bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractSystematic 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

AbstractThe 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

AbstractAs 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

AbstractConfusion 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

AbstractA 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

AbstractThe 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

AbstractAccording 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

AbstractThe 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

AbstractRecent 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

AbstractThe 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

AbstractArenaria 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

AbstractNuclear 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

AbstractThe 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

AbstractGenipa 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

AbstractWe 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

AbstractThe 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

AbstractPhoradendron 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.