bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bristly versus juicy: Phylogenetic position and taxonomy of Sphaerocoma (Caryophyllaceae)
Authors: Kool Anneleen , Perrigo Allison , Thulin Mats 
Published: February 2019

AbstractThe 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

AbstractThe 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

AbstractThe 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

AbstractHerbarium 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

AbstractA 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

AbstractJumellea 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

AbstractSpecies 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

AbstractDuring 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

AbstractWe 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

AbstractA 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

AbstractIn 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

AbstractSenecio 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.
A NOTE ON PREDICATIVE ORDINAL ANALYSIS I: ITERATED COMPREHENSION AND TRANSFINITE INDUCTION
Authors: KENTARO SATO 
Published: February 2019

AbstractWe 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.
Local knowledge and attitude towards the Vulnerable Bhutan takin Budorcas whitei among residents living within its seasonal range
Authors: Sangay Tiger , Rajanathan Rajaratnam , Vernes Karl , Tighe Matthew 
Published: February 2019

AbstractWe assessed local knowledge of and attitudes towards a large, endemic bovid, the Bhutan takin Budorcas whitei, within its seasonal range in Jigme Dorji National Park, Bhutan. Using semi-structured questionnaires, data were collected in March 2015 from interviews with 169 park residents. A conditional inference tree analysis was used to explore associations between demography, locality, and secondary response variables through questions relating to respondents’ knowledge of the takin's status as a protected species, a Vulnerable species, and as the national animal. Most respondents knew the takin was Bhutan's national animal, and of those, a significantly high proportion also knew of its protected status. Significantly more respondents residing in the species’ summer, rather than winter, range were aware of the takin's Vulnerable status. Most respondents expressed positive feelings towards the takin and supported its protection. This strong positive attitude, in conjunction with awareness-raising efforts, could be valuable for promoting the takin as a montane flagship species.
Alexithymia and frontal–amygdala functional connectivity in North Korean refugees
Authors: Kim Nambeom , Park Inkyung , Lee Yu Jin , Jeon Sehyun , Kim Soohyun , Lee Kyung Hwa , Park Juhyun , Kim Hang-Keun , Gwaq Ah Reum , Jun Jin Yong , Yoo So Young , Lee So Hee , Kim Seog Ju 
Published: February 2019

AbstractBackgroundRefugees commonly experience difficulties with emotional processing, such as alexithymia, due to stressful or traumatic experiences. However, the functional connectivity of the amygdala, which is central to emotional processing, has yet to be assessed in refugees. Thus, the present study investigated the resting-state functional connectivity of the amygdala and its association with emotional processing in North Korean (NK) refugees.MethodsThis study included 45 NK refugees and 40 native South Koreans (SK). All participants were administered the Toronto Alexithymia Scale (TAS), Beck Depression Inventory (BDI), and Clinician-administered PTSD Scale (CAPS), and differences between NK refugees and native SK in terms of resting-state functional connectivity of the amygdala were assessed. Additionally, the association between the strength of amygdala connectivity and the TAS score was examined.ResultsResting-state connectivity values from the left amygdala to the bilateral dorsolateral prefrontal cortex (dlPFC) and dorsal anterior cingulate cortex (dACC) were higher in NK refugees than in native SK. Additionally, the strength of connectivity between the left amygdala and right dlPFC was positively associated with TAS score after controlling for the number of traumatic experiences and BDI and CAPS scores.ConclusionsThe present study found that NK refugees exhibited heightened frontal–amygdala connectivity, and that this connectivity was correlated with alexithymia. The present results suggest that increased frontal–amygdala connectivity in refugees may represent frontal down-regulation of the amygdala, which in turn may produce alexithymia.