, Chillania Roivainen, and Websteria (Poir.) S. Hooper—which have been variously included or excluded from Eleocharis in different classifications. These genera, while morphologically distinct, show characteristics that fall within the range of variation seen in Eleocharis. The relationship between the clade containing Eleocharis and these segregate genera (i.e., Eleocharideae) and the rest of Cyperaceae has also been difficult to determine from previous studies, and numerous conflicting hypotheses have been suggested. To address these uncertainties, we sequenced cpDNA from the ndhF and psbB-psbH marker regions and used it to reconstruct the phylogenetic history of Eleocharis and a broad sample of other Cyperaceae. We found that Egleria and Websteria are derived from within Eleocharis, and that this clade, representing the Eleocharideae, is sister to the Abildgaardieae. Chillania could not be included in the molecular dataset, but its morphology suggests it should be included in Eleocharis. New nomenclature is suggested to place the species of Chillania, Egleria, and Websteria in Eleocharis. Our phylogenetic reconstructions also indicate several other instances of generic paraphyly in other Cyperaceae lineages.
A molecular phylogeny of Solanum sect. Pteroidea (Solanaceae) and the utility of COSII markers in resolving relationships among closely related species
Authors: Tepe Eric J. , Bohs Lynn 
Published: February 2019

AbstractSolanum sect. Pteroidea is a lineage of ten species of neotropical herbs and vines with a center of distribution in the eastern Andean slopes. It is a member of the Potato clade of Solanum, a group that includes the potato (S. tuberosum) and tomato (S. lycopersicum). Members of S. sect. Pteroidea are characterized by inflorescences that emerge from the leaf axils and rugose, sharply pointed fruits in most species. The aim of this study is to infer phylogenetic relationships among sixteen species of Solanum, including all ten species of S. sect. Pteroidea, using DNA sequence data from the chloroplast trnT-trnF and five nuclear regions: ITS, the granule bound starch synthase gene (GBSSI or waxy), and three Conserved Orthologous Set II (COSII) markers. Results provide strong support for the monophyly of S. sect. Pteroidea and for its sister group relationship to S. sect. Herpystichum. Solanum mite, one of the most widespread and morphologically variable species in the section, is not monophyletic. Bayesian analyses using a total evidence concatenated approach and a coalescent approach implemented in BEST produced largely congruent topologies. The total evidence trees, however, were much more highly supported than the BEST trees. Although not useful individually in S. sect. Pteroidea, the three COSII markers were easy to amplify, provided clean sequences, and were tremendously useful in increasing resolution and support among the closely related species of S. sect. Pteroidea in combined analyses.
Systematics and character evolution of Tabernaemontaneae (Apocynaceae, Rauvolfioideae) based on molecular and morphological evidence
Authors: Simões André O. , Endress Mary E. , Conti Elena 
Published: February 2019

AbstractTabernaemontaneae (Rauvolfioideae, Apocynaceae) are small trees with mainly animal–dispersed fleshy fruits and arillate seeds represented in the tropics of Africa, Asia, the Pacific and America. The tribe is characterized by complex indole alkaloids, thus its species play a prominent role in traditional medicine. Taxonomically, the Tabernaemontaneae have a convoluted history fraught with contention as to tribal, subtribal, generic and sectional delimitation, with some authors recognizing Ambelanieae and Macoubeeae as separate tribes and others including them in an expanded Tabernaemontaneae s.l. In the species–rich pantropical genusTabernaemontana, seven sections and up to 30 segregate genera have been described during the past 100 years, giving it the dubious distinction of being the most disputed genus in Apocynaceae s.str. Here 420 new chloroplast DNA sequences from 104 species, including representatives of all satellite genera ever recognized in the Tabernaemontaneae, were analyzed phylogenetically to evaluate previous circumscriptions of Tabernaemontaneae and test the sectional treatment ofTabernaemontana. The Tabernaemontaneae s.l. as currently circumscribed was shown to be monophyletic. Of the 19 genera recognized in the most recent classification, 15 are maintained. The generaBonafousia, Stemmadenia, StenosolenandWoytokowskiaare nested withinTabernaemontana. Of the seven current sections ofTabernaemontana, the four that included taxa from more than one continent were found to be para– or polyphyletic. All natural groups recovered withinTabernaemontanawere found to correspond to geographic areas. Mapping of 29 selected morphological characters onto the molecular tree recovered recurrent suites of co–occurring character states and identified three synapomorphies characterizing the Tabernaemontaneae s.l.: (1) specialized anthers with massive lignified guide–rails; and a differentiated style–head with (2) a five–lobed upper crest and (3) a thickened basal flange. A new combination for the subtribe Ambelaniinae and the necessary new combinations resulting from mergingStemmadeniaintoTabernaemontanaare made.
Geometric morphometrics: A powerful tool for the study of shape evolution in Menispermaceae endocarps
Authors: Jacques Frédéric M.B. , Zhou Zhekun 
Published: February 2019

AbstractWithin Menispermaceae, endocarp shape is highly variable and often characteristic. This study applied geometric morphometrics to the investigation of horseshoe–shaped endocarps that characterized the former Menispermeae tribe. The shape of 823 endocarp specimens, representing 66 species and 16 genera, were described on the lateral face by the means of 4 landmarks and 18 semilandmarks. The general Procrustes analysis was used to remove size and orientation of the specimens. Using thin–plate splines, we were able to visualize and describe the variation in shape for each genus and/or species. The main differences concern the symmetry/asymmetry of endocarp, the relative size of condyle, the relative length of ventral face and the concavity of ventral face. The results of a PCA reveal that for all genera exceptDiploclisia, generic variability is explained by a continuum in intra– and interspecific variability. Endocarp shape differed significantly between genera, demonstrating the potential for geometric morphometrics in fossil identification. Allometry explained only a small part of shape variation. Phylogenetic content is evaluated by comparing the results of cluster analysis with recent molecular phylogenies. Endocarp shape affinities appear to be quite different from phylogenetic relationships, demonstrating the low phylogenetic signal in endocarp shape at the family level. However, stronger variation is found in the lineages leading to modern genera. With a known phylogeny, geometric morphometrics is a good tool to understand shape evolution.
Taxonomic revision of Sargassum sect. Acanthocarpicae (Fucales, Phaeophyceae)
Authors: Mattio Lydiane , Payri Claude E. , Verlaque Marc , de Reviers Bruno 
Published: February 2019

AbstractSargassum is one of the morphologically most complex phaeophyceaen genera, and is divided into subgenera, sections, subsections, series and species groups based on highly polymorphic characters. Recent DNA analyses have highlighted incongruities in the traditional classification of the genus and especially within Sargassum subg. Sargassum sect. Acanthocarpicae. Our goal was to re–assess the relationships among taxa currently attributed to this section in the Pacific basin. We undertook the taxonomic study in two main steps: (1) the morphological examination of large collections from inter–tropical Pacific islands and type specimens from worldwide localities; and (2) DNA analyses using a set of three markers (ITS–2, partial rbcLS–operon, cox3). Morphological and DNA analyses confirmed that S. sect. Acanthocarpicae is based on unsuitable morphological characters and is not monophyletic. On the basis of this study, we propose (1) abandoning subsections within S. sect. Acanthocarpicae; (2) synonymization of S. sect. Acanthocarpicae and sect. Malacocarpicae with sect. Sargassum; and (3) the elevation of S. ser. Ilicifoliae and ser. Binderianae to sectional rank as well as their re–description according to new sets of morphological characters.
Typification and nomenclature of Podocarpus angustifolius Griseb. and Podocarpus aristulatus Parl. (Podocarpaceae)
Authors: Mill Robert R. , Stark Schilling Darian M. 
Published: February 2019

AbstractThe nomenclature of Podocarpus angustifolius Griseb. and P. aristulatus Parl., names applied to two taxonomically distinct Cuban species of Podocarpus sect. Pumilis (Podocarpaceae), is discussed. Both names are based on material collected by Charles Wright. The complexities of typifying names based on this collector's material are summarised, emphasising that material bearing the same “Wright number” cannot always be considered duplicate type material, Wright's numbers being distribution not collection numbers. In this particular case, the dioecy of Podocarpus further complicates matters because the original material of P. angustifolius at GOET, formerly regarded as a holotype, consists of two shoots of different sexes, plus detached seeds that are more mature than those on the mounted female shoot. We demonstrate that these three elements all have different provenances and must be regarded as syntypes. The name Podocarpus angustifolius Griseb. is lectotypified by the detached seeds at GOET, and a supporting epitype designated to fix the application of the name. Podocarpus aristulatus Parl. was based partly on the type of the earlier name P. angustifolius Griseb. of which Parlatore was unaware. However, Parlatore did not see all syntypes present in Grisebach's original material of that name; moreover his name P. aristulatus has been consistently applied to a taxonomically different entity from eastern Cuba, rather than western Cuba where the lectotype of Podocarpus angustifolius was collected. In order to maintain nomenclatural stability it is recommended that P. aristulatus be either lectotypified or conserved with a new conserved type. The latter option is favoured and a separate proposal to that effect is being published simultaneously.
Monophyly and paraphyly: A discourse without end?
Authors: Podani János 
Published: February 2019

AbstractThe ongoing discourse on monophyly versus paraphyly shows apparent lack of mutual understanding among schools of biological taxonomy. The principal reason behind the frozen disagreement is that these terms were redefined repeatedly. Although terminological discrepancy has long been recognized, relatively few attempts have been made to clarify this. As a consequence, contemporary taxonomy still uses three different definitions of monophyly, and therefore paraphyly. Resolution is possible provided that the terms (a) monophyly and paraphyly are used for diachronous classifications and phylogenetic trees; (b) monoclady and paraclady for synchronous classifications and cladograms of contemporaneous organisms; and (c) monothety and non‐monothety for groups in classifications derived by the pattern cladistic approach.
Origin and phylogenetic relationships of the Old World Gesneriaceae with actinomorphic flowers inferred from ITS and trnL-trnF sequences
Authors: Wang Yin-Zheng , Liang Rong-Hua , Wang Bo-Han , Li Jia-Mei , Qiu Zhi-Jing , Li Zhen-Yu , Weber Anton 
Published: February 2019

AbstractThe phylogenetic placement of the Old World Gesneriaceae genera Ramonda, Conandron, Bournea, Thamnocharis, and Tengia, all characterized by actinomorphic flowers, has been the subject of much debate. Actinomorphy in Gesneriaceae is rare, with most species exhibiting zygomorphic flowers. The actinomorphic genera have historically been considered “primitive” and lumped in the tribe Ramondeae separate from the remaining Old World Gesneriaceae. In this study, we used nuclear (ITS) and plastid (trnL‐F) DNA for molecular phylogenetic analysis of these five genera along with representative species across the Cyrtandroideae. Our results show that the actinomorphic genera are scattered over several otherwise zygomorphic clades within Cyrtandroideae, and along with previous data, indicate that Ramondeae is an unnatural group. Floral actinomorphy has evolved convergently in different alliances of Old World Gesneriaceae. Ramonda is sister to Haberlea, Bournea is apparently paraphyletic, Conandron seems rather isolated, and Tengia is close to Petrocodon and sister to a group of Chirita sect. Gibbosaccus together with Calcareoboea. We hypothesize that the evolution from zygomorphy to actinomorphy with novel combinations of characters is possibly due to shifts in pollination strategies, such as a switch from nectar‐ to pollen‐rewards.
Contribution of mitochondrialcox1intron sequences to the phylogenetics of tribe Orchideae (Orchidaceae): Do the distribution and sequence of this intron in orchids also tell us something about its evolution?
Authors: Inda Luis A. , Pimentel Manuel , Chase Mark W. 
Published: February 2019

AbstractIn this paper, we use the mitochondrial regioncox1to assess the usefulness of this marker in addressing evolutionary relationships within the tribe Orchideae. Despite the low overall variation uncovered in this region, one good phylogenetic marker was identified. A large group I intron was shared across subtribe Orchidinae and some species of Habenariinae sensu Dressler. The clades identified in thecox1tree were weakly supported, but consistent with previous studies based on nuclear ribosomal spacers (nrITS). Moreover, the phylogenetic analysis of the combinedcox1/ITS data matrix allowed us to highly improve the resolution of the ITS‐only analysis and confirm several previously controversial relationships. A second purpose of this study was to analyse the evolution of the group Icox1intron in Orchideae. This intron has a patchy distribution in angiosperms that has been claimed to be mostly due to horizontal transfer events. Our results suggest that, despite the differences observed in the co‐conversion tracts in the tribe, vertical transfer is more consistent with the observed phylogenetic trees.
Phylogeny of Solanum series Piurana and related species in Solanum section Petota based on five conserved ortholog sequences
Authors: Ames Mercedes , Spooner David M. 
Published: February 2019

AbstractTaxonomic complexity in wild potatoes (Solanum L. sect. Petota Dumort.) has led to widely conflicting treatments. Solanum ser. Piurana Hawkes is one of 21 series recognized in S. sect. Petota in the latest comprehensive taxonomic treatment by Hawkes in 1990. They are distributed from southern Colombia south through Ecuador to central Peru. The taxonomic limits of the series and validity of its constituent species were not resolved with previous studies. In the present study, a set of five conserved orthologous DNA markers (cos II) with 5342 bp of aligned length were used to infer the phylogeny of putative members of Solanum ser. Piurana and outgroups. The results agreed with a three‐clade topology shown by previous studies within S. sect. Petota. Solanum ser. Piurana is expanded to include some species formerly included in S. sers. Conicibaccata, Cuneoalata, Ingaefolia, Olmosiana, Simplicissima, Tuberosa and Yungasensa. This expanded group is supported morphologically by the presence of moniliform tubers and coriaceous leaves in most species.