bluuebunny/crossref_metadata_2025_split huggingface dataset:
A preliminary molecular phylogeny of Pennisetum and Cenchrus (Poaceae‐Paniceae) based on the trnL‐F, rpl16 chloroplast markers
Authors: Donadío Sabina , Giussani Liliana M. , Kellogg Elizabeth A. , Zuolaga Fernando O. , Morrone Osvaldo 
Published: February 2019

ABSTRACTPennisetum (80–140 species) and Cenchrus (16–22 species) are closely related genera of Paniceae, both distributed in tropical and sub‐tropical regions. The distinction between Pennisetum and Cenchrus is not clearly defined, and currently no comprehensive taxonomic treatment is available for either genus. Chloroplast DNA sequence data (rpl16, trnL‐F region) were analyzed to test their monophyly, species relationships, and infrageneric classifications. Phylogenetic analyses of individual genomic regions, and a combined dataset, including indel‐coded information, were performed under parsimony and Bayesian inference. Selected geographical, chromosomal and morphological characters were mapped onto the phylogeny to investigate evolutionary trends. Our results support a monophyletic bristle clade and the close relationship between Pennisetum and Cenchrus. Excluding Pennisetum lanatum, Pennisetum is paraphyletic because Cenchrus is nested within it. Sections Pennisetum and Gymnotrix are polyphyletic. Our molecular phylogenetic results show a close relationship among the domesticated species P. glaucum, P. purpureum, P. squamulatum, P. nervosum, and P. sieberianum, suggesting the potential use of these species in crop improvement. The Pennisetum‐Cenchrus clade shows an independent reduction (x = 5, 7, 8) or duplication (x = 17) of the basic chromosome number from the ancestral x = 9. American Pennisetum and Cenchrus species appear to have originated from Old World species more than once. A core group of American species of Cenchrus with a basic chromosome number of x = 17 and retrorsely barbed bristles could be restricted to Cenchrus s. str.
Arabidopsis family ties: molecular phylogeny and age estimates in Brassicaceae
Authors: Franzke Andreas , German Dmitry , Al-Shehbaz Ihsan A. , Mummenhoff Klaus 
Published: February 2019

ABSTRACTThe Brassicaceae family is of great scientific interest because it contains the plant model organism Arabidopsis thaliana. Currently, contemporary plant research activities expand to other Brassicaceae taxa. Despite that, the phylogeny of this family is only partly understood. The present study deepens our understanding of a family‐wide phylogeny by using two new approaches in phylogenetic family‐wide research. We used a molecular marker from the mitochondrial genome and utilised a relaxed molecular dating method. Our data generally confirms a recent tribal alignment of Brassicaceae. We present for the first time a biogeographical scenario for the broad‐scale Brassicaceae evolution. We suggest that Brassicaceae most likely evolved some 19 mya in or near the eastern Mediterranean region from a common ancestor of its sister family Cleomaceae. The early Brassicaceae formed a lineage adapted to more open/drier habitats than its capparoid progenitors. The early Brassicaceae evolution was very rapid and the radiation was most likely driven by climatic changes that created open habitats and the well‐documented expansion of open grass‐dominated ecosystems. Moreover, our dating suggests that the radiation events correlate with an ancient genome duplication in the early history of the family, which is evidenced by recent genomic studies.
Systematics of Dombeyoideae (Malvaceae) in the Mascarene archipelago (Indian Ocean) inferred from morphology
Authors: Péchon Timothée Le , Cao Nathanaël , Dubuisson Jean-Yves , Gigord Luc D.B. 
Published: February 2019

ABSTRACTThe Mascarene Archipelago is characterized by remarkable fauna and flora, mainly due to its high rate of endemism. The Dombeyoideae Beilschm. is one of the most diversified groups of angiosperms in the Mascarenes with 22 species, 21 of which are endemic. We used parsimony analysis of morphological characters to examine the relationships between the endemic Dombeyoideae from the Mascarenes and the members of Dombeyoideae from Africa, Madagascar and Asia. A morphological matrix was created including 36 representative species and 42 characters. Among the most parsimonious trees (MPTs) those with the highest number of secondary homologies were identified. The Dombeyoideae from the Mascarenes are polyphyletic and split into nine clades. Trochetia appears monophyletic and more closely related to Eriolaena and Helmiopsis than to Dombeya. All Dombeya taxa are included in a clade together with Ruizia and Astiria, which makes Dombeya paraphyletic. In terms of breeding systems the Malagasy Dombeyoideae are hermaphroditic, whereas those of the Mascarenes are considered dioecious. The polyphyly of the Mascarene Dombeyoideae suggests that dioecy has been acquired several times. At least five colonization events from Madagascar to the Mascarene archipelago are inferred. The evolutionary history of two lineages of Mascarene Domeyoideae seems to be related to adaption to xeric habitats.
Circumscription of European taxa within the Sciuro-hypnum reflexum complex (Brachytheciaceae, Bryophyta), based on molecular and morphological data
Authors: Draper Isabel , Hedenäs Lars 
Published: February 2019

ABSTRACTITS, rpl16 and trnG sequences, together with morphological data, were used to circumscribe the European problematic taxa within the Sciuro-hypnum reflexum complex. Strongly supported monophyletic clades sustain several of the target taxa as distinct species (S. reflexum, S. starkii, S. tromsoeense, S. glaciale, S. dovrense, S. latifolium). The segregation of S. nelsonii and Brachythecium glaciale var. gelidum is found to be inconsistent with our results and the two taxa are therefore synonymized.
Taxonomy and species delimitation in Sporodictyon (Verrucariaceae) in Northern Europe and the adjacent Arctic—reconciling molecular and morphological data
Authors: Savić Sanja , Tibell Leif 
Published: February 2019

ABSTRACTMorphological variation in Sporodictyon is scrutinized in an effort to reconcile it with monophyletic groups based on molecular evidence. Molecular data (nucITS, nucLSU, RPB1) are investigated by Bayesian and parsimony phylogenetic analyses, statistical parsimony, and split decomposition. Morphological variation within and between the monophyletic groups is evaluated. Four monophyletic groups strongly supported by molecular data correspond to morphologically well‐characterized species. Sporodictyon schaererianum and S. terrestre are morphologically variable, especially with respect to thallus structure. Two distinct subclades are found in both species, but they could, however, not be distinguished morphologically and may be regarded as cryptic species. A combination of ascoma size, spore pigmentation, spore size and thallus structure characterizes the species recognized, whereas thallus thickness, involucrellum thickness and excipulum pigmentation are found to be quite plastic. A taxonomic revision of Sporodictyon in Northern Europe and the adjacent Arctic is provided, recognizing five species. Two new species, S. arcticum and S. minutum, are described. The name Polyblastia theleodes has been misapplied for S. schaererianum. Several taxonomic synonyms are proposed, particularly for S. terrestre, and lectotypes for several species names are designated.
On the identity and typification of Koeleria lobata (M. Bieb.) Roem. & Schult. (Pooideae, Gramineae)
Authors: Quintanar Alejandro , Glazkova Elena , Castroviejo Santiago 
Published: February 2019

ABSTRACTSome authors have recently considered Koeleria lobata (M. Bieb.) Roem. & Schult. to be the correct name for those grasses traditionally named K. splendens C. Presl. Koeleria lobata is in fact the correct name for another species that has been named as K. brevis Steven or K. degenii Domin. Although the clarification of the true identity of K. lobata solves the current nomenclatural confusion between K. lobata and K. splendens, preserving the use of this last name, the restitution of K. lobata to its correct use would cause notable nomenclatural confusion thus making it compulsory to propose its rejection.
Nomenclature and typification of J.G.C. Lehmann and H. Buek names in Lobostemon (Boraginaceae), with enquiries into the contributions by O. Swartz and C.P. Thunberg
Authors: Buys Matt H. , Nordenstam Bertil 
Published: February 2019

ABSTRACTJ.G.C. Lehmann and H. Buek described 18 species of Lobostemon Lehm., in addition to making new combinations of taxa previously placed in Echium L. Some of Lehmann’s Echium taxa were supplied by Olof Swartz in Stockholm who also provided Thunberg with the same material. This led to more or less simultaneous publication of some homonyms in Echium by Lehmann and Thunberg. Previous confusions on publication dates of Thunberg and Lehmann names are clarified. Author citations and priority of homonyms ascribed to Thunberg, Swartz and Lehmann are rectified. Many types are identified, including 17 new lectotypes (MEL, S, SAM, SBT, UPS) and one neotype. The role of Sonder in selling material to S while breaking off bits and pieces and supplying his friend Baron F. von Mueller in MEL is also investigated and the presence of Lehmann’s hand on a SAM specimen is reported on.
Typification of names based on the Angolan collections of Friedrich Welwitsch
Authors: Albuquerque Sara , Brummitt R.K. , Figueiredo Estrela 
Published: February 2019

ABSTRACTThe background to Friedrich Welwitsch’s seven year expedition to Angola and the subsequent fate of his herbarium of 10,000 collections are reviewed. In typifying the approximately 1,000 species names based on his collections, it is important to know where the specimens were at the time of publication of the names. In most cases there are no holotypes, and lectotypifications have to be made. It has not been generally realised that Welwitsch lumped together under one number all the collections which he considered to be conspecific, which means that designation of isotypes is open to serious misinterpretation. Data added retroactively to labels by copying from Hiern’s Catalogue may be erroneous. The collection has now been distributed to at least 24 different herbaria.
Molecular phylogenetic analysis of the tribe Alberteae (Rubiaceae), with description of a new genus,Razafimandimbisonia
Authors: Kainulainen Kent , Mouly Arnaud , Khodabandeh Anbar , Bremer Birgitta 
Published: February 2019

AbstractThe tribe Alberteae, presently classified in the subfamily Ixoroideae (Rubiaceae), has historically been an artificial grouping of genera. In the present study, phylogenetic analyses of the chloroplast DNA markersrbcL, ndhF, trnS‐G, trnT‐FandtrnH‐psbAas well as the ITS region of the nuclear ribosomal DNA, are done to assess the delimitation of Alberteae. The resulting phylogenetic hypothesis is highly resolved, with most clades strongly supported. The genusAlbertais found to be paraphyletic as presently circumscribed. As a consequence, we propose the new genusRazafimandimbisoniaKainul. & B. Bremer to accommodate the Malagasy species. The newly delimitedAlbertais distinguished by having two calycophylls that expand after anthesis as well as awl‐shaped stigma lobes.Razafimandimbisoniais distinguished from the remaining Alberteae by having dehiscent fruits and anthers without basal appendages. We demonstrate that the generaAirosperma, Boholia and Crossopteryx are not associated with Alberteae, as has previously been suggested. Alberteae is considered restricted to the genusAlbertaendemic to Southeast Africa, and the two Malagasy endemic generaNematostylisandRazafimandimbisonia.
Systematic position of the enigmatic genus Sheareria ( Asteraceae)—evidence from molecular, morphological and cytological data
Authors: Gao Tian-Gang , Wang Wei , Bayer Randall J. , Li De-Zhu 
Published: February 2019

AbstractThe systematic position of the monoecious rheophyte, Sheareria (Asteraceae), a genus endemic to China, has been long disputed and never rigorously examined. In this study, two molecular datasets (trnL‐F, ITS), plus morphological and cytological characters, were used to assess the systematic position of Sheareria. The broader phylogenetic analyses based on the trnL‐F data placed Sheareria in the tribe Astereae with strong support. This placement was also supported by the lanceolate style, “Asteroid type” ligule epidermis, yellow anthers, green achenes, and basic chromosome number of x = 9. Analysis of the tribe Astereae based on the ITS dataset showed that Sheareria and three East Asian genera (Kalimeris, Aster, Rhynchospermum) formed a strongly supported clade characterized by flat, 2‐ribbed, glandular disc achenes. Detailed morphological comparisons indicate that Sheareria is more similar to Kalimeris than to Rhynchospermum. Within this clade, Sheareria is distinguished from other genera by its monoecious breeding system (vs. gynomonoecious). Based on fossil and geological evidence, the development of monoecy in Sheareria is discussed. Within Sheareria, only one species, S. nana, is recognized; S. leshanensis, a newly described species, is placed in synonymy.
Historical biogeography of a disjunctly distributed, Spanish alpine plant, Senecio boissieri (Asteraceae)
Authors: Peredo Elena L. , Revilla M. Ángeles , Jiménez-Alfaro Borja , Bueno Álvaro , Prieto J. Antonio Fernández , Abbott Richard J. 
Published: February 2019

AbstractLittle is known about the historical biogeography of alpine plants that are disjunctly distributed across the mountains of the Iberian Peninsula. Randomly Amplified Polymorphic DNA (RAPD) and chloroplast microsatellite (cpSSR) variation were surveyed in the Spanish alpine endemic, Senecio boissieri, to resolve the causes of its disjunct distribution in the southern Sierra Nevada and Baza, centrally located Sierra Guadarrama, and northern Cordillera Cantábrica. RAPD analysis identified two divergent genetic groups, one containing individuals from the Cordillera Cantábrica and another comprising individuals from the three other mountain ranges. Chloroplast DNA variation was much more limited with only one of forty‐two cpSSR loci examined showing polymorphism. At this locus the same allele occurred at high frequency in material from each mountain range. A possible reason for RAPD divergence in the Cantabrian material is its derivation from plants surviving the last glacial maximum in a northern refugium, isolated from the main distribution of the species spanning the area between the southern and central Spanish sierras. Postglacial fragmentation of the species range in southern and central Iberia would have resulted in the current disjunction of genetically similar populations in southern and centrally located mountains.
New molecular and morphological insights prompt transfer ofBlechumtoRuellia(Acanthaceae)
Authors: Tripp Erin A. , Daniel Thomas F. , Lendemer James C. , McDade Lucinda A. 
Published: February 2019

AbstractThe genusBlechumP. Browne (Acanthaceae) is best known by the widespread tropical weed formerly referred to asBlechum pyramidatum(Lam.) Urb. (recently re‐established asRuellia blechumL.). Some species ofBlechumhave been transferred toRuelliabased on macromorphological and molecular data, but comprehensive study of taxa assigned toBlechumis lacking. We reexamined morphological characters that have been used to distinguishBlechumfrom Ruellia including inflorescence structure and pollen and capsule morphology. Second, we conducted phylogenetic analyses including nine accessions from five of six species traditionally treated inBlechum(and that we here consider valid species) plus a synoptic sample of species of Ruellia based on the work of the first author. Results indicate thatBlechumis nested within Ruellia with strong support. An alternative phylogenetic hypothesis of monophyly of Ruellia exclusive of species traditionally treated inBlechumwas rejected under a likelihood but not a parsimony criterion. Based on morphological similarities, common chromosome numbers, and molecular data, we transfer the genusBlechumto Ruellia. Third, we studied specimens and images of specimens of as many pertinent historical collections as we could acquire. This study resulted in nomenclatural and taxonomic renovations that include several new taxonomic synonyms (reduction ofBlechum killipii, Blechum linnaei, andBlechum trinitense), two new combinations (Ruellia haughtiiandRuellia panamensis), one new lectotypification (Blechum browneiαsubcordatumf.albiflorum), and additional recommendations for future typification. Based on our morphological and molecular studies, six species ofRuelliaare treated as constituting theBlechumlineage ofRuellia. A preliminary key is provided to distinguish these species, but theBlechumlineage as a whole deserves further attention and fieldwork to determine the precise limits of each taxon.
Klackenbergia (Gentianaceae – Exaceae), a new endemic genus from Madagascar
Authors: Kissling Jonathan , Buerki Sven , Mansion Guilhem 
Published: February 2019

AbstractSeveral lines of evidence (morphological, karyological and molecular) support the exclusion of both Sebaea madagascariensis Klack. and S. condensata Klack. from Sebaea Sol. ex. R. Br. (Gentianaceae – Exaceae), resulting in the establishment of a new genus Klackenbergia Kissling and two new species combinations: K. stricta (Schinz) Kissling (= S. madagascariensis) and K. condensata (Klack.) Kissling. Klackenbergia is endemic to Madagascar and is morphologically recognized by its inflorescence with long bracts and bracteoles and subsessile flowers arranged in axillary fascicules at each node. Affinities with the other genera of the tribe Exaceae (Exacum, Gentianothamnus, Ornichia, Sebaea, Tachiadenus) are discussed.
Shape analysis for the automated identification of plants from images of leaves
Authors: Hearn David J. 
Published: February 2019

AbstractSpecies identification is a necessary component of most studies of biological diversity, and computational approaches are beginning to automate it. In particular, leaves of plants provide taxon‐specific information that has successfully been applied to plant identification. Prior studies have not investigated the number of leaves or the resolution of the digitized leaf image required to represent a species’ shape. Moreover, the relationship between accuracy and the size of the leaf shape database, and methods to integrate automated approaches with more traditional dichotomous keys have yet to be explored. Here, I use a database of 2,420 leaves from 151 species to address these issues. Using distance metrics derived from Fourier and Procrustes analyses, it is found that a minimum of 10 leaves of each species, 100 margin points, and 10 Fourier harmonics are required to accurately represent leaf shape of a species. These results are used to assess the success of species identification from images of leaves: 72% for all 151 species. The tight relationship between database size and accuracy is then used in conjunction with results from probability theory to predict accuracy of species identification when dichotomous multiple‐entry keys and combined Fourier and Procrustes analysis are used together. Combining these two approaches to identification can greatly improve identification accuracy. Open‐source software is available to implement the automated distance‐based approach.
Non‐parametric bootstrapping of partitioned datasets
Authors: Torres-Carvajal Omar 
Published: February 2019

AbstractNon‐parametric bootstrapping is one of the most commonly used methods for branch support assessment. Unlike Bayesian posterior probability values, which are influenced by a priori data partitioning, non‐parametric bootstrapping is usually applied to unpartitioned (combined) datasets. The resulting bootstrap support values are misleading in that they do not measure how well clades are supported by all the partitions, unless all partitions are equal in size (i.e., number of characters). Since most empirical studies include data partitions that are heterogeneous in size, our current bootstrapping approach for partitioned datasets (i.e., bootstrapping the combined dataset) is not adequate. Here I propose a simple modification to non‐parametric bootstrapping that takes a priori data partitioning into account by obtaining bootstrap replicates for each partition separately and combining them in such a way that the size (i.e., number of characters) of each partition is taken into account. With this “corrected” bootstrap support value, characters from smaller partitions will have greater influence on final bootstrap values, and those in larger partitions relatively less influence than they would for unpartitioned data.
Revised lectotypification of Lycopodium complanatum L. (Lycopodiaceae)
Authors: Thulin Mats , Aagaard Sunniva M.D. , Wikström Niklas , Jarvis Charlie 
Published: February 2019

AbstractThe currently accepted lectotype of the circumboreal species Lycopodium complanatum L., or Diphasiastrum complanatum (L.) Holub, is a specimen of the related species L. tristachyum Pursh, or D. tristachyum (Pursh) Holub, mainly distributed in eastern North America and Europe. This lectotype, in LINN, is here superseded in favour of an alternative original element in the Celsius herbarium in Uppsala, supported by an epitype, on the grounds of serious conflict with the protologue. Thereby the traditional usage of the well‐known name L. complanatum can be maintained.
Typification of names of temperate North American plants proposed by Linnaeus
Authors: Reveal James L. , Jarvis Charles E. 
Published: February 2019

AbstractLectotypifications are proposed for the names of the following 36 temperate North American species proposed by Carl Linnaeus: Allium canadense, Amaranthus lividus, Aristolochia arborescens, Asarum canadense, Aster tenuifolius, Baccharis foetida, Bartsia pallida, Chenopodium anthelminticum, Croton argenteus, Erigeron carolinianus, Gentiana villosa, Hedysarum viridiflorum, Hedysarum volubile, Hippophaë canadensis, Iris versicolor, Lonicera dioica, Lonicera symphoricarpos, Lupinus perennis, Lysimachia ciliata, Lythrum petiolatum, Myrica aspleniifolia, Oenothera sinuata, Onoclea sensibilis, Polypodium bulbiferum, Rudbeckia laciniata, Rudbeckia triloba, Ruellia strepens, Rumex verticillatus, Sideroxylon decandrum, Sideroxylon lycioides, Smilax lanceolata, Solidago lateriflora, Tabernaemontana amsonia, Tragia urens, Triosteum angustifolium and Verbena carolina. In addition, neotypes are established for six Linnaean names that lack original material: Agave virginica, Blechnum virginicum, Juglans cinerea, Magnolia virginiana var. grisea, Menispermum carolinum and Teucrium virginicum.
Genistein protects against doxorubicin‐induced cardiotoxicity through Nrf‐2/HO‐1 signaling in mice model
Authors: Bai Zhifeng , Wang Zhijian 
Published: February 2019

AbstractDoxorubicin (DOX)‐induced cardiomyopathy is a lethal disease. DOX‐induced cardiotoxic effects are attributed towards increased redox status and apoptotic signaling. In this study, we show that genistein offers protection against DOX‐induced cardio toxicity in the mice model. DOX‐mediated increase in serum cardiac troponin and redox markers (ROS, LPO, 4‐hydroxynonenal‐protein adducts [HNE] levels) was significantly reduced by genistein treatment. Significantly increased TNF‐α, IL‐6, IL‐8 expressions during DOX‐induced inflammatory responses were down regulated by genistein treatment. Further, we found that genistein regulated antioxidant response through increased Nrf‐2, HO‐1, NQO1 protein expressions. In addition, DOX downregulated survival proteins (p‐Akt, Bcl‐2) with concomitant upregulation in Erk (1/2), Bax and cleaved caspase‐3 expressions. The apoptotic activation was significantly downregulated by genistein treatment through suppression of apoptosis. Altogether, these findings show that genistein protects against DOX‐induced cardiotoxic effects through activation of Nrf‐2/HO‐1 signaling.