bluuebunny/crossref_metadata_2025_split huggingface dataset:
Botanical nomenclature and plant fossils
Authors: Cleal Christopher J. , Thomas Barry A. 
Published: February 2019

AbstractThe provisions in the Code for naming plant fossil taxa have changed substantially over the years. The history of these changes reflects the tension between palaeobotanists (including palynologists studying plant microfossils) who need a flexible set of regulations, and the tendency for the Code to include nomenclatural regulations that constrain taxonomic decisions. The current Vienna Code now provides for plant fossils to be named as fossil taxa, which is a flexible taxonomic concept that should suit the needs of most palaeobotanists. However, the Vienna Code also incorporates the more restrictive concept of morphotaxa and most palaeobotanists seem to be under the misapprehension that plant fossils can only be named as morphotaxa. In our view, the concept of morphotaxa is logically flawed and unnecessary in practice, and should be removed from the Code.
Typification of the name Smilax lanceolata L.
Authors: Acosta Lilian Ferrufino , Greuter Werner 
Published: February 2019

AbstractA mislabelled specimen in the Clifford herbarium (BM) is identified as the single extant original element on which Linnaeus based Smilax lanceolata. It is here designated as the lectotype of the name, corroborating its placement in the synonymy of S. laurifolia L.
Xylosma congesta (Lour.) Merr. (Salicaceae) the correct name for the species otherwise known as X. japonica or X. racemosa
Authors: Zmarzty Sue 
Published: February 2019

AbstractXylosma congesta (Lour.) Merr. is the correct name for a species for which two additional names are in common use: Xylosma japonica A. Gray and X. racemosa (Siebold & Zucc.) Miq. This paper aims to stabilize the name of the species.
Evolution and systematic value of fruit and seed characters in Adoxaceae (Dipsacales)
Authors: Jacobs Bart , Huysmans Suzy , Smets Erik 
Published: February 2019

AbstractThis study presents a description of the morphology and anatomy of the fruits and seeds of Adoxa, Sambucus, and Viburnum. A phylogenetic study included Adoxa moschatellina, Sinadoxa corydalifolia, Sambucus, Tetradoxa omeiensis, and Viburnum. All major clades of Caprifoliaceae, the sister family of Adoxaceae, were sampled and used as outgroup. Maximum parsimony and Bayesian inference optimality criteria were used to analyze three datasets, molecular data (ITS, trnK, matK), morphological data (21 fruit and seed characters), and a combined dataset. We used parsimony optimization to study character evolution. Results of the phylogenetic analyses were congruent with previously published results. Viburnum is the basalmost lineage in the family and sister to subfamily Adoxoideae. In Adoxoideae, Sambucus is sister to the Adoxina clade (i.e., Adoxa, Sinadoxa, and Tetradoxa). Our results also confirmed the sister relationship between Sinadoxa corydalifolia and Adoxa plus Tetradoxa. For the first time, clear autapomorphies are described for Sambucus, such as a long, slender, cylindrical embryo, sclereids with a u–shaped sclerification pattern, a rugose endocarp surface, and numerous, small calcium oxalate crystals in the endocarp sclereids. Character evolution in Sambucus, however, is complex and a broader sampling is required to draw firm conclusions. The evolution toward Viburnum is marked by a number of shifts such as the development of small, amorphous crystals in endosperm cells and a well–developed, parenchymatous seed coat. Based on our results and previous studies we hypothesize a paedomorphic event took place at the origin of Adoxina. Evidence supporting this hypothesis is the presence of green fruits, weakly sclerified endocarp sclereids, small seeds, and semi–inferior ovaries in Adoxina. Finally, our results indicate that the first Adoxaceae were characterized by tricarpellate ovaries with an endocarp composed of an outer layer of sclereids and an inner layer of fibers. A thorough study of the fruits and seeds of Sinadoxa and Tetradoxa is vital to fully understand fruit and seed evolution in Adoxaceae.
The botanical and zoological codes impede biodiversity research by discouraging publication of unnamed new species
Authors: Oliver Paul M. , Lee Michael S.Y. 
Published: February 2019

AbstractMolecular systematics is advancing rapidly, while the pool of taxonomic expertise dwindles: thus, the lag between recognising potential new species, and formally describing those species, will increase. Given the urgency of the biodiversity crisis, the existence of potential new undescribed species should be communicated as rapidly and widely as possible, thus highlighting the relevance and importance of systematics to other sciences, and to biodiversity managers, policy makers, and the general public. However, under the current botanical and zoological codes, scientists who reveal the existence of unrecognised taxa are vulnerable to having those candidate species rapidly named by unscrupulous individuals using unrefereed (and often self‐published) works. This compelling argument for peer review in nomenclature has been largely overlooked in previous debates about the codes. The botanical and zoological codes need to be immediately updated to discourage such taxonomic piracy; this would encourage taxonomists to disseminate their vital biodiversity data as quickly and broadly as possible.
Polymorphism of postmating reproductive isolation within plant species
Authors: Scopece Giovanni , Lexer Christian , Widmer Alex , Cozzolino Salvatore 
Published: February 2019

AbstractSpeciation can be viewed as the evolution of reproductive isolation between formerly interbreeding populations. Recent years have seen great advances in our understanding of the genetic mechanisms underlying postmating reproductive isolation during plant speciation. Nevertheless, little is known about the early stages of species divergence and the evolution of reproductive isolation at the within species level. Direct or indirect evidence indicates that intrinsic postzygotic mechanisms are prevalent and often polymorphic among allopatric conspecific populations of plants. We review studies that report direct or indirect evidence for polymorphism of genic (i.e., gene‐based) postmating reproductive isolation within species' ranges. Specifically, we focus on three genic mechanisms often held responsible for reproductive isolation between species: Bateson‐Dobzhansky‐Muller (BDM) incompatibilities and two widespread types of genomic conflict, transmission ratio distortion and cytonuclear interactions. We further highlight the close similarity between reported cases of outbreeding depression among conspecific populations, especially those that correspond to the intrinsic co‐adaptation model, and the origin of genetic incompatibilities. This association holds great promise to help improve our understanding of the processes involved in the initial stage of speciation, and it highlights the close (and often overlooked) relationship between evolutionary and conservation biology.
What we still don't know about polyploidy
Authors: Soltis Douglas E. , Buggs Richard J.A. , Doyle Jeff J. , Soltis Pamela S. 
Published: February 2019

AbstractDuring the past decade there has been a tremendous resurgence of interest in polyploidy that has in large part been stimulated by the development of increasingly powerful genetic and genomic tools. The result has been numerous new insights into the genomic and genetic consequences of polyploidy. The plethora of new discoveries has dramatically reshaped traditional views and concomitantly revealed that polyploidy is a highly dynamic and ubiquitous process. These recent advances in our understanding of polyploidy have stimulated numerous reviews, most focused on the various genetic, epigenetic, and genomic consequences of polyploid evolution. Whereas genetic and genomic attributes of polyploidization have received considerable attention, other crucial areas of polyploid evolution have received much less (e.g., ecology, pollination biology, physiology). The focus of this paper is not to review again recent discoveries, but to emphasize what we do not yet know about polyploidy, which despite all that has been learned about genome doubling is still an enormous amount. Our list is not meant to be comprehensive, but includes a range of topics that we have placed in several general categories, including mode of formation, ecological and physiological consequences, and genomic rules. Questions include: What is (are) the most frequent mechanism(s) of polyploidization? What factors promote/facilitate polyploidization? What factors favor autopolyploid vs. allopolyploid formation? Do multiple origins result in lineages with differing evolutionary trajectories and/or cryptic species? Our major goals are to stimulate discussion and promote further research.
How many of Cassini anagrams should there be? Molecular systematics and phylogenetic relationships in the Filago group (Asteraceae, Gnaphalieae), with special focus on the genus Filago
Authors: Galbany-Casals Mercè , Andrés-Sánchez Santiago , Garcia-Jacas Núria , Susanna Alfonso , Rico Enrique , Martínez-Ortega M. Montserrat 
Published: February 2019

AbstractThe Filago group (Asteraceae, Gnaphalieae) comprises eleven genera, mainly distributed in Eurasia, northern Africa and northern America: Ancistrocarphus, Bombycilaena, Chamaepus, Cymbolaena, Evacidium, Evax, Filago, Logfia, Micropus, Psilocarphus and Stylocline. The main morphological character that defines the group is that the receptacular paleae subtend, and more or less enclose, the female florets. The aims of this work are, with the use of three chloroplast DNA regions (rpl32‐trnL intergenic spacer, trnL intron, and trnL‐trnF intergenic spacer) and two nuclear DNA regions (ITS, ETS), to test whether the Filago group is monophyletic; to place its members within Gnaphalieae using a broad sampling of the tribe; and to investigate in detail the phylogenetic relationships among the Old World members of the Filago group and provide some new insight into the generic circumscription and infrageneric classification based on natural entities. Our results do not show statistical support for a monophyletic Filago group. The traditional generic circumscription of most of the genera, as well as the traditional infrageneric classification of the genus Filago, do not correlate with the inferred phylogenetic relationships. A monophyletic circumscription of Filago and a new subgeneric treatment for this genus are proposed, this involving description of a new subgenus (Filago subg. Crocidion Andrés‐Sánchez & Galbany, subg. nov.) and four new combinations (Filago subg. Pseudevax (DC.) Andrés‐Sánchez & Galbany, comb. et stat. nov.; Filago discolor (DC.) Andrés‐Sánchez & Galbany, comb. nov.; Filago gaditana (Pau) Andrés‐Sánchez & Galbany, comb. et stat. nov. and Filago griffithii (A. Gray) Andrés‐Sánchez & Galbany, comb. nov.). The genera Cymbolaena, Evacidium and Evax are synonymised under Filago. Several incongruences found between chloroplast and nuclear DNA sequence analyses, as well as a notable degree of intraspecific sequence variation in all regions sequenced are documented and discussed.
Report on the Special Committee on the Nomenclature of Fungi with a Pleomorphic Life Cycle
Authors: Redhead Scott A. 
Published: February 2019

AbstractHistorically, nonlichenized fungi in two phyla, Ascomycota and Basidiomycota, with pleomorphic life cycles may have more than one acceptable legitimate name with priority given to names typified by teleomorphs. This idea has been challenged amidst considerable prolonged debate. An intermediate step towards normalized nomenclature was made in Vienna through the introduction of teleomorph epitypes. A Special Committee was formed to provide guidance on another proposal to prohibit future dual nomenclature and to review the need for Article 59. Committee membership fluctuated between ten and twelve individuals whose opinions were divided over three options: (1) delete Article 59, (2) remove the option for epitypification, or (3) revise the Article further. The Committee reached an impasse and as a body could not recommend acceptance or rejection of any particular proposal. A set of proposals discussed by the Committee is made separately and independently.
Nomenclature and typification of names of genera and subdivisions of genera inCypereae(Cyperaceae): 1. Names of genera in theCyperusclade
Authors: Huygh Wim , Larridon Isabel , Reynders Marc , Muasya A. Muthama , Govaerts Rafaël , Simpson David A. , Goetghebeur Paul 
Published: February 2019

AbstractThe morphological diversity and the presence of several convergent evolutionary lineages in the Cypereae tribe (Cyperaceae) have given rise to various conflicting classifications. These conflicts do not only arise in the delimitation of genera and their subdivisions, but also in the use of similar subdivisional names for different species groups and different names for similar species groups. This has resulted in the publication of approximately 350 names of genera and subdivi sions of genera to accommodate the ca. 950 species in Cyperus and its segregate genera. This complex nomenclature has led to an accumulation of errors in the assessment of valid publication, priority and legitimacy, and in typification in almost all existing taxonomic treatments for the group. Renewed interest in the phylogeny and taxonomy of Cypereae reveals the need to evaluate the nomenclature of generic names and names of subdivisions of genera. In this paper, the first in a series of four papers, we present a survey of all generic names described in the Cyperus clade, designate types where needed, and evaluate priority and legitimacy.
Underestimated endemic species diversity in the dry inter‐Andean valley of the Río Marañón, northern Peru: An example from Mimosa (Leguminosae, Mimosoideae)
Authors: Särkinen Tiina E. , Marcelo-Peña José Luis , Yomona A. Daza , Simon Marcelo F. , Pennington R. Toby , Hughes Colin E. 
Published: February 2019

AbstractMolecular phylogenies which include multiple accessions of species and near complete taxon sampling can be an important tool for estimating species diversity when used in combination with traditional morphology‐based taxonomy. Here we use a densely sampled plastid gene tree for a morphologically complex group within the legume genus Mimosa (sect. Batocaulon ser. Andinae) to improve estimates of species limits and diversity in the poorly known dry inter‐Andean valley of the Río Marañón, northern Peru. Based on the plastid gene tree, Mimosa ser. Andinae, which previously comprised four species, is re‐circumscribed to include six Andean dry‐forest species from northern Peru, Ecuador and southern Colombia, including the new species, M. jaenensis, described here. A further three candidate species are identified within the section based on high levels of sequence variation among accessions. With the additional species, the Marañón valley is now known to harbour nine narrowly restricted endemic species of Mimosa, a pattern of multiple congeneric endemics mirrored in many other plant genera as well as several animal groups. Our results, in combination with other published studies, suggest that overall species diversity in the Marañón has been significantly under‐estimated. Further work is needed to identify conservation priority areas in the Marañón in order to protect its unique flora.
Report of the Nomenclature Committee for Fungi: 16
Authors: Norvell Lorelei L. 
Published: February 2019

AbstractThe following five generic names are recommended for conservation: Cladia against Heterodea; Hemipholiota against Nemecomyces; Lactarius with conserved type; Mixia against Phytoceratiomyxa; Stirtonia A.L. Sm. against Stirtonia R. Br. bis; the following five specific names are also recommended for conservation: Aspicilia aquatica against Lichen mazarinus; Dermatocarpon bucekii (Placopyrenium bucekii) against Placidium steineri; Hebeloma cylindrosporum against Hebeloma angustispermum; Psoroma versicolor (Degeliella versicolor) against Psoroma subdescendens; Thelephora comedens (Vuilleminia comedens) with conserved type. Lecidea epiploica is recommended for rejection under Art. 56 and it is recommended that Verrucaria thelostoma and Pyrenula umbonata not be rejected under Art. 56. As a result of reference under Art. 53.5, it is recommended that the following two pairs of names be treated as homonyms: Calongea Healey & al. and Calongia D. Hawksw. & Etayo; and Phyllocratera Sérus. & Aptroot and Phyllocrater Wernham.
Ancient allopolyploidy in the everlasting daisies (Asteraceae: Gnaphalieae): Complex relationships among extant clades
Authors: Smissen Rob D. , Galbany-Casals Mercè , Breitwieser Ilse 
Published: February 2019

AbstractPhylogenetic analyses have suggested that the everlasting daisy tribe Gnaphalieae colonized the globe repeatedly and rapidly from southern Africa. However, both the circumscription of monophyletic groups of “out of Africa” Gnaphalieae genera and the identification of their sister groups in southern Africa has proved difficult. We have analysed sequences of nrDNA spacers (ITS, ETS), cpDNA (ndhF, trnL intron, trnL‐trnF intergenic spacer, trnK intron), and low‐copy nuclear markers to examine selected relationships within the crown radiation of the tribe. We focused on relationships among two putative clades suggested by previous studies and a representative sampling of genera endemic to Australasia. Incongruities between nrDNA and cpDNA trees are frequent and some involve robustly supported clades. However, trees generated for two low‐copy nuclear markers are largely congruent with each other but imply that allopolyploidy preceded the radiations of at least four separate extant lineages within the tribe, one largely or entirely restricted to Australasia, one almost global, and two still poorly sampled. Collectively, these four putative allopolyploid lineages may account for more than half of the described species diversity of the tribe.
First detection of porcine circovirus type 3 in Colombia and the complete genome sequence demonstrates the circulation of PCV3a1 and PCV3a2
Authors: Vargas‐Bermudez Diana S. , Campos Fabricio S. , Bonil Laura , Mogollon Darío , Jaime Jairo 
Published: February 2019

AbstractPorcine circovirus 3 (PCV3) was recently discovered and is a new species of the genus circovirus. Clinically, it is associated with absence of symptoms or with different clinical syndromes. It has been reported in different countries of America, Europe and Asia. Last year, in Colombia, some farms have reported symptoms similar to those caused by PCV2. Samples were taken from two farms located in the centre of the country, and the presence of PCV3 was determined by PCR in two samples, one from a pool of sera and another from mesenteric lymph node. The strains were fully sequenced (GenBank accession numbers MH327784 and MH327785) and classified into subgroups a1 and a2. According to this classification and its analysis, strain a2 is located within the group called “Linker” that may be evolving towards group “b”. In addition to the above, the two Colombian strains were compared with 104 strains reported in the GenBank database. The phylogenetic tree obtained grouped according to the classification of subgroups a1, a2, b1 and b2. It was found that subgroups a1 and a2 were well grouped when comparing whole genomes, but the same was not observed with the strains of group “b”. In the latter, no subgroups were evidenced when comparing complete genomes. It is suggested that a new classification of PCV3 subgroups should be proposed, based on whole genome sequences. This is the first report of PCV3 in Colombia and its complete genome sequence.
Actants and aktionsart: The Norwegian verb få as the dynamic counterpart to ha / Actants et mode d'action : le verbe norvégien få comme contrepartie dynamique de ha
Authors: Halmøy Madeleine 
Published: February 2019

AbstractFollowing Denis Bouchard's neo-Saussurean Sign Theory of Language, with a focus on the notion of Grammar Semantics, this article sketches a proposal for a unified understanding of the most multifunctional among Norwegian verbs, namely få ‘get’. Based on Bouchard's analysis of French être ‘be’ and avoir ‘have’ and corresponding signs in other languages, I propose that få is the dynamic version of ha ‘have’, which is a bivalent transitive copula. This abstract semantic value is shown to form the basis for the many contextual interpretations få receives, in its use both as a main verb and as an auxiliary. To my knowledge, a monosemic, unified understanding of få that covers all its uses and interpretations has not yet been proposed, especially not one that highlights its relationships with være ‘be’, ha ‘have’ and bli ‘be, become, get’. The study also includes a contrastive analysis of få and the English verb get.
Disaster Preparedness in Hospitals in the Middle East: An Integrative Literature Review
Authors: Alruwaili Abdullah , Islam Shahidul , Usher Kim 
Published: February 2019

ABSTRACTDisasters occur rarely but have significant adverse consequences when they do. Recent statistics suggest that millions of lives and billions of US dollars have been lost in the last decade due to disaster events globally. It is crucial that hospitals are well prepared for disasters to minimize their effects. This integrative review study evaluates the preparedness level of hospitals in the Middle East for disasters using the Preferred Reporting Items for Systematic and Meta-Analyses (PRISMA) guidelines. The key terms include disaster preparedness OR disaster management OR emergency response AND Middle East AND hospitals. The study reviews articles published between January 2005 and December 2015, which focused on the hospitals’ preparedness for disasters in the Middle East nations. Based on their meeting 5 eligibility criteria, 19 articles were included in the review. Twelve of the articles focused on both natural and man-made disasters, whereas 6 of them were based on mass casualty events and 1 on earthquake. Thirteen of the reviewed articles ranked the level of preparedness of hospitals for disasters to be generally “very poor,” “poor,” or “moderate,” whereas 6 reported that hospitals were “well” or “very well prepared” for disasters. Factors affecting preparedness level were identified as a lack of contingency plans and insufficient availability of resources, among others. (Disaster Med Public Health Preparedness. 2019;13:806–816).
Statistical state dynamics analysis of buoyancy layer formation via the Phillips mechanism in two-dimensional stratified turbulence
Authors: Fitzgerald Joseph G. , Farrell Brian F. 
Published: February 2019

Horizontal density layers are commonly observed in stratified turbulence. Recent work (e.g. Taylor & Zhou, J. Fluid Mech., vol. 823, 2017, R5) has reinvigorated interest in the Phillips instability (PI), by which density layers form via negative diffusion if the turbulent buoyancy flux weakens as stratification increases. Theoretical understanding of PI is incomplete, in part because it remains unclear whether and by what mechanism the flux-gradient relationship for a given example of turbulence has the required negative-diffusion property. Furthermore, the difficulty of analysing the flux-gradient relation in evolving turbulence obscures the operating mechanism when layering is observed. These considerations motivate the search for an example of PI that can be analysed clearly. Here PI is shown to occur in two-dimensional Boussinesq sheared stratified turbulence maintained by stochastic excitation. PI is analysed using the second-order S3T closure of statistical state dynamics, in which the dynamics is written directly for statistical variables of the turbulence. The predictions of S3T are verified using nonlinear simulations. This analysis provides theoretical underpinning of PI based on the fundamental equations of motion that complements previous analyses based on phenomenological models of turbulence.