bluuebunny/crossref_metadata_2025 huggingface dataset:
The Prometheus Description Model: an examination of the taxonomic description‐building process and its representation
Authors: Pullan Martin R. , Armstrong Kate E. , Paterson Trevor , Cannon Alan , Kennedy Jessie B. , Watson Mark F. , McDonald Sarah , Raguenaud Cédric
Published: May 2010

A model for representing taxonomic descriptive data is presented. The model has been developed in response to the growing requirement for the global exchange of descriptive data. Meaningful exchange of data requires that data be represented in a form that can be consistently parsed and interpreted, requiring a common data model and the constrained and explicitly defined use of descriptive terms. The model presented here is divided into two parts that address both of these issues. A new data model for the representation and storage of taxonomic descriptive data is proposed that builds on and extends the best features of current descriptive data models and formats. An ontology‐based model for defining and constraining the use of descriptive terms is also presented. The model is based on an analysis of current taxonomic working practices and the processes involved in generating a description. The model takes a specimen‐oriented approach allowing descriptive data to be represented through a range of levels of abstraction from actual measurements of structures on a specimen to abstract descriptions of the features expected to be found on a specimen that is a member of a particular taxon. A comparison and discussion of the important aspects of the new model relative to existing models is presented.
Making the first step: practical considerations for the isolation of low‐copy nuclear sequence markers
Authors: Schlüter Philipp M. , Stuessy Tod F. , Paulus Hannes F.
Published: May 2010

In many plant groups, the use of low‐copy nuclear sequence markers for phylogenetics and population genetics has been hindered by their limited availability. Although it may be possible to PCR amplify low‐copy markers using primers designed for use with other plant groups, this does not always yield the desired results. Here, we suggest several alternative approaches to begin the isolation and characterisation of novel low‐copy markers when there is little or no sequence information available. These alternatives are: (1) the design of new primers from information in the sequence databases; (2) isolation of homologous DNA using a gene probe from another organism; (3) characterisation of sequence markers from DNA fingerprints; and (4) obtaining novel sequences via cDNA cloning.
Comparison of the Munsell and Royal Horticultural Society’s color charts in describing flower color
Authors: Griesbach Robert J. , Austin S.
Published: May 2010

The flower color of daylily (Hemerocallis L.) cultivars at the U. S. National Arboretum, Washington, D.C. was documented using the Royal Horticultural Society Colour Chart (RHSCC) and the Munsell Book of Color (MBC). The RHSCC descriptions did not allow discrimination between cultivars that were distinguishable by eye. The MBC, however, allowed the description of colors that fell between color chart chips, and had the ability to compare the specific color attributes of different cultivars of similar color. The ability to interpolate colors with the MBC allows a greater accuracy in documentation and discrimination of floral color.
Typification and synonymization in Primula sect. Auricula (Primulaceae)
Authors: Zhang Li-Bing , Zhang Li-Bing , Kadereit Joachim W.
Published: May 2010

Supplementing a recent systematic study of Primula sect. Auricula, we here lectotypify or neotypify 27 names applicable to taxa in this section and the name of one related genus. These are P. auricula var. widmerae Pax, P. balbisii Lehm., P. ciliata Moretti, P. cottia Widmer, P. crenata Lam., P. oenensis Thomas ex Gremli, P. glaucescens Moretti, P. glutinosa Wulfen, P. integrifolia L., P. latifolia var. cynoglossifolia Widmer, P. laevigata Duby ex Rchb., P. longobarda Parta, P. lutea Vill., P. marginata Curtis, P. microcalyx Lehm., P. minima L., P. parlatorii Porta ex Caruel, P. villosa Wulfen, P. villosa var. daonensis Leyb., P. viscosa Vill., P. [unranked] Brevibracteae Widmer, P. [unranked] Rufiglandulae Widmer, P. [unranked] Longibracteatae Widmer, P. [unranked] Cartilagineo‐marginatae Widmer, P. [unranked] Luteae Widmer, P. [unranked] Nothobritanica Schott and P. [unranked] Saniculina Schott. We also publish two new combinations: P. lutea subsp. widmerae (Pax) L. B. Zhang and P. lutea subsp. tatriaca (L. B. Zhang) L. B. Zhang. We further synonymize 233 names referable to P. sect. Auricula, including P. glaucescens subsp. longobarda (Porta) Widmer, P. grignensis D. M. Moser and P. pedemontana subsp. iberica Losa et P. Monts. Through extensive herbarium and literature surveys, we further located the types of an additional 32 names in the section, many of which had been thought to be lost or unclear to science.
The basionym of Eucladium verticillatum (Pottiaceae)
Authors: Ochyra Ryszard , Zijlstra Gea
Published: May 2010

Evidence is provided that the first person to validly publish a name for the species that Linnaeus termed “Bryum verticillatum” in 1753 was Withering in 1801, and that his name actually constitutes the basionym of the well‐known moss name, correctly cited as Eucladium verticillatum (With.) Bruch & Schimp. (Bryophyta, Pottiaceae). “Weissia verticillata (Hedw.) ex Brid.” of 1801, which has hitherto been considered the basionym of this binomial, is a nomen nudum; the combination Weissia verticillata was validly published by Bridel in 1806. Bryum verticillatum With. is lectotypified here with a specimen from Cumberland, England, that is preserved at BM.
Neotypification of Potamogeton ×fluitans Roth and the distribution of this hybrid
Authors: Kaplan Zdenek
Published: May 2010

The identity of the name Potamogeton fluitans Roth has for a long time been uncertain. An analysis of the history of the name and its use is presented and the identity of the extant material ascribed to Roth discussed. The name P. fluitans is neotypified with a specimen from a population of the hybrid P. lucens L. × P. natans L. recently studied morphologically, anatomically and electrophoretically. Nomenclature of the hybrid is summarized and lectotypes for a further four names designated. Distribution of the hybrid is described and a list of representative specimens given.
Evolutionary trends in the simple thalloid liverworts (Marchantiophyta, Jungermanniopsida subclass Metzgeriidae)
Authors: Crandall-Stotler Barbara J. , Forrest Laura L. , Stotler Raymond E.
Published: May 2010

The phylogenetic history of and evolutionary trends within the simple thalloid liverworts (Jungermanniopsida, subclass Metzgeriidae) are reconstructed in a combined analysis of molecular and morphological data. The molecular dataset comprises loci from all three genomes, including trnL-F, rps4, rbcL, atpβ and psbA from the chloroplast, SSU rRNA and LSU rRNA from the nucleus, and nad5 from the mitochondrion, and 65 characters are scored in the morphological dataset. An initial analysis of a molecular dataset that included 16 outgroup and 50 ingroup taxa resolved a Haplomitrium/Treubiaceae clade as the earliest diverging lineage of the ingroup. Subsequent analyses of ingroup only datasets, rooted on this clade, resolve Metzgeriidae as paraphyletic, with Blasiaceae sister to Marchantiopsida in all analyses. A combined analysis of morphological and molecular datasets resolves basically the same clades as analyses of the molecular dataset alone, except for the resolution of a weak sister group relationship between Metzgeriineae and the leafy liverworts. Reconstructions of morphological character evolution on the combined analysis topology confirm that there is substantial homoplasy in the morphology dataset, even in characters that have been traditionally considered diagnostic of hierarchial relationships, such as apical cell geometry, calyptral type and capsule wall thickness. Ancestral state reconstructions contradict many prevailing hypotheses of character evolution in hepatics, including the model of the ancestral liverwort prototype as an erect, radially symmetric plant. Instead, a more likely model is a prostrate, bilaterally symmetric plant with the diagnostic features of a simple thalloid liverwort.
Spatio‐temporal relationships of the Macaronesian endemic flora: a relictual series or window of opportunity?
Authors: Carine Mark A.
Published: May 2010

Convolvulus is represented in Macaronesia by two endemic clades. The first (Clade I) has a predominantly western Mediterranean sister group whilst the second (Clade II) is nested within a predominantly eastern Mediterranean clade. The Relictual Series Hypothesis (RSH) predicts that degree of geographical disjunction between Macaronesian groups and their sister taxa is related to time available for continental extinction to occur and this would provide a possible explanation for the observed pattern in Convolvulus if Clade I is younger than Clade II. To test this hypothesis, mean relative divergence times for the two Macaronesian Convolvulus clades are estimated using a nrITS dataset. The results do not support the age‐disjunction hypothesis and indicate that the mean divergence time for Clade I predates that of Clade II, although the difference between mean divergence times is small and the standard deviations are large. The inconsistency between this result and the RSH might be explained by the stochastic nature of evolution: with continental extinction events occurring during a similar time period, there may have been inadequate time for a clear spatio‐temporal pattern to develop. An alternative explanation, termed the "Colonisation Window Hypothesis" (CWH), is also presented. This hypothesis emphasises island establishment rather than continental extinction as the prime determinant of spatio‐temporal relationships of Macaronesian groups and predicts that opportunities for colonisation into Macaronesia has been temporally constrained to discrete waves of colonisation. Whilst the Convolvulus results are consistent with both RSH and CWH, a framework for establishing the ability of these two hypotheses to explain the spatial relationships of the Macaronesian endemic flora is presented.
Phylogenetic patterns and polyploid evolution within the Mediterranean genusCentaurium(Gentianaceae ‐ Chironieae)
Authors: Mansion Guilhem , Zeltner Louis , Bretagnolle François
Published: May 2010

The genusCentaurium(centauries) comprises ca. 27 annual species and subspecies primarily distributed in the Mediterranean basin. Phylogenetic relationships, inferred from sequences of both nrDNA (internal transcribed spacer, ITS) and cpDNA (trnLintron andtrnL‐Fspacer) regions, confirm the monophyly ofCentauriumand reveal the importance of polyploidy within the genus. In each ITS clade, diploid to hexaploid species of centauries occur. Furthermore, polyploidization is often associated with hybridization events, as suggested by the importance of additive polymorphic sites detected in the ITS region. Hence, reticulation appears to be the main cause of phylogenetic incongruence—and resulting systematic controversies—detected in the genus. Based on molecular and cytological evidence, the origin of several polyploid systems is discussed. Allopolyploidy, associated or not with introgression, appears to be the main evolutionary trend inCentaurium, and only a few autopolyploid taxa have been detected so far.
Temporal and spatial diversification of Circum‐Mediterranean Compositae‐Anthemideae
Authors: Oberprieler Christoph
Published: May 2010

A combination of dispersal‐vicariance analysis (DIVA) and molecular clock dating of a calibrated, ratesmoothed maximum‐likelihood tree based on sequence information from the internal transcribed spacer region of the ribosomal repeat (nrDNA ITS) was used to reconstruct the biogeographical history of the Circum‐Mediterranean clade of Compositae‐Anthemideae. The reconstructions suggest that the ancestor of this clade diverged from the basal African lineages in the late Early Miocene (18 Myr), presumably in conjunction with the collision of the African and Eurasian platform through the Arabian plate. Recurrent dispersal/vicariance events during the Middle and Late Miocene (16–11 Myr) both between the eastern and western Mediterranean regions and (in the latter region) between the northern and southern Peri‐Tethys platforms caused the further diversification of the clade and may have been triggered by episodes of marine regression/transgression events on the Eurasian platform and in the area of the Strait of Gibraltar, respectively. The analyses further show that both the western part of the North African platform and the Anatolian region played a paramount role in the radiation of different subclades of the Circum‐Mediterranean Anthemideae, leading to the present day genus‐richness of the western subclade and to the species‐richness in the large genera (Achillea, Anthemis, Cota, Tanacetum, Tripleurospermum) of the eastern subclade. Whereas in the present analyses these radiations are reconstructed as sympatric speciation events, they may actually correspond to allopatric speciation events on a finer geographical scale within the two main centres of diversification (NW Africa, Anatolia). The Messinian salinity crisis (5.96–5.33 Myr) and the following re‐inundation of the Mediterranean basin (Early Pliocene) triggered dispersal/vicariance events observable today on the level of species or species groups, as did the climatic changes during the Pleistocene.
Contrasting nuclear‐plastidial phylogenetic patterns in the recently diverged IberianPhlomis crinitaandP. lychnitislineages (Lamiaceae)
Authors: Albaladejo Rafael G. , Aguilar Javier Fuertes , Aparicio Abelardo , Feliner Gonzalo Nieto
Published: May 2010

Systematic and evolutionary relationships within the diploid Western MediterraneanPhlomis crinita/lychnitiscomplex remain controversial apparently due to hybridization and introgression. This study examines patterns of sequence variation in the nuclear ribosomal DNA (ITS region) and three non‐coding plastid DNA regions (trnH‐psbA,trnT‐trnLandatpB‐rbcL) in this complex in an aim to clarify whether hybridization, introgression or lineage sorting resulting from recent diversification is mainly responsible for poorly understood relationships. Information recovered from nuclear and chloroplast markers was found to be strongly incongruent. Phylogenetic analysis of inferred nuclear ITS ribotypes is consistent with previous morphometric and taxonomic results in distinguishing two sister lineages,P.crinitas.l. andP.lychnitis. In addition, the high number of additive polymorphisms detected in ITS sequences suggests the sharing of ancestral variability and local patterns of gene flow within the complex. In contrast, the pattern of chloroplast haplotype variation is geographic rather than taxonomic, which might be caused by low mutation rates combined with frequent instances of interspecific hybridization. To integrate the apparently discordant plastid and nuclear evidence, we suggest that both lineage sorting and horizontal transfer have been involved. Even though pinpointing cases due to either phenomenon is difficult, the available data provide evidence of two sister lineages where hybridization events can be identified despite the inheritance of ancestral polymorphisms.
Amphilogia gen. nov. for Cryphonectria‐like fungi from Elaeocarpus spp. in New Zealand and Sri Lanka
Authors: Gryzenhout Marieka , Glen Hugh F. , Wingfield Brenda D. , Wingfield Michael J.
Published: May 2010

The ascomycete genera Cryphonectria and Endothia are closely related members of Diaporthales. Recent DNA sequence comparisons have shown that isolates from Elaeocarpus spp. in New Zealand, previously identified as Cryphonectria radicalis and Cryphonectria gyrosa, represent a phylogenetic group distinct from those including other species of Cryphonectria and Endothia. Cryphonectria gyrosa applies to a species that occurs on Elaeocarpus glandulifer in Sri Lanka, the same host genus but a different species from which the New Zealand collections were made. The aim of this study was to provide a name for the fungi residing in the phylogenetic group from New Zealand. Morphological characters that define these fungi include superficial conical conidiomata, conidia of variable size, and ascospores with one to three septa. These characteristics are not found in other species of Cryphonectria. We also recognise a second species in the group from New Zealand that has distinctly larger ascospores. Herbarium specimens of C. gyrosa exhibit the same primary characteristics as the specimens from New Zealand and C. gyrosa is regarded as conspecific with one of the species in the New Zealand collections. A new genus, Amphilogia, is described for the collections of C. gyrosa from Sri Lanka and New Zealand, which also contains the second species from New Zealand, Amphilogia major sp. nov.
Plant Red Data List assessments in southern Africa: financial costs of a collaborative regional project
Authors: Siebert Stefan J. , Smith Gideon F.
Published: May 2010

As part of the activities of the Southern African Botanical Diversity Network (SABONET), funds were made available by the World Conservation Union (IUCN) to compile plant Red Data Lists for the ten participating countries. Analysis of costs involved in terms of human and financial resources to perform conservation assessments of threatened plants revealed interesting trends, especially cost savings due to sound co‐ordination followed by stakeholder participation and data collection. Data dissemination proved the most expensive. Data collection did not include costs involved in gathering species information, because these contributions were voluntary and cost‐free. SABONET has demonstrated that with sound management and co‐ordination, and selective regional participatory consultation and peer review, it is possible to assess conservation status of threatened plants at around $US 18/taxon and produce a complete product at $US 40/taxon. Cost‐effective expenditure for generating conservation‐oriented information is often overlooked in donor‐funded projects. This article presents a project case study of how a low financial input can lead to high returns (useful information and skills that can improve decisions about conservation).
The restoration of Ipomoea muricata (L.) Jacq. (Convolvulaceae)
Authors: Staples George W. , Wiersema John H. , Chambers Neil A. , Austin Daniel F.
Published: May 2010

Confusion about the dates of publication for Ipomoea muricata (L.) Jacq. and I. muricata Cav. has resulted in both names being set aside in favour of later names proposed for these two distinct taxa. Investigation of the publication date for Jacquin’s Plantae Rariorum Horti Caesari Schoenbrunnensis clarifies the nomenclature for these two tropical morning glories. Ipomoea muricata (L.) Jacq. is the earlier name, and it is herein reinstated for the plant recently called I. turbinata Lagasca by some authors. Ipomoea capillacea (Kunth) G. Don is the correct name for I. muricata Cav.
Phylogeography of Japanese alpine plants: biogeographic importance of alpine region of Central Honshu in Japan
Authors: NoriyukiFujii Kei , Senni
Published: May 2010

A preliminary synthesis of the geographic distribution patterns of intraspecific cpDNA variations in Japanese alpine plants is presented by studying five species, namely, Pedicularis chamissonis, Primula cuneifolia, Loiseleuria procumbens, Cardamine nipponica, and Anemone narcissiflora. Nucleotide sequences of the noncoding regions of cpDNA recognized multiple cpDNA haplotypes in these species. Phylogenetic analyses of these haplotypes suggest two or three major cpDNA clades; each clade has a clearly disjunct distribution pattern in the northern parts of Japan, and in the central parts of Japan. The southernmost clades endemic to central Honshu in Japan were found in all the species (Central Honshu clade). We estimate that the major clades of Pedicularis chamissonis and Primula cuneifolia separated from a common ancestor before the last glacial period (>0.6 and 0.47 million years ago, respectively). We speculate that the common distribution patterns of the cpDNA clades observed in central Honshu were formed by dynamic climatic changes (e.g., glacial events in the Pleistocene) and that the alpine regions of central Honshu acted as refugia for alpine plants during warm interglacial periods.
The phylogeographic structure of Japanese coniferous species as revealed by genetic markers
Authors: Tsumura Yoshihiko
Published: May 2010

The phylogeography of Japanese conifers studied using polymorphic allozyme and organelle (chloroplast and mitochondrial) DNA markers is reviewed. Three Abies species showed a clear geographical cline based on mtDNA polymorphisms. Allozyme markers revealed a clear genetic cline in A. mariesii, with no mtDNA polymorphism. Refugia of these species during the last glaciation were probably located along the southwestern Pacific side of Japan. Based on allozyme analysis, Pinus pumila may have migrated from Siberia southward from Hokkaido to higher mountains in central Japan. Mitochondrial DNA polymorphisms clearly differentiated the pentaphylla and parviflora varieties of Pinus parviflora and suggest that refugia of the latter species were located south of the central mountains of Chubu district during the last glaciation. Current populations in the Chubu highlands, Tohoku, and Hokkaido presumably became established by colonization from these refugia. Phylogeographic analysis of Cryptomeria japonica using allozymes and DNA markers did not reveal distinct patterns. However, microsatellite analysis revealed highest allelic diversity in putative refugia of the last glaciation. Allozyme analysis of Chamaecyparis obtusa revealed a clear cline. Recently, substantial numbers of loci based on expressed sequence tags for population and genome mapping were developed. Cryptomeria japonica and Chamaecyparis obtusa belong to different families, but molecular phylogeny based on chloroplast sequence data revealed that they are closely related and that sequence tag site markers of C. japonica are highly applicable to C. obtusa. Using such markers, researchers have attempted to clarify the genetic structure of the two species. This paper also discusses the most successful approaches (to date) for elucidating the genetic structure of the above‐mentioned species and other phylogeographic issues related to Japanese conifers.
Phylogenetics of South American Asclepiadoideae (Apocynaceae)
Authors: Rapini Alessandro , Chase Mark W. , Konno Tatiana U. P.
Published: May 2010

According to analyses of plastid DNA, New World Asclepiadoideae (Apocynaceae) fall into four clades; most species, however, are included in just one clade endemic to the New World that comprises Metastelmatinae, Oxypetalinae and Gonolobinae (the MOG clade). Looking for better support and resolution inside the MOG core group, we sequenced the nuclear ribosomal DNA region ITS and increased the number of plastid regions (trnS‐G and matK) sequenced. Because of high levels of intra‐individual polymorphisms and complex alignment among subtribes, ITS could not be used at the subtribal level. According to combined analysis of the plastid regions, Blepharodon lineare and Funastrum clausum are confirmed as sister group to the rest of Metastelmatinae and Oxypetalinae, respectively. The analysis indicates that Ditassa is polyphyletic. A highly supported clade composed of shrubby species with minute leaves that were traditionally classified in Ditassa comes out as sister to the rest of the subtribe apart from B. lineare. These data clearly support the recognition of a new genus in Metastelmatinae.
On the phylogeny of the genus Calceolaria (Calceolariaceae) as inferred from ITS and plastid matK sequences
Authors: Andersson Stephan
Published: May 2010

The chloroplast gene matK and the nuclear internal transcribed spacer region (ITS) were used to explore taxonomic placement of and phylogeny within Calceolaria and related genera of Calceolarieae (= Calceolariaceae), a group traditionally referred to the polyphyletic Scrophulariaceae. Calceolarieae appear as a strongly supported monophyletic group and receive moderate support as the sister group of the family Gesneriaceae. The monotypic genus Porodittia is deeply nested inside Calceolaria and is reduced to synonymy under the latter genus. The phylogenetic trees retrieved for Calceolaria reveal that many presently recognised sections are polyphyletic. They also suggest that temperate species have retained the most ancestral character states in the genus. The phylogeny of Calceolaria features a number of well supported clades, which are difficult to characterize morphologically. A renewed interpretation of morphological characters diagnosing natural groups within Calceolaria is called for. The role of the Huancabamba Deflection as an important factor in the biogeography of Calceolaria is strongly alluded by the inferred phylogeny.
A new phylogeny‐based generic classification of Costaceae (Zingiberales)
Authors: Specht Chelsea D. , Stevenson Dennis Wm.
Published: May 2010

Recent cladistic analysis of multiple molecular data from chloroplast and nuclear genomes as well as morphological data have indicated that a reclassification of the family Costaceae is necessary in order to appropriately reflect phylogenetic relationships. The previously described genera Tapeinochilos, Monocostus, and Dimerocostus are all upheld in the new classification. Monocostus and Dimerocostus are found to be sister taxa. The large pantropical genus Costus is found to be polyphyletic and is thus divided into four genera, three of which are new (Cheilocostus, Chamaecostus, Paracostus). Costus has now a more concise generic concept including morphological synapomorphies previously absent due to the polymorphic nature of the prior non‐monophyletic assemblage. Of the three new genera, one (Paracostus) was previously recognized as a subgenus of Costus. Cheilocostus comprises several Asian taxa and is sister to Tapeinochilos, whereas Chamaecostus comprises entirely neotropical taxa and is sister to a neotropical Monocostus + Dimerocostus clade. A reevaluation of the traditional taxonomy indicates that floral characters and pollination syndromes commonly used to identify groups exhibit homoplasy when analyzed in a cladistic framework and are thus unreliable as taxonomic indicators.
Taxonomic and nomenclatural history of Fragilaria (Bacillariophyceae)
Authors: Silva Paul C. , Hasle Grethe R.
Published: May 2010

The genus Fragilaria Lyngb. 1819 originally comprised eight species of filamentous diatoms, six of which were marine whereas two were freshwater. Subsequently, two of the eight species have been referred to Melosira C. Agardh 1824 (nom. cons.), two to Grammatophora Ehrenb. 1840, and one each to Diatoma Bory 1824 (nom. cons.) and Striatella C. Agardh 1832. Of the remaining species, Fragilaria pectinalis (O. F. Müll.) Lyngb. (Conferva pectinalis O. F. Müll.), from fresh water, was designated lectotype by Boyer in 1927. The last species, F. striatula Lyngb., from marine habitats, can be accommodated by Grammonema C. Agardh 1832. Because authentic material of Conferva pectinalis has not been found and Müller's published figures are not identifiable, the application of that name, and hence the application of the generic name Fragilaria, has remained uncertain. Fragilaria capucina Desm., which has been assumed to include the material in Lyngbye's hand, has served as a de facto lectotype. However, current studies by Tuji & Williams (2006) reveal that the type of F. capucina is not conspecific with the species to which that name has traditionally been applied. They therefore have proposed an epitype for C. pectinalis that will ensure the continued application of the generic name Fragilaria in the present‐day sense.
Phylogenetic and phylogeographic analysis of the western Mediterranean Arenaria section Plinthine (Caryophyllaceae) based on nuclear, plastid, and morphological markers
Authors: Valcárcel Virginia , Vargas Pablo , Feliner Gonzalo Nieto
Published: May 2010

Arenaria sect. Plinthine is an easily distinguishable morphologically cohesive group encompassing 14 species and five additional subspecies. To explore phylogenetic relationships and search for phylogeographic patterns in a group that is restricted to the western Mediterranean, independent and combined analyses of four datasets (morphological characters and sequences from nuclear and plastid DNA: nrITS, trnT–trnL, trnL–trnF) were conducted using Maximum Parsimony, Neighbour–Joining, Maximum Likelihood and Bayesian Inference. Monophyly of the section is supported by the data, the ITS sequences show full agreement with taxonomy for one third of the taxa, and the high number of trnL–F haplotypes found in SE Spain (7 of 11) is consistent with the fact that this region is one of the hotspots of biodiversity in the Mediterranean. However, a number of less easily interpretable results have been obtained, despite considerable ITS variation (43 parsimony informative characters within the ingroup) and a reasonable intraspecific sampling for this marker. These results are: low resolution at deep nodes of the ingroup, partial discordance between taxonomy and ITS sequences particularly for widespread taxa, and lack of congruence not only between the topologies of the plastid and nuclear trees but also between the two plastid trees. It is proposed that a combination of factors (rampant aneuploidy, polyploidy, hybridization, lineage sorting, and concerted evolution of ITS sequences) are responsible for the incongruent but not totally unexpected results.
Molecular phylogenetics of Oreobolus (Cyperaceae) and the origin and diversification of the American species
Authors: Chacón Juliana , Madriñán Santiago , Chase Mark W. , Bruhl Jeremy J.
Published: May 2010

Nuclear ribosomal DNA Internal Transcribed Spacer (ITS) and plastid trnL intron and trnL–F intergenic spacer regions were sequenced for 14 species of Oreobolus (Cyperaceae) from throughout most of its distribution range (South America, Australasia, and Hawai'i), with the exception of the Malesian species; Costularia laxa was used as outgroup. Phylogenetic trees were produced for ITS and trnL–F datasets using maximum parsimony and maximum likelihood. We estimated species divergence times by enforcing a molecular clock on the Maximum Likelihood ITS tree, using the appearance of O. furcatus in Hawai'i, no earlier than 5.1 mya, as a calibration point. Our results support the monophyly of the South American species with the southern O. obtusangulus as sister to the rest. This South American clade is sister to the Australian O. pumilio, and the Australasian and Hawaiian species sampled form a basal grade. Oreobolus oligocephalus is embedded within Oreobolus, rejecting its separation in the monotypic genus Schoenoides. The transformed branch lengths of the ITS tree indicate a recent (5.5–6 mya) origin of the South American clade, followed by a northward migration and diversification of species along the Andes.
The phylogeny and classification of Neuropogon and Usnea (Parmeliaceae, Ascomycota) revisited
Authors: Wirtz Nora , Printzen Christian , Sancho Leopoldo G. , Lumbsch Thorsten H.
Published: May 2010

The phylogeny of usneoid lichens with black pigmentation in the cortex was reconstructed using Bayesian and maximum parsimony analyses of nuclear ITS rDNA sequences. Fifty new partial sequences of 14 taxa were generated and assembled with 74 sequences from GenBank. Our results indicate that Neuropogon is polyphyletic with a core group nested within Usnea subgen. Usnea as sister–group to section Usnea. In addition an undescribed species is basal to the section Usnea clade and the Neuropogon species U. acanthella and U. durietzii have unresolved relationships in the Usnea subgen. Usnea clade. Monophyly of Neuropogon not nested within Usnea subgen. Usnea is rejected using three independent tests. Consequently, it is proposed to synonymise Neuropogon with Usnea. We recommend a conservative approach regarding nomenclatural changes from phylogenetic studies especially at the generic level when few taxa are studied.
Six species of MadagascanGenipatransferred toHyperacanthus(Rubiaceae–Gardenieae) and new data on general morphology, placentation and ovary structure inHyperacanthus
Authors: Rakotonasolo Franck , Davis Aaron
Published: May 2010

Genipa in Madagascar currently comprises 11 species of Rubiaceae. These species do not belong in the New World genus Genipa (Gardenieae) but instead should be placed in Old World genera belonging to the tribes Gardenieae and Octotropideae. Six species can be confidently placed in the genus Hyperacanthus (Gardenieae), and the appropriate new combinations are made. Five species belong to the tribe Octotropideae but can not be unequivocally placed in genera at the present time and consequently no combinations are proposed. Three new types of placentation are recorded in Hyperacanthus, which broaden the morphological characterization of the genus. These placentation types are apparently unique within Rubiaceae and perhaps even within Asterideae. Species descriptions, additional material examined, distribution, ecology and conservation assessments are given for each of the six new combinations in Hyperacanthus.
A new subgeneric classification forEuphorbia(Euphorbiaceae) in southern Africa based on ITS andpsbA-trnHsequence data
Authors: Bruyns Peter V. , Mapaya Ruvimbo J. , Hedderson Terrence J.
Published: May 2010

We use data from the internal transcribed spacer (ITS) region of the nuclear rDNA cistron and the chloroplast psbA–trnH intergenic spacer to reconstruct the phylogenetic relationships among southern African species of Euphorbia. The results indicate that major re–organization is necessary of the groupings within Euphorbia that have been recognised in the past, since most of them turn out to be polyphyletic. Furthermore, in its present circumscription, Euphorbia itself is not monophyletic, nor do the southern African species form a monophyletic group. Both datasets show that the southern African species fall into four major groups, which we recognise as subgenera: Chamaesyce Raf., Esula Pers., Euphorbia and Rhizanthium (Boiss.) Wheeler. To accommodate the southern African species, subg. Chamaesyce is divided into sect. Chamaesyce, sect. Frondosae Bruyns, sect. nov., sect. Articulofruticosae Bruyns, sect. nov. and sect. Espinosae Pax & Hoffm. Subgenus Euphorbia is divided into sect. Euphorbia, sect. Monadenium (Pax) Bruyns, sect. Goniostema H. Baill. ex Boiss. and sect. Tirucalli Boiss. To re–establish the monophyly of Euphorbia, the genera Endadenium L. C. Leach, Monadenium Pax and Synadenium Boiss. are reduced to synonymy under Euphorbia subg. Euphorbia sect. Monadenium and the species are all transferred to Euphorbia. Consequently the subtribe Euphorbiinae now consists of the single, very large, very widely distributed and very diverse genus Euphorbia. Three of the subgenera (Chamaesyce, Esula, Euphorbia) are nearly cosmopolitan, showing the great age and wide extent of the radiation that has occurred within Euphorbia. The remaining subg. Rhizanthium is mainly African.
Determining the potential utility of datasets for phylogeny reconstruction
Authors: Wortley Alexandra H. , Scotland Robert W.
Published: May 2010

The utility of morphological and molecular data in phylogenetic inference has been widely debated. Potential utility is intrinsically related to size, so the importance of morphological data in phylogenetic inference is becoming increasingly uncertain as molecular datasets grow rapidly larger. To test the continuing relevance of morphological data, we present an empirical investigation of size in a selection of recent data matrices and contrast the possible methods of measuring relative potential utility. Molecular datasets contained significantly more variable and parsimony–informative characters, and implied a greater number of parsimony–informative character–state changes than morphological ones. The latter is suggested to be the most useful measure of potential utility in phylogeny reconstruction, and shows much greater variability and overlap between molecular and morphological datasets. Morphological datasets often have much greater phylogenetic utility than is apparent from their size, and thus molecular datasets are not always more useful simply because they contain a greater number of aligned characters. We recommend these more accurate measures of utility should be more widely reported in phylogenetic research.
A review of Peruvian Phoradendron (Viscaceae) species names published by Paczoski and typified by material collected by Augusto Weberbauer
Authors: León Blanca , Granda Arturo , Roque G. José , Vilcapoma Graciela
Published: May 2010

Phoradendron englerianum and P. ernstianum, described by Jozef Paczoski based on Peruvian material have been recently neotypified. The original types, collected by Augusto Weberbauer in the Berlin herbarium (B) were destroyed during World War II. However, prior to these neotypifications, the two species names were inadvertently lectotypified using duplicate material for the original types kept at the Herbario Weberbauer (MOL) in Lima, Peru. Additional information on another Paczoski name, P. leucocarpum, a species transferred to Dendrophthora, is also provided.
Sectional classification of Gymnosporia (Celastraceae), with notes on the nomenclatural and taxonomic history of the genus
Authors: Jordaan Marie , van Wyk Abraham E.
Published: May 2010

Gymnosporia (Wight & Arn.) Hook. f. (Celastraceae) is an Old World genus of about 99 species and 19 infraspecific taxa. A historical review of the genus and its conserved status are given. Sectional subdivision of Gymnosporia into eight sections is based mainly on characters from fruit morphology and leaf anatomy. Taxonomically useful characters at section level include: presence or absence of leaf and fruit indumentum, number of valves in the fruit, aril colour and the degree to which it covers the seed. Diagnostic leaf anatomical characters are epidermis cell size, presence or absence of a hypodermis, uni–or multi–seriate epidermis, dorsiventral or isobilateral mesophyll and presence or absence of trichomes or papillae. The newly described sections (species/infraspecific taxa in brackets) are Buxifoliae (29); Capitatae (1); Gymnosporia (6/3); Mossambicenses (11/4); Vaccinifoliae (1/2); Pubescentes (1); Putterlickioides (1/2) and Tenuispinae (49/8). A key to the sections and a list of species in each section are provided. Morphological as well as leaf anatomical characters to assist in the identification of sections are tabulated. Eleven new name combinations, three new ranks and two new names are proposed.
ETS sequences support the monophyly of the eucalypt genus Corymbia (Myrtaceae)
Authors: Parra-O. Carlos , Bayly Michael , Udovicic Frank , Ladiges Pauline
Published: May 2010

The generic classification of the eucalypts, especially recognition of the genus Corymbia, has been controversial. The phylogeny of Corymbia and related eucalypt groups was investigated using nuclear ETS sequences, and combined ETS and ITS sequences. Both the ETS and combined datasets support the monophyly of Corymbia. Three major eucalypt clades are confirmed: Corymbia + Angophora; Eucalyptus s.s.; and the Eucalyptopsis group. Within Corymbia, relationships are broadly consistent with phylogenies based on morphological and anatomical characters; sections Ochraria, Blakearia, and Politaria are all supported as monophyletic; sect. Rufaria is monophyletic with the inclusion of the monotypic sect. Apteria. Within Eucalyptus s.s., relationships are generally consistent with those shown by previous molecular studies. Within the Eucalyptopsis group, Allosyncarpia is sister to the clade Stockwellia + Eucalyptopsis. Relationships between the major eucalypt clades are equivocal, but combined analysis of ETS and ITS data shows Corymbia + Angophora as sister to Eucalyptus—the rainforest taxa of the Eucalyptopsis group being outside this clade. Patterns of relationship and distribution are consistent with differentiation of major lineages of Corymbia prior to the isolation of taxa (now relictual) in eastern and south‐western Australia, arguably before the mid‐Miocene.
Phylogenetic delimitation of Isoglossinae (Acanthaceae: Justicieae) and relationships among constituent genera
Authors: Kiel Carrie A. , McDade Lucinda A. , Daniel Thomas F. , Champluvier Dominique
Published: May 2010

Phylogenetic relationships of Isoglossinae (Acanthaceae: Justicieae) were studied with a taxon sample including all but one genus putatively placed in the lineage and a dataset composed of DNA sequences from three genic regions (nrITS, cp trnS/G, trnT/L). Two members each of the lineages of Justicieae previously shown to be phylogenetically adjacent to Isoglossinae were included to test monophyly of Isoglossinae. The Malagasy genera Forcipella and Populina were excluded from Isoglossinae by our analysis. The former was placed outside of Justicieae. The latter was placed with plants representing the Tetramerium lineage of Justicieae. Our results do not provide strong support for placement of Ptyssiglottis with Isoglossinae but also cannot refute this placement. Core Isoglossinae (i.e., members of Old World Conocalyx, Isoglossa, Brachystephanus and New World Kalbreyeriella, Stenostephanus s.l., Razisea) are monophyletic; these plants share "Gürtelpollen", hypothesized to be a morphological synapomorphy for the group. Malagasy Conocalyx is part of the clade that includes all sampled species of Isoglossa and does not seem distinct from the latter genus. Sister to Isoglossa (including Conocalyx) is a lineage including all sampled species of Brachystephanus plus all New World Isoglossinae. Plants belonging to this last clade share monothecous stamens as a morphological synapomorphy. Our data do not support but cannot refute reciprocal monophyly of Brachystephanus and New World Isoglossinae. There is, in fact, very little variation among these taxa such that the problem is lack of resolution rather than support for relationships that conflict with current taxonomy. NW plants in particular are richly diverse in morphology and it is remarkable that this diversification is not reflected in variation in these three DNA regions.
A classification for extant ferns
Authors: Smith Alan R. , Pryer Kathleen M. , Schuettpelz Eric , Korall Petra , Schneider Harald , Wolf Paul G.
Published: May 2010

We present a revised classification for extant ferns, with emphasis on ordinal and familial ranks, and a synopsis of included genera. Our classification reflects recently published phylogenetic hypotheses based on both morphological and molecular data. Within our new classification, we recognize four monophyletic classes, 11 monophyletic orders, and 37 families, 32 of which are strongly supported as monophyletic. One new family, Cibotiaceae Korall, is described. The phylogenetic affinities of a few genera in the order Polypodiales are unclear and their familial placements are therefore tentative. Alphabetical lists of accepted genera (including common synonyms), families, orders, and taxa of higher rank are provided.
A reassessment of the sections of the genus Cytisus Desf. (Cytiseae, Leguminosae)
Authors: Cristofolini Giovanni , Troìa Angelo
Published: May 2010

Recent morphological and molecular research on Cytisus and allied genera has produced a great deal of new data relevant to systematics, which have not yet been incorporated into a consistent classification system of the genus. We have compared and evaluated recently published cladograms and phenograms based on morphological and molecular (nuclear and plastid DNA) characters. The genus Cytisus sensu lato, including Calicotome, Chamaecytisus, Chronanthus, and Lembotropis, appears to be monophyletic. A subdivision of the genus Cytisus in 13 sections is presented; one species, C. tribracteolatus, remains incertae sedis. A new section (C. sect. Dendrocytisus) and two new combinations for taxa in C. sect. Calicotome are proposed.
Studies in Perenniporia: Polyporus unitus, Boletus medulla-panis, the nomenclature of Perenniporia, Poria and Physisporus, and a note on European Perenniporia with a resupinate basidiome
Authors: Decock Cony , Stalpers Joost A.
Published: May 2010

The status and identities of Polyporus unitus, type of Perenniporia Murrill, of Boletus medulla‐panis, their supposed synonymy, and the nomenclatural status of Perenniporia, Poria, and Physisporus are discussed. It is demonstrated, based on the study of its type, that Pol. unitus is not a synonym of B. medulla‐panis even in the historically wider context than that recognised here. Although not precisely identifiable, the type of Pol. unitus does not belong to Perenniporia in its current sense, which is based on B. medulla‐panis. Poria Pers. and Physisporus Chevall. are discussed as possible generic names for B. medulla‐panis and related taxa. However, in view of the need for nomenclatural stability, it is proposed to maintain Perenniporia as currently accepted, with B. medulla‐panis as conserved type. This name is epitypified and Perenniporia medulla‐panis redefined. Based on a study of European specimens, two species are recognized within the historical circumscription of P. medulla‐panis, Perenniporia meridionalis being described as new. Both species are compared with other European taxa with resupinate basidiomes and a key to all these taxa is presented.
Lectotypification of Echites campanulata Sessé & Moç. (Apocynaceae)
Authors: Williams Justin K. , Morales J. Francisco
Published: May 2010

A lectotype is designated for Echites campanulata Sessé & Moç. The lectotype is identified as Laubertia contorta (Mart. & Gal.) Woodson, making E. campanulata a synonym of that name, and provides a further step towards a full account of the species of Echites described by Sessé and Moçiño.
Lectotypification of the names of three moss species described by Hedwig
Authors: Ederra Alicia
Published: May 2010

As a part of a study for the project "Flora Briofítica Ibérica" three names, Bartramia halleriana Hedw., Bartramia pomiformis Hedw. and Anictangium aquaticum Hedw. [≡ Cinclidotus aquaticus (Hedw.) Bruch & Schimp.] described by Johannes Hedwig, are lectotypified.
RNA editing and phylogenetic reconstruction in two monocot mitochondrial genes
Authors: Petersen Gitte , Seberg Ole , Davis Jerrold I. , Stevenson Dennis W.
Published: May 2010

The mitochondrial genome of land plants has a high level of evolutionary plasticity that may impair its use in phylogenetic analyses. Among the most challenging properties are RNA editing and retroprocessing of edited mRNA into the mitochondrial and/or nuclear genome as processed paralogs. Using mtDNA sequence data encoding for apocytochrome B (cob) and the alpha subunit of F1‐ATP synthase (atp1) across the monocots, and in two subclades, alismatids and Agavaceae, it is shown that edited sites, despite being more homoplasious than non‐edited sites, perform well on the trees, and that they are not randomly distributed among taxa but have a clade specific distribution. Indirect evidence for the presence of processed paralogs is presented and their likely evolutionary fate discussed.
A reassessment of Hemizygia and Syncolostemon (Ocimeae—Lamiaceae)
Authors: Otieno Donald F. , Balkwill Kevin , Paton Alan J. , Savolainen Vincent
Published: May 2010

The relationships between Hemizygia and Syncolostemon are investigated. Parsimony analyses of morphological data and sequences of the trnL intron, trnL‐trnF intergenic spacer and the rps16 intron were carried out separately and in combination. All analyses largely show strong support for the two genera as a monophyletic group; neither genus as currently circumscribed is monophyletic. They are herein merged under the earliest name Syncolostemon. The clade can be diagnosed by the presence of fused anterior stamens. Bremer’s ancestral area analysis method suggests that the Afroalpine and Afromontane archipelago‐like Regional Centre of Endemism may be the ancestral area for Syncolostemon s.l.