bluuebunny/crossref_metadata_2025 huggingface dataset:
The evolutionary history of BeringianSmelowskia(Brassicaceae) inferred from combined microsatellite and DNA sequence data
Authors: Carlsen Tor , Elven Reidar , Brochmann Christian
Published: February 2019

We used the genusSmelowskia, which is distributed in Asia and North America and comprises both diploids and polyploids, as an example to address phylogeny, biogeography and polyploidization in the recently (ca. 3 million years ago) formed arctic biome with particular reference to the Beringian area. We combined data from high–resolution nuclear markers (seven SSR loci) with sequences from two nuclear regions (the low copyRPA2region and the multicopy nrITS region) and five plastid regions (trnLUAA and rps16 introns, trnHGUG–psbA, trnLUAA–trnFGAA, and 5′prs12–rpl20spacers). The different nuclear markers showed a congruent pattern that fits well with that observed in morphology and geography, while the plastid data showed some incongruence. Both sequence and SSR data support merging ofSmelowskia porsildii, S. spathulatifolia, andS. jurtzeviiinto a single species (S. porsildii). An Asian origin of the Beringian taxa was inferred, resulting in two separate lineages of American–Beringian/American taxa. The SSR data confirmed polyploidy in several species, supporting the major role of this process in the evolution of the arctic flora.
A phylogeny of the Areae (Araceae) implies thatTyphonium, Sauromatum, and the Australian species ofTyphoniumare distinct clades
Authors: Cusimano Natalie , Barrett Matthew D. , Hetterscheid Wilbert L.A. , Renner Susanne S.
Published: February 2019

With in excess of 70 species, the Southeast Asian/Australian genusTyphoniumis the largest genus of the Areae, a tribe that includes up to nine smaller genera of whichSauromatumandLazarumhave recently been reduced to the synonymy ofTyphonium.To test the circumscription and relationships ofTyphoniumto the other Areae, we used chloroplast and nuclear DNA sequences (4319 aligned nucleotides) for 86 of the total 153 species, including representatives of all relevant genera. In the resulting phylogeny,Typhoniumspecies fall into three well–supported clades: the first comprises mostTyphoniumspecies, including the type, T. trilobatum ; the second consists of the type ofSauromatum, S. guttatum, and other species formerly placed in that genus; the third includes only Australian endemics. Each of the remaining six genera of Areae is monophyletic. Sauromatum andTyphoniumare not sister groups, requiring the recognition ofSauromatum. The Australian clade also needs to be ranked as a genus to achieve similar levels of morphological, geographic, and genetic distinctness among the genera of Areae. However, since only 10 of the 16 described Australian endemics currently placed inTyphoniumhave so far been sequenced, not including the type of the name of the Australian genusLazarum, we refrain from applying this name to the Australian clade. Among the nomenclatural and taxonomic results of this study are a key to the nine species ofSauromatum, and five new combinations. We also report two new chromosome counts and discuss the implications of the molecular phylogeny for the evolution ofSauromatumkaryotypes.
Intercontinentally disjunct species are derived rather than relictual in the moss genus Daltonia (Bryophyta)
Authors: Yu Jing , Devos Nicolas , Majestyk Piers , Shaw A. Jonathan
Published: February 2019

We present a phylogenetic analysis of the moss genus Daltonia based on nucleotide sequences from three plastid loci (psbT, trnL, trnG) plus the nuclear ribosomal RNA gene (ITS), including 9 of 21 species in this genus. Of the nine species, seven are well–supported as monophyletic, even when multiple accessions came from different continents. Early diverging species in the genus have relatively restricted ranges that are limited to a single continent, whereas most or all later–diverging species have broad intercontinental distributions. The observation that intercontinental distributions are repeated in multiple monophyletic species suggests that a key innovation underlying enhanced abilities for long dispersal evolved within Daltonia, and that this potential was inherited among derived species from their common ancestor. The nature of this (these) innovation(s) remains obscure, but may be related to both relaxation of ecological limitations on establishment, and to effective dispersal of spores per se.
Geographical speciation related to Pleistocene range shifts in the western Mediterranean mountains (Reseda sect. Glaucoreseda, Resedaceae)
Authors: Martín-Bravo Santiago , Valcárcel Virginia , Vargas Pablo , Luceño Modesto
Published: February 2019

Reseda sect. Glaucoreseda is a monophyletic group composed of five endemic tetraploid species with a disjunct distribution in the high mountains and plateaus of the Iberian Peninsula and Morocco. It was previously suggested that range shifts induced by Quaternary glaciations played an important role in the speciation of the group. We studied the evolution of R. sect. Glaucoreseda in order to infer historical range dynamics and speciation processes, and to understand current distributional patterns. Phylogeographic analyses were performed using nuclear ribosomal ITS and plastid trnL–F and rps16 sequences. Cloning of additive ITS sequences was carried out to elucidate the origin of intra–individual polymorphisms. A dated phylogeny based on ITS and cpDNA (rbcL, matK, trnL–F) sequences was used to estimate divergence times of R. sect. Glaucoreseda. Time estimates using Penalized Likelihood analyses indicate a late Pleistocene diversification of R. sect. Glaucoreseda. Incomplete lineage sorting of ancestral polymorphisms due to recent divergence, rather than rampant hybridisation, is suggested as the main cause of the phylogenetic incongruence detected between nuclear and plastid datasets. Our results support the vicariance hypothesis for population disjunctions in the Iberian Peninsula, in which an ancestral, widespread species could have undergone differentiation by Quaternary interglacial fragmentation. In contrast, long–distance dispersal across the Strait of Gibraltar may have been involved in the colonisation of North African plateaus by R. battandieri.
The phylogenetic significance of vestured pits in Boraginaceae
Authors: Rabaey David , Lens Frederic , Smets Erik , Jansen Steven
Published: February 2019

The bordered pit structure in tracheary elements of 105 Boraginaceae species is studied using scanning electron microscopy to examine the systematic distribution of vestured pits. Forty–three species out of 16 genera show a uniform presence of this feature throughout their secondary xylem. Most vestures are small, unbranched and associated with the outer pit aperture of bordered intervessel pits. The feature is likely to have originated independently in the distantly related subfamilies Boraginoideae (tribe Lithospermeae) and Ehretioideae. The distribution of vestures in Ehretia agrees with recent molecular phylogenies: (1) species with vestured pits characterise the Ehretia I group (incl. Rotula), and (2) species with non–vestured pits belong to the Ehretia II group (incl. Carmona). The occurrence of vestured pits in Hydrolea provides additional support for excluding this genus from Hydrophylloideae, since Hydrolea is the only species of this subfamily with vestured pits. Functional advantages of vestured pits promoting parallel evolution of this conservative feature are suggested. The hydraulic benefits of poorly developed vestures remain underinvestigated.
A re–examination of the type specimens of Yuania H.C. Sze 1953 and its junior synonym Russellites Mamay 1968 (Noeggerathiales)
Authors: Wang Jun , Chaney Dan
Published: February 2019

The noeggerathialean fossil names Yuania H.C. Sze and Russellites Mamay are shown to be synonymous, with the latter being the junior synonym of the former. Examination and re–illustration of the type material of both Yuania and Russellites shows that they are indistinguishable taxonomically. Both sets of material have pinnules with clasping bases and concave apices in which the veins converge but do not anastomose. Sze's original description of Yuania was incorrect in indicating that the leaves were petiolate and that the veins converged. Yuania may be the first plant taxon identified in the Permian floras of China and North America with vegetative and reproductive organs represented on both continents.
Latin diagnosis: Time to let go
Authors: Figueiredo Estrela , Moore Gerry , Smith Gideon F.
Published: February 2019

Article 36.1 of the International code of botanical nomenclature (McNeill & al., 2006) requires that, as from 1 January 1935, all names of new plant taxa (algae and fossils excepted) can be validly published only if they are accompanied by a Latin description or diagnosis or by a reference to an effectively published Latin diagnosis or description. Although several past Nomenclature Section meetings have voted on proposals to have this requirement lifted, the liberation of plant nomenclature, and by implication plant taxonomy, from this impediment remains elusive. We argue that the Latin requirement must be removed now as it represents a relict that does not serve the purposes for which it was originally intended. Previous proposals to delete the requirement of a Latin description or diagnosis for the valid publication of a plant name have all had strings attached. We propose (Figueiredo & al. in Taxon 59: 659–660, this issue) that, as from the effective date of the Melbourne Code (a suitable date after the Melbourne Congress), a diagnosis or description in any language would suffice to effect valid publication of a plant name, the algae and fossils excepted, provided all of the other provisions for valid publication have been satisfied.
Origin and distribution of autopolyploids via apomixis in the alpine species Ranunculus kuepferi (Ranunculaceae)
Authors: Cosendai Anne-Caroline , Rodewald Jan , Hörandl Elvira
Published: February 2019

The evolution of polyploids is strongly influenced by their mode of origin. Autopolyploidy is often hampered by disturbances of chromosome pairing and segregation at meiosis, while allopolyploids exhibit fewer meiotic problems and potentially have selective advantages because of hybridity. Apomixis, the asexual reproduction via seed in flowering plants, can overcome problems of meiotic reduction, favouring range expansions of polyploids. We elucidate the origin and genetic structure of apomictic cytotypes of the alpine species Ranunculus kuepferi by analyzing five microsatellite loci (SSRs) and Amplified Fragment Length Polymorphisms (AFLPs) on eight diploid and twelve polyploid populations from across the range of the species. Multiple allelism appears in three SSR loci in all polyploid cytotypes and is likely a result of facultative unbalanced meiotic events, as it is typical for autopolyploids. Low frequencies of private AFLP fragments (3%) and SSR alleles (4%) in tetraploids suggest that they evolved from diploid populations without the contribution of another divergent parental gene pool. A Neighbor‐joining tree of AFLPs revealed a low genetic divergence of cytotypes and at least three independent origins of tetraploid populations. Autopolyploidy is in R. kuepferi likely evolutionarily young and still has signatures of a facultative unbalanced meiosis. The shift to apomixis avoided consequences of meiotic problems and therefore enhanced rapid establishment of autotetraploids. The lack of hybridity in polyploids suggests that apomixis is successful even without genomic novelty. The distributional success of polyploid cytotypes is probably more due to the benefits of apomictic reproduction than to genetic consequences of polyploidization.
Southern European glacial refugia: A tale of tales
Authors: Feliner Gonzalo Nieto
Published: February 2019

Interpretations of current diversity patterns based on the contraction/expansion model forced by climatic oscillations during the last two million years are commonplace in phylogeographic literature. Of the wealth of scientific studies accumulated during the past two decades in Europe, the ones we understand best are those mostly from higher latitudes, probably because patterns were simplified to a great extent by major losses of diversity during glacial periods. In Southern European regions (or in general, in those places where ice effects were less severe) the situation is quite different and to some extent opposite. These regions are referred to as refugia because they are known to contain more genetic diversity than elsewhere. This is not only due to preservation of genotypes that went extinct in other places, however, but also to the intensity and accumulation of a number of processes in a patchy landscape across a varied topography. A lack of general phylogeographic patterns in these regions is one consequence. Speaking of a single refugium to refer to each of the peninsulas, however, is an oversimplification. Even speaking of multiple unconnected refugia does not adequately reflect the complexity of the processes that shaped the current genetic and specific diversity.
Phylogenetic analyses of DNA sequences with chromosomal and morphological data confirm and refine sectional and series classification within Melampodium (Asteraceae, Millerieae)
Authors: Stuessy Tod F. , Blöch Cordula , Villaseñor José L. , Rebernig Carolin A. , Weiss-Schneeweiss Hanna
Published: February 2019

The genus Melampodium consists of 40 species distributed throughout Mexico and Central America with extensions into the southwestern United States and Colombia and Brasil of South America. The genus reflects broad chromosomal evolution involving dysploidy and polyploidy withn = 9, 10, 11, 12, 14, 18, 20, 23, 24, 27, 28, 30, and 33 having been documented (x = 9, 10, 11, 12, and 14). The most recent classification of the genus, based primarily on morphology and chromosome num bers, recognized six taxonomic sections: Alcina, Bibractiaria, Melampodium, Rhizomaria, Serratura, and Zarabellia. Section Melampodium, which contains 22 species, was divided into five series: Cupulata, Leucantha, Longipila, Melampodium, and Sericea. This hypothesis had been tested by previous morphological phenetic and cladistic analyses, and several problem areas had been highlighted, especially involving section Alcina, but no modifications to the classification have been made. Recent molecular studies utilizing nrITS, 5S rDNA spacer and low‐copy nuclear PgiC gene, plus plastid matK and psbA‐trnH regions allow the classificatory hypothesis to be tested more precisely. Congruence between ITS and matK phylogenies for all species reveals sections Bibractiaria, Rhizomaria, and Serratura to be holophyletic. The largest section Melampodium is holophyletic with both plastid markers, but M. longipilum is shown as an outlier (tying to sect. Rhizomaria) in all nuclear marker phylogenies (ITS, PgiC and 5S rDNA spacer). Section Zarabellia appears holophyletic in matK but biphyletic with ITS, suggesting recogni tion of two distinct series. Section Alcina is the most problematic, being triphyletic in ITS and matK, and with the species not connecting to the same relatives. These insights recommend recognition of three sections from within section Alcina, one hous ing M. nutans (Nutantia Stuessy, sect. nov.) another M. glabrum (Glabrata Stuessy, sect. nov.) and a third M. perfoliatum (sect. Alcina (Cav.) DC.). These may represent ancient independent lines that have diverged from original x = 11 ancestors. Within section Melampodium, 5S rDNA NTS, PgiC and psbA‐trnH, in addition to ITS and matK, provide insights on relationships among taxonomic series. Series Leucantha and Longipila are holophyletic, and series Cupulata nearly so, with M. glabribracteatum deserving treatment in a series of its own. The most complex relationships are between series Melampodium, Cupulata, and Sericea, the latter comprising five exclusively polyploid taxa (4x and 6x). Molecular and cytogenetic data reveal allopolyploid origins for all of these polyploids, in some cases involving hybridization between the two series Cupulata and Melampodium / Sericea, such as with M. mayfieldii and M. longicorne, which exacerbates taxonomic circumscription.
Phylogeny and divergence times of Bactridinae (Arecaceae, Palmae) based on plastid and nuclear DNA sequences
Authors: Eiserhardt Wolf L. , Pintaud Jean-Christophe , Asmussen-Lange Conny , Hahn William J. , Bernal Rodrigo , Balslev Henrik , Borchsenius Finn
Published: February 2019

Bactridinae include about 150 species of spiny Neotropical palms in five genera that are ecologically important in several vegetation types such as open woodland (Acrocomia), lowland rainforest (Astrocaryum, Bactris), and montane forest (Aiphaness). The subtribe also includes the only exclusively lianescent palm genus in the Neotropics (Desmoncus). We present a fully resolved molecular phylogeny of 41 species of Bactridinae, representing all genera as well as most of the currently ac ‐ cepted infrageneric taxa (subgenera, sections etc.) and recently proposed informal groups. Analyses are based on five plastid DNA regions (matK, trnQ‐rps16, rps16 intron, trnD‐trnT, trnL‐trnF) and three nuclear markers (PRK, RPB2, ITS). A combined dataset was analysed with likelihood and parsimony methods. The results show that all accepted taxa at and above the generic level are monophyletic with high support. Astrocaryum alatum and A. mexicanum, recently segregated into a genus of their own (Hexopetion), form a strongly supported monophyletic group sister to the remaining Astrocaryum species. Desmoncus and Acrocomia are resolved as sister genera, and together they are sister to the remaining Bactridinae. This finding contrasts with that of two previous studies reporting Acrocomia to be sister to the rest of the subtribe. Aiphanes is resolved as sister to Bactris and Astrocaryum. Species‐level relationships recovered within Astrocaryum and Bactris disagree to a large extent with previous morphology‐based infrageneric classifications, suggesting that those characters are homoplasious, particularly within Bactris. A Bayesian dating analysis using the relaxed‐clock model indicates that most genera of Bactridinae diverged during a relatively short period around the Eocene–Oligocene boundary, which might explain the difficulties in resolving the phylogenetic backbone of the group. The mostly Andean genus Aiphanes shows an initial radiation of early lineages in the Oligocene (around 25 Ma ago) corresponding to an early uplift phase of the cordillera. These taxa are nowadays restricted to the mountain forests of Colombia and Ecuador. The main diversification of Andean Aiphanes began in the Miocene (around 11 Ma ago). This study provides the first substantial insight into Bactridinae phylogeny and sets the stage for more comprehensively sampled species‐level studies analysing drivers of diversity of Neotropical palms, speciation patterns, character evolution, or biogeography.
Phylogeny, morphology, and biogeography of Haplophyllum (Rutaceae), a species‐rich genus of the Irano‐Turanian floristic region
Authors: Salvo Gabriele , Manafzadeh Sara , Ghahremaninejad Farrokh , Tojibaev Komiljon , Zeltner Louis , Conti Elena
Published: February 2019

Haplophyllum A. Juss. is one of the most species‐rich, but poorly‐known genera of Rutaceae (citrus family), reaching maximum species diversity in Turkey, Iran, and Central Asia. Many of its species exhibit a narrow geographic range ("narrow endemics"), which makes them particularly vulnerable to extinction. Despite its importance for the characterization of the Irano‐Turanian floristic region, the evolution of species diversity in Haplophyllum has never been examined in a phylogenetic and biogeographic context. We generated gene trees from DNA sequences of four regions of the chloroplast genome for 118 accessions, representing 66% of the species diversity of the genus. Additionally, Haplophyllum was examined morphologically. The phylogenetic analyses showed that several species of the genus do not form reciprocally monophyletic groups. Optimization of morphological characters on the chloroplast DNA phylogeny indicated that most of the species, in particular those with a widespread geographic distribution, can only be diagnosed by combinations of homoplasious character states. Homoplasy notwithstanding, the main morphological characters traditionally used to classify the genus are consistent with the molecular phylogeny of Haplophyllum. Finally, the Mediterranean representatives of Haplophyllum were found to be embedded within a clade that includes primarily Irano‐Turanian species, suggesting multiple invasions of the Mediterranean basin from the east.
The fate of Acacia
Authors: Linder H. Peter , Crisp Mike
Published: February 2019

We propose a once‐off "special committee" to developed a proposal that could resolve the entrenched positions in the case of the typification of Acacia. It is important that such a proposal has a broad, consensual, support, rather than rely on a "winner takes all" approach.
Phylogeny and taxonomy of Tribulocarpus (Aizoaceae): A paraphyletic species and an adaptive shift from zoochorous trample burrs to anemochorous nuts
Authors: Thulin Mats , Thiede Joachim , Liede-Schumann Sigrid
Published: February 2019

The phylogenetic position and circumscription of the disjunct African genus Tribulocarpus is investigated with DNA sequences from plastid rps16 and trnL‐F, and nuclear ITS. Representatives from all four subfamilies of Aizoaceae are included in the analyses, most of them from Aizooideae and Sesuvioideae. The position of Tribulocarpus as sister to the rest of Sesuvioideae is confirmed, and we agree that the genus should be referred to this subfamily. Tetragonia retusa is found to be part of the Tribulocarpus clade with strong support. A new taxonomy of Tribulocarpus with two species is proposed and the new combination Tribulocarpus retusus is made. A lectotype is designated for Tetragonia somalensis. Tribulocarpus dimorphanthus, disjunctly distributed in south‐western and north‐eastern Africa, is retrieved as paraphyletic with regard to T. retusus, endemic in Somalia, as the latter is sister to the north‐east African part of T. dimorphanthus only. Despite the genetic difference between the samples from the disjunct populations of T. dimorphanthus no morphological differences could be detected. Tribulocarpus dimorphanthus–T. retusus is suggested as an example of a progenitor‐derivative species pair, where T. retusus has budded off from the north‐eastern partial area of distribution of T. dimorphanthus. The compound and spiny fruits of T. dimorphanthus versus the simple and broadly winged fruits of T. retusus indicate a rapid adaptive shift from zoochorous trample burrs to anemochorous nuts.
Bristly versus juicy: Phylogenetic position and taxonomy of Sphaerocoma (Caryophyllaceae)
Authors: Kool Anneleen , Perrigo Allison , Thulin Mats
Published: February 2019

The phylogenetic position of the Afro‐Asian genus Sphaerocoma is investigated using DNA sequences from plastid rps16 and ndhF, as well as from nuclear ITS and RPB2. Seven accessions of Sphaerocoma, representing all three currently recognized taxa, are analyzed along with sequences from genera that have been found to be closely related to Sphaerocoma in broader studies of Caryophyllaceae. The Afro‐Arabian Pollichia is indicated as sister to Sphaerocoma, and this Sphaerocoma‐Pollichia clade is sister to a clade with Macaronesian Polycarpaea and the widely distributed Polycarpon prostratum. A close relationship between the anemochorous Sphaerocoma and the endozoochorous Pollichia has never previously been suggested, but some similarities in, e.g., floral characters are pointed out. Sphaerocoma is strongly supported as monophyletic, but no significant molecular variation within the genus could be detected. A new taxonomy of Sphaerocoma is proposed, where a single species with two geographically and morphologically defined subspecies are recognized: S. hookeri subsp. hookeri in coastal areas along the Red Sea in Egypt, Sudan and Saudi‐Arabia, near Aden in Yemen, and in Somalia, and S. hookeri subsp. aucheri comb. & stat. nov. in coastal areas in south‐eastern Yemen, Oman, United Arab Emirates, Bahrain, Iran, and Pakistan. A lectotype is designated for S. hookeri.
Infrageneric classification of Calibrachoa (Solanaceae) based on morphological and molecular evidence
Authors: Fregonezi Jéferson Nunes , de Freitas Loreta Brandão , Bonatto Sandro L. , Semir João , Stehmann João Renato
Published: February 2019

The genus Calibrachoa (Solanaceae) comprises approximately 27 species that are found in open areas of southern South America, with the exception of C. parviflora, which also occurs in North America and Europe, probably as a result of introduction from South America and subsequent naturalization. The genus is closely related to Petunia, but differs in characteristics such as chromosome number, corolla aestivation, seed morphology, and leaf anatomy. Previous publications have shown that C. parviflora and C. pygmaea have morphological, ecological, and molecular features that differ from those of the other species of Calibrachoa, which had also been shown in a phylogenetic study using cpDNA RFLPs. In this paper, we present phylogenies based on chloroplast sequence data from psbB-psbH, trnS-trnG, and trnL-trnF intergenic spacers and the trnL intron, which corroborate the segregation of Calibrachoa species in two highly supported clades. On the basis of these results and the morphological and ecological evidence, we propose that each Calibrachoa clade be recognized at the subgeneric level. A new subgenus, Calibrachoa subg. Stimomphis, is recognized, which includes 25 species, whereas C. parviflora and C. pygmaea are in C. subg. Calibrachoa. A list of species that belong to each subgenus is provided, and lectotypes, neotypes, or epitypes are designated for eight names in Calibrachoa.
Annual plants colonizing the Arctic? Phylogeography and genetic variation in theEuphrasia minimacomplex (Orobanchaceae)
Authors: Gussarova Galina , Alsos Inger Greve , Brochmann Christian
Published: February 2019

The high‐arctic environment supports very few annual plants, but more annuals can be expected to move northwards following climate warming. Here we address the history of the amphi‐Atlantic, hemiparasiticEuphrasia minimacomplex, which is taxonomically intricate and consists of annuals typically growing in alpine, north boreal, and low‐arctic habitats. Recently it has also been discovered at three distantly separated sites in the high‐arctic archipelago of Svalbard. We analyzed Amplified Fragment Length Polymorphism (AFLP) and chloroplast DNA (cpDNA) variation in populations from most of the range of the complex. The main split observed in both datasets, dated to nearly 6 Ma ago, was between one central/southern European alpine lineage (E. minimas.str.) and one northern amphi‐Atlantic lineage (E. wettsteinii). TheE. wettsteiniilineage consisted of two cpDNA sublineages, both amphi‐Atlantic and partly sympatric, estimated to have diverged 1.7 Ma ago. Two main northern subgroups were also revealed in the AFLP dataset, partly consistent with the cpDNA sublineages: one E Atlantic subgroup (N Russia, extending into Scotland and Colesdalen in Svalbard), and one mainly W Atlantic subgroup (NE Canada, Greenland, and Iceland, extending into N Norway). A third subgroup was restricted to two of the three Svalbard populations, Bockfjorden and Ossian Sarsfjellet. Assignment tests of the Svalbard populations suggest that Colesdalen was derived from N Russian source populations and Bockfjorden from N Norwegian ones; the assignment of the Ossian Sarsfjellet population was uncertain. However, as all Svalbard populations were distinctly divergent from each other as well as from all other populations in AFLP marker frequencies, it is unlikely that their establishment in Svalbard is caused by the current climate warming or recent human activities. Their divergence is probably due to founder effects and genetic drift following independent earlier immigrations, possibly during the postglacial warm period 9500 to 4000 years ago.
Automatic extraction of leaf characters from herbarium specimens
Authors: Corney David P.A. , Clark Jonathan Y. , Tang H. Lilian , Wilkin Paul
Published: February 2019

Herbarium specimens are a vital resource in botanical taxonomy. Many herbaria are undertaking large‐scale digitization projects to improve access and to preserve delicate specimens, and in doing so are creating large sets of images. Leaf characters are important for describing taxa and distinguishing between them and they can be measured from herbarium specimens. Here, we demonstrate that herbarium images can be analysed using suitable software and that leaf characters can be extracted automatically. We describe a low‐cost digitization process that we use to create a set of 1895 images of Tilia L. specimens, and novel botanical image processing software. The output of the software is a set of leaf characters. As a demonstration of this approach, we extract the length and width of a large number of leaves automatically from images of whole herbarium specimens. We show that the lengths and widths that we extract are very strongly correlated with values in a published account of cultivated species, but are also consistently smaller. We discuss some particular features of herbarium specimens that may affect the results of this form of analysis, and consider further applications to extract characters such as leaf shape and margin characters.
Revised generic delimitations for Oxypolis and Ptilimnium (Apiaceae) based on leaf morphology, comparative fruit anatomy, and phylogenetic analysis of nuclear rDNA ITS and cpDNA trnQ–trnK intergenic spacer sequence data
Authors: Feist Mary Ann E. , Downie Stephen R. , Magee Anthony R. , Liu Mei Rebecca
Published: February 2019

A phylogenetic study of Oxypolis and Ptilimnium, two small genera of tribe Oenantheae (Apiaceae: subfamily Api–oideae), was carried out. Generic circumscriptions and infrageneric and infraspecific relationships were investigated through parsimony and Bayesian inference analyses of nuclear rDNA ITS and cpDNA trnQ–5’rps16 and 3’rps16–5’trnK intergenic spacer sequences. Fruit anatomical characters were also examined and used in conjunction with leaf morphology to corroborate the results of the phylogenetic analyses. Each genus as currently delimited has both compound–leaved and rachis–leaved species. Results of the phylogenetic analyses show that neither Oxypolis nor Ptilimnium is monophyletic; each genus is split into two strongly supported clades that correspond to differences in leaf morphology within the groups. Fruit anatomical characters support these splits. The fruits of compound–leaved and rachis–leaved Oxypolis species differ in the number of commissural vittae per mericarp, the branching of the vittae, and the lignification of mericarp around the seed. The fruits of compound–leaved and rachis–leaved Ptilimnium species differ in the compression of the mericarps and the development of the marginal ribs. The fruits of rachis–leaved Oxypolis and rachis–leaved Ptilimnium species also differ in the compression of the mericarps and the development of the marginal ribs. Based on analyses of molecular data and corroboration with morphological and fruit anatomical data, new circumscriptions for the genera Oxypolis and Ptilimnium are formalized. Each of the two polyphyletic genera (Oxypolis and Ptilimnium) is split, two genera (Tiedemannia and Harperella) are resurrected, and three new combinations are made.
Molecular systematics and evolutionary trends and relationships in the genus Jumellea (Orchidaceae): Implications for its species limits
Authors: Rakotoarivelo Fanny P. , Razafimandimbison Sylvain G. , Mallet Bertrand , Faliniaina Lucien , Pailler Thierry
Published: February 2019

Jumellea is an orchid genus centered on Madagascar but also occurs on some of the neighboring oceanic islands (the Mascarenes and Comoros) and in southern and eastern Africa. Prior to our study the genus contained ca. 55 morphologically distinct species, of which six are found in the Comoros (three endemic, three shared with Madagascar), nine in the Mascarenes (four endemic, four shared with Madagascar), two in southern and eastern Africa (both endemic), and 41 species endemic to Madagascar. We perform Bayesian and parsimony phylogenetic analyses of Jumellea based on combined chloroplast (matK, trnL-F, rps16, ycf1) and nuclear (nrITS) data from 60 specimens representing 47 species, four subspecies, and two varieties of Jumellea: (1) to assess the phylogenetic value of growth form, leaf, bract and lip shape, and spur length, presently used for recognizing informal groups within the genus; and (2) to test the monophyly of some variable species (e.g., J. gracilipes, J. lignosa). We find no support for the informal groups of Jumellea, as all the characters tested are evolutionarily labile. Jumellea lignosa (comprising J. lignosa subsp. lignosa, subsp. tenuibracteata, subsp. acutissima, and subsp. latilabia) is not monophyletic unless subsp. tenuibracteata is excluded. Jumellea gracilipes s.l. (including J. ambongensis, J. imerinensis, and J. unguicularis) is polyphyletic. As a result, we resurrect these three latter species, and recognize J. lignosa subsp. tenuibracteata at species level. Furthermore, we propose new circumscriptions for the following species: the Comorian J. arachnantha (including the Malagasy J. sagittata); the Reunionese J. exilis (including the Malagasy J. flavescens); the Reunionese J. recta (including the Malagasy Jumellea sp. 1); the Reunionese J. recurva (including the Malagasy J. pandurata); and the Reunionese J. steno-phylla (including the Malagasy J. gracilipes 2 and 3). Finally, Jumellea arborescens and J. maxillarioides are recorded from Madagascar and the Comoros. Finally, the number of species of Jumellea has now increased from 55 to 57: seven species in the Comoros (four shared with Madagascar), nine species in the Mascarenes (four shared with Madagascar), two species in Africa, and 39 species, three subspecies, and two varieties restricted to Madagascar.
Integrating different tools to disentangle species complexes: A case study in Epidendrum (Orchidaceae)
Authors: Pessoa Edlley Max , Alves Marccus , Alves-Araújo Anderson , Palma-Silva Clarisse , Pinheiro Fábio
Published: February 2019

Species delimitation remains a central problem in systematic, taxonomic and evolutionary studies. However, the precise delimitation of species depends on the criteria used to identify lineages and the specific species concept that is applied. Recently, multidisciplinary studies using different data sources have significantly improved the delimitation of species within complex taxonomic groups, leading to an integrative taxonomy. To investigate the species delimitation within the Atlantic clade of Epidendrum (subg. Amphyglottium), four different species criteria were examined (phenetic differentiation, mono–phyly, diagnosability, absence of genetic intermediates). Morphometrics, plastid DNA sequences and nuclear microsatellite markers were used to explore the agreement between patterns recovered and species criteria tested. The conflicts among species criteria are discussed in light of pollination ecology, patterns of gene flow, reproductive isolation mechanisms and selective pressures currently acting in deceptive orchid species. Four currently recognized species from the Atlantic clade could be delimitated, including one newly described species, Epidendrum flammeus. Three out of five species satisfied the monophyly criterion, and few diagnostic flower characters were found among species. In contrast, nuclear microsatellite data correctly assigned individuals to their respective species, even in the presence of weak reproductive isolation and extensive hybridization events reported in the literature. One important implication of this finding is that phylogenetic studies in Epidendrum spp. should make use of single– or low–copy nuclear loci instead of plastid markers, which may be true for other plant groups. The results also indicate that the generalized pollination syndrome found among species of the Atlantic clade, the different levels of gene flow observed between nuclear and plastid markers, and hybridization events are commonly observed as the main evolutionary forces within this orchid group. Finally, we discuss evolutionary processes and taxonomic limits among these species, and we highlight the need to increase the inter–disciplinary approach to investigate species limits in complex plant groups.
A contribution toward clarifying the nomenclature of Veronica L. (Plantaginaceae)
Authors: Agudo Jose Ángel Sánchez , Martínez-Ortega M. Montserrat , Cafferty Steve , Rico Enrique
Published: February 2019

During a taxonomic revision of the genus Veronica L. for the Flora iberica project, an attempt was made to fix the correct status of the names cited in the study area. With this aim, here we have designated lectotypes, neotypes and epitypes for 18 previously untypified names, mainly belonging to annual species, some of them widely distributed such as V. persica and V. praecox. These newly proposed types support the current use of the names concerned and therefore contribute to establishing the correct nomenclature of the genus.
BrassiBase: Tools and biological resources to study characters and traits in the Brassicaceae—version 1.1
Authors: Koch Marcus A. , Kiefer Markus , German Dmitry A. , Al-Shehbaz Ihsan A. , Franzke Andreas , Mummenhoff Klaus , Schmickl Roswitha
Published: February 2019

We are developing an online­accessible knowledge and database system of cross­referenced information and resources on Brassicaceae (Cruciferae) taxonomy, systematics and evolution, including chromosome numbers, traits and characters, germplasm resources, and accurate enumeration of all species, genera and tribes. Biological, molecular and evolutionary knowledge is exponentially increasing in the mustard family. However, because of the complex and overwhelming biological diversity of the family, it is difficult to assess research results within a larger evolutionary framework. Many species have proven to be remarkable study objects but are rarely available. Biological material and resources, either collected directly in the wild or held in germplasm collections, have often been taxonomically misidentified; and only very rarely has the material been further characterized and documented. There is also no comprehensive survey of character and trait distribution among Brassicaceae lineages, though family­wide phylogenies are meanwhile available. In order to close these gaps, we will make accessible to the scientific community the research data focusing on adaptive characters and their evolution in the Brassicaceae. In this context, we will also provide a comprehensive documentation of the taxonomy and systematics of the entire family. This will include a database with all relevant taxonomic, systematic and phylogenetic literature, a comprehensive data collection of characters and traits, a DNA­based identification tool for genera and species, electronic interactive keys for the identification of genera and species, and a setup of a carefully selected and documented germplasm collection representing main lineages of the family. This knowledge database, hereafter BrassiBase, has been launched within the framework of the DFG priority programme SSP 1529 “Adaptomics – Evolutionary plant solutions to ecological challenges/Molecular mechanisms underlying adaptive traits in the Brassicaceae s.l.”
A review of Polygala trichosperma Jacq. (Polygalaceae)
Authors: Pastore José Floriano Barêa
Published: February 2019

A review of the name Polygala trichosperma, including its authority, orthography, and typification, is provided. It is determined that this name was first validly published by Jacquin and not Linnaeus. However, under the Code, the specific epithet’s original spelling, “trichisperma” t is to be corrected to “trichosperma”, the spelling originally used by Linnaeus. The name P. trichosperma is lectotypified by a Jacquin specimen at BM.
Pertya scandens and P. glabrescens (Asteraceae: Pertyeae) revisited
Authors: Zhang Cai-Fei , Deng Yun-Fei , Ohi-Toma Tetsuo , Li Liang-Qian , Gao Tian-Gang
Published: February 2019

In Japan, there are two common suffruticose species of the genus Pertya Sch. Bip. (Asteraceae: Pertyeae),P. scandens (Thumb.) Sch. Bip. and P. glabrescens Sch. Bip. ex Nakai, the former with pilose stems and leaves and the latter with glabrous to glabrate stems and leaves. Recently, however, it was concluded that the two species should be referred to as P. ovata Maxim. and P. scandens, the application of the latter name shifting to the species with glabrous stems. The lectotype of Erigeron scandens Thunb. (= P. scandens) was carefully examined and it was identified as the species with pilose stems and leaves. Pertya glabrescens Sch. Bip. ex Nakai was determined to be the correct name for the glabrous species. Lectotypes for P. glabrescens, as well as the synonyms P. scandens f. maximowicziana Franch., P. scandens f. schulziana Franch., and P. glabrescens var. viridis Nakai are designated.
A phylogenetic analysis and new delimitation of Senecio sect. Crociseris (Compositae: Senecioneae), with evidence of intergeneric hybridization
Authors: Calvo Joel , Álvarez Inés , Aedo Carlos , Pelser Pieter B.
Published: February 2019

Senecio sect. Crociseris is one of the three main sections of western Eurasian/northern African Senecio species. Previous studies indicated that species commonly assigned to this section are closely related to those of sect. Doria. The aim of the research presented here was to test the morphology–based delimitation of sect. Crociseris using phylogenetic analyses of plastid and nuclear DNA sequence data. The results of these studies are used to propose a new delimitation of sect. Crociseris. Species of sect. Doria were nested within a clade formed by species of sect. Crociseris. Section Doria is therefore best considered a synonym of sect. Crociseris. In addition, S. racemosus, traditionally included in sect. Crociseris, is transferred to the genus Jacobaea. One of the two J. kirghisica specimens that were sequenced contains ITS copies that are most closely related to those of sect. Crociseris as well as copies that nest among ITS accessions of Jacobaea. This suggests intergeneric hybridization between Senecio and Jacobaea.
Effective field theories in Rξ gauges
Authors: Misiak M. , Paraskevas M. , Rosiek J. , Suxho K. , Zglinicki B.
Published: February 2019

Abstract

In effective quantum field theories, higher dimensional operators can affect the canonical normalization of kinetic terms at tree level. These contributions for scalars and gauge bosons should be carefully included in the gauge fixing procedure, in order to end up with a convenient set of Feynman rules. We develop such a setup for the linear R

ξ
-gauges. It involves a suitable reduction of the operator basis, a generalized gauge fixing term, and a corresponding ghost sector. Our approach extends previous results for the dimension-six Standard Model Effective Field Theory to a generic class of effective theories with operators of arbitrary dimension.
Multipartite dark matter with scalars, fermions and signatures at LHC
Authors: Bhattacharya Subhaditya , Ghosh Purusottam , Sahu Narendra
Published: February 2019

Abstract

Basic idea of this analysis is to achieve a two-component dark matter (DM) framework composed of a scalar and a fermion, with non-negligible DM-DM interaction contributing to thermal freeze out (hence relic density), but hiding them from direct detection bounds. We therefore augment the Standard Model (SM) with a scalar singlet (S) and three vectorlike fermions: two singlets (χ
1
, χ
2) and a doublet (N). Stability of the two DM components is achieved by a discrete

$$ {\mathcal{Z}}_2 \times {\mathcal{Z}}_2^{\prime } $$

Z
2

×

Z
2
′

symmetry, under which the additional fields transform suitably. Fermion fields having same

$$ {\mathcal{Z}}_2 \times {\mathcal{Z}}_2^{\prime } $$

Z
2

×

Z
2
′

charge (N, χ
1 in the model) mix after electroweak symmetry breaking (EWSB) and the lightest component becomes one of the DM candidates, while scalar singlet S is the other DM component connected to visible sector by Higgs portal coupling. The heavy fermion (χ
2) plays the role of mediator to connect the two DM candidates through Yukawa interaction. This opens up a large parameter space for the heavier DM component through DM-DM conversion. Hadronically quiet dilepton signature, arising from the fermion dark sector, can be observed at Large Hadron Collider (LHC) aided by the presence of a lighter scalar DM component, satisfying relic density and direct search bounds through DM-DM conversion.
A NOTE ON PREDICATIVE ORDINAL ANALYSIS I: ITERATED COMPREHENSION AND TRANSFINITE INDUCTION
Authors: KENTARO SATO
Published: February 2019

We determine the proof-theoretic ordinals (i) of ${\cal C} - {\bf{TI}}[\alpha ]$, the transfinite induction along α, for any hyperarithmetical level ${\cal C}$, in the first order setting and (ii) of any combination of iterated arithmetical comprehension and ${\cal C} - {\bf{TI}}[\alpha ]$ for ${\cal C}\, \equiv \,{\rm{\Pi }}_k^i ,{\rm{\Sigma }}_k^i$ ($i\, = \,0,1$) in the second order setting.
WEDDING IMAGERY IN THE TALOS EPISODE: APOLLONIUS RHODIUS,ARGONAVTICA4.1653–88
Authors: Cassidy Sarah
Published: February 2019

AtArgon.4.1653–88, Medea steps forward among the Argonauts and asserts that their harbourage on Crete will not be blocked by the bronze giant Talos, who stands menacingly throwing rocks at their ship. She claims that she alone can subdue him, and then steps forward and proceeds to do so. Using a sequence of ‘magical’ ritualistic acts, she causes Talos to scrape his vulnerable heel on a rock and fall down dead, as the ichor pours from his wound. This scene is the last in which Medea appears in the epic, and accordingly it forms the final opportunity to bridge the gap between the Medea of theArgonauticaand the future Medea, one whose actions are already well known from such works as Pindar's fourthPythian Odeand Euripides’Medea. The importance for Apollonius to create a plausible transition between the Medea of earlier myth and the Argonautic Medea is evident. A clear-cut break from tradition would allow Medea to become an alternative Medea, perhaps akin to the alternative portrayal of Helen by Euripides; a continuation would allow corroboration with earlier sources, which would lend authority and validation to Apollonius’ version. It is now the common consensus that Apollonius tried, however successfully, to bridge the gap between a young and an adult Medea and between tradition and innovation in her character.
β-Carotene in the human body: metabolic bioactivation pathways – from digestion to tissue distribution and excretion
Authors: Bohn Torsten , Desmarchelier Charles , El Sedef N. , Keijer Jaap , van Schothorst Evert , Rühl Ralph , Borel Patrick
Published: February 2019

β-Carotene intake and tissue/blood concentrations have been associated with reduced incidence of several chronic diseases. Further bioactive carotenoid-metabolites can modulate the expression of specific genes mainly via the nuclear hormone receptors: retinoic acid receptor- and retinoid X receptor-mediated signalling. To better understand the metabolic conversion of β-carotene, inter-individual differences regarding β-carotene bioavailability and bioactivity are key steps that determine its further metabolism and bioactivation and mediated signalling. Major carotenoid metabolites, the retinoids, can be stored as esters or further oxidised and excreted via phase 2 metabolism pathways. In this review, we aim to highlight the major critical control points that determine the fate of β-carotene in the human body, with a special emphasis on β-carotene oxygenase 1. The hypothesis that higher dietary β-carotene intake and serum level results in higher β-carotene-mediated signalling is partly questioned. Alternative autoregulatory mechanisms in β-carotene / retinoid-mediated signalling are highlighted to better predict and optimise nutritional strategies involving β-carotene-related health beneficial mediated effects.