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Nannoplankton taxonomy and the International Code of Nomenclature for algae, fungi, and plants (ICN)
... In accordance with ICN, Art. 9, Note 1, (Turland et al., 2018) this specimen must be accepted as the holotype of Baker's name, and consequently G. manicata Linden was inadvertently neotypified. Subsequently, Wanntorp et al. (2002) neotypified G. manicata Linden ex André (based on André, 1873) using this same specimen, unaware of the previous typification. ...
Gunnera x cryptica J.M.H.Shaw representing the hybrid G. manicata Linden ex André × G. tinctoria (Molina) Mirb. is described from spontaneous seedlings in cultivation. It is widespread in the British Isles, and appears to have completely replaced G. manicata in cultivation. Details of the earliest publication, authorship and typification of G. manicata are provided, along with the origin and history of the hybrid, and notes on G. tinctoria including a previously overlooked synonym G. thyrsiflora Ruiz ex Barreiro.
... The word "Taxonomy" generally refers to principles and techniques of scientific classification into different ranks and categories. Scientists of biology use taxonomy principles to classify and rank the organisms such as animals, plants, viruses and bacteria (Turland & Wiersema, 2018). Benjamin Bloom is an American educational psychologist who developed in 1950s Bloom's taxonomy for education objective classification based on knowledge, skills, and competences categories (Thomas, 2014;Bloom, 1956). ...
This paper aims to present and discuss phases of planning and designing campuses for Higher Education Institutions (HEIs). The authors argue that creating a taxonomy to control an environment conducive to learning is of the same order of importance as that for education as depicted by Bloom, given the size, financial burden, and influence on learning outcomes. A specific model is proposed for the taxonomy of planning campuses for HEIs with four ordered phases: educational programming, spaces programming, master planning, and detailed design. The researchers followed four methodologies to support the proposed model: A literature review to seek relevant knowledge and terms used in previous studies; a descriptive discussion of the proposed campus planning and design taxonomy model; a survey of experts in educational and campus planning to examine the proposed phases; and, a case study of the campus of Kingdom University in Bahrain where the phases of taxonomy were implemented. This latter case study further exhibits how the executed campus planning process is developed in adherence with state-of-the-art educational demands and trends. This paper is concluded with guidelines of HEIs campus planning as illustrated a diagram for the proposed model of taxonomy showing the process and illustrating the model domains, together with its phases and planning process considerations. The model also analyses the relationship between the domains that are ordered according to the process flow starting with educational programming up to the detailed design phases.
... Rossman et al. [16] recommended the name Exserohilum over Setosphaeria according to Article 57.2 of the International Code of Nomenclature for algae, fungi and plants [17]. MycoBank currently lists 38 taxa in Exserohilum, most of which are associated with diseases of grasses [18,19]. ...
... Stemphylium is a dematiaceous hyphomycete genus and the asexual morph has been recorded in Pleospora allies (Ariyawansa et al. 2015c;Woudenberg et al. 2017). Based on morphological studies, multi-gene phylogeny analyses, and ecological evidence, the use of Stemphylium over Pleospora has been recommended (Köhl et al. 2009;McNeill et al. 2012;Rossman et al. 2015;Woudenberg et al. 2017;Wijayawardene et al. 2018). Stemphylium is typified with S. botryosum. ...
The cosmopolitan plant genus Clematis contains many climbing species that can be found worldwide. The genus occurs in the wild and is grown commercially for horticulture. Microfungi on Clematis were collected from Belgium, China, Italy, Thailand and the UK. They are characterized by morphology and analyses of gene sequence data using an integrated species concept to validate identifications. The study revealed two new families, 12 new genera, 50 new species, 26 new host records with one dimorphic character report, and ten species are transferred to other genera. The new families revealed by multigene phylogeny are Longiostiolaceae and Pseudomassarinaceae in Pleosporales (Dothideomycetes). New genera are Anthodidymella (Didymellaceae), Anthosulcatispora and Parasulcatispora (Sulcatisporaceae), Fusiformispora (Amniculicolaceae), Longispora (Phaeosphaeriaceae), Neobyssosphaeria (Melanommataceae), Neoleptosporella (Chaetosphaeriales, genera incertae sedis), Neostictis (Stictidaceae), Pseudohelminthosporium (Neomassarinaceae), Pseudomassarina (Pseudomassarinaceae), Sclerenchymomyces (Leptosphaeriaceae) and Xenoplectosphaerella (Plectosphaerellaceae). The newly described species are Alloleptosphaeria clematidis, Anthodidymella ranunculacearum, Anthosulcatispora subglobosa, Aquadictyospora clematidis, Brunneofusispora clematidis, Chaetosphaeronema clematidicola, C. clematidis, Chromolaenicola clematidis, Diaporthe clematidina, Dictyocheirospora clematidis, Distoseptispora clematidis, Floricola clematidis, Fusiformispora clematidis, Hermatomyces clematidis, Leptospora clematidis, Longispora clematidis, Massariosphaeria clematidis, Melomastia clematidis, M. fulvicomae, Neobyssosphaeria clematidis, Neoleptosporella clematidis, Neoroussoella clematidis, N. fulvicomae, Neostictis nigricans, Neovaginatispora clematidis, Parasulcatispora clematidis, Parathyridaria clematidis, P. serratifoliae, P. virginianae, Periconia verrucose, Phomatospora uniseriata, Pleopunctum clematidis, Pseudocapulatispora clematidis, Pseudocoleophoma clematidis, Pseudohelminthosporium clematidis, Pseudolophiostoma chiangraiense, P. clematidis, Pseudomassarina clematidis, Ramusculicola clematidis, Sarocladium clematidis, Sclerenchymomyces clematidis, Sigarispora clematidicola, S. clematidis, S. montanae, Sordaria clematidis, Stemphylium clematidis, Wojnowiciella clematidis, Xenodidymella clematidis, Xenomassariosphaeria clematidis and Xenoplectosphaerella clematidis. The following fungi are recorded on Clematis species for the first time: Angustimassarina rosarum, Dendryphion europaeum, Dermatiopleospora mariae, Diaporthe ravennica, D. rudis, Dichotomopilus ramosissimum, Dictyocheirospora xishuangbannaensis, Didymosphaeria rubi-ulmifolii, Fitzroyomyces cyperacearum, Fusarium celtidicola, Leptospora thailandica, Memnoniella oblongispora, Neodidymelliopsis longicolla, Neoeutypella baoshanensis, Neoroussoella heveae, Nigrograna chromolaenae, N. obliqua, Pestalotiopsis verruculosa, Pseudoberkleasmium chiangmaiense, Pseudoophiobolus rosae, Pseudoroussoella chromolaenae, P. elaeicola, Ramusculicola thailandica, Stemphylium vesicarium and Torula chromolaenae. The new combinations are Anthodidymella clematidis (≡ Didymella clematidis), A. vitalbina (≡ Didymella vitalbina), Anthosulcatispora brunnea (≡ Neobambusicola brunnea), Fuscohypha kunmingensis (≡ Plectosphaerella kunmingensis), Magnibotryascoma rubriostiolata (≡ Teichospora rubriostiolata), Pararoussoella mangrovei (≡ Roussoella mangrovei), Pseudoneoconiothyrium euonymi (≡ Roussoella euonymi), Sclerenchymomyces jonesii (≡ Neoleptosphaeria jonesii), Stemphylium rosae (≡ Pleospora rosae), and S. rosae-caninae (≡ Pleospora rosae-caninae). The microfungi on Clematis is distributed in several classes of Ascomycota. The analyses are based on morphological examination of specimens, coupled with phylogenetic sequence data. To the best of our knowledge, the consolidated species concept approach is recommended in validating species.
... Starting with the International Code of Nomenclature for algae, fungi and plants (McNeill et al. 2012), only one scientific name may be used for a single species of fungus. At present, both Marssonina coronariae for the asexual morph and Diplocarpon mali for the sexual morph have been applied to this fungus as shown in the literature. ...
Seven new genera, 26 new species, 10 new combinations, two epitypes, one new name, and 20 interesting new host and / or geographical records are introduced in this study. New genera are: Italiofungus (based on Italiofungus phillyreae ) on leaves of Phillyrea latifolia (Italy); Neolamproconium (based on Neolamproconium silvestre ) on branch of Tilia sp. (Ukraine); Neosorocybe (based on Neosorocybe pini ) on trunk of Pinus sylvestris (Ukraine); Nothoseptoria (based on Nothoseptoria caraganae ) on leaves of Caragana arborescens (Russia); Pruniphilomyces (based on Pruniphilomyces circumscissus ) on Prunus cerasus (Russia); Vesiculozygosporium (based on Vesiculozygosporium echinosporum ) on leaves of Muntingia calabura (Malaysia); Longiseptatispora (based on Longiseptatispora curvata ) on leaves of Lonicera tatarica (Russia). New species are: Barrmaelia serenoae on leaf of Serenoa repens (USA); Chaetopsina gautengina on leaves of unidentified grass (South Africa); Chloridium pini on fallen trunk of Pinus sylvestris (Ukraine); Cadophora fallopiae on stems of Reynoutria sachalinensis (Poland); Coleophoma eucalyptigena on leaf litter of Eucalyptus sp. (Spain); Cylindrium corymbiae on leaves of Corymbia maculata (Australia); Diaporthe tarchonanthi on leaves of Tarchonanthus littoralis (South Africa); Elsinoe eucalyptorum on leaves of Eucalyptus propinqua (Australia); Exophiala quercina on dead wood of Quercus sp., (Germany); Fusarium californicum on cambium of budwood of Prunus dulcis (USA); Hypomyces gamsii on wood of Alnus glutinosa (Ukraine); Kalmusia araucariae on leaves of Araucaria bidwillii (USA); Lectera sambuci on leaves of Sambucus nigra (Russia); Melanomma populicola on fallen twig of Populus canadensis (Netherlands), Neocladosporium syringae on branches of Syringa vulgarishorus (Ukraine); Paraconiothyrium iridis on leaves of Iris pseudacorus (Ukraine); Pararoussoella quercina on branch of Quercus robur (Ukraine); Phialemonium pulveris from bore dust of deathwatch beetle (France); Polyscytalum pinicola on needles of Pinus tecunumanii (Malaysia); Acervuloseptoria fraxini on Fraxinus pennsylvanica (Russia); Roussoella arundinacea on culms of Arundo donax (Spain); Sphaerulina neoaceris on leaves of Acer negundo (Russia); Sphaerulina salicicola on leaves of Salix fragilis (Russia); Trichomerium syzygii on leaves of Syzygium cordatum (South Africa); Uzbekistanica vitis-viniferae on dead stem of Vitis vinifera (Ukraine); Vermiculariopsiella eucalyptigena on leaves of Eucalyptus sp. (Australia).
... A mikológusok, taxonómusok többsége a jogszabályokhoz alkalmazkodik, ennek legutóbbi összefoglaló gyűjteménye a 2011-es ún. Melbourne Code, a Nemzetközi Szabályzat az algák, gombák és növények nevezéktanára (International Code of Nomenclature for algae, fungi and plants, ICN) (McNeill et al., 2012). ...
Mycologists have recorded a few hundred thousand Latin names for fungi and these are thought to refer to 70 000 or so separate species. The use of molecular techniques in fungal taxonomy and systematics in the last 25 years has provided massive amounts of information to clarify phylogenetic relationships, encouraged grant support, and complicated the jobs of classically-trained mycologists. Taxonomists have a reputation for being traditionalists, but the community has recently embraced the modernization of the nomenclatural rules by discarding the requirement for Latin descriptions, endorsing electronic publication, and ending the dual system of nomenclature, viz. teleomorph and anamorph names, which used parallel for the sexual and asexual phases of pleomorphic species. A group of taxonomists accepted ’The Amsterdam Declaration on Fungal Nomenclature’ and its basic principle the ’One fungus – one name’ has been incorporated in the Code of Nomenclature (’Melbourne Code’) in 2011. The next, and more difficult step will be to develop community standards for sequence-based classification. As the’One fungus – One name’ theory is a brand-new issue for the Hungarian plant doctors and practical specialists, it seems reasonable to review this to promote conversations between generations in Hungarian language.
... Nomenclatural changes were made according to the Code (McNeill et al. 2012). Names of species and authors follow IPNI (continuously updated). ...
Seringia botak Cheek sp. nov., based on a collection made by the authors in 2017, is described from metalliferous grassland and savannah habitats in Indonesian New Guinea. Initially this appeared to be the first verified record of Seringia from SE Asia and to extend the range of the genus c. 1500 km further north than the previously recorded northern limit in Northern Territory, Australia. Further research, however, showed two previous specimens of the taxon from New Guinea, which had been overlooked. The extinction risk of Seringia botak is assessed as Endangered using the IUCN 2016 standard.
... For a long time, these descriptions had to be in Latin but recently also English descriptions became valid. For plants, the rules were fixed in different editions of the International Code of Botanical Nomenclature (ICN, last version: McNeill et al. 2012). This code determines, however, only how the naming has to be done and not the criteria that define systematic entities like species, genera, families, etc. ...
Barley refers to the cereal Hordeum vulgare subsp. vulgare but also more generally to the barley genus Hordeum that, apart from cultivated barley, comprises more than 30 wild grass species distributed in temperate and arid regions of the world. Like wheat and rye, Hordeum belongs to the Triticeae tribe of grasses, most conspicuously characterized by their inflorescence that is a spike instead of the panicle that occurs in most other grasses. The wild progenitor of the cereal is H. vulgare subsp. spontaneum from Southwest Asia. Together with bulbous barley (Hordeum bulbosum), the closest relative of the crop, and wall barley (Hordeum murinum) these species are grouped within subgenus Hordeum, while all other species belong to subgenus Hordeastrum. The crop is easily crossable with its wild progenitor (forming the primary gene pool of barley), while hybrids between cultivated and bulbous barley (secondary gene pool) exhibit low fertility. All other species belong to the tertiary gene pool, resulting in sterile hybrids that can only be established through embryo rescue techniques. However, barley’s tertiary gene pool holds traits for pathogen resistances and adaptations to extreme environmental conditions, which are of high value if they can be transferred into cultivated barley or other cereals. Taxonomic and nomenclatural issues are discussed here in the light of recent findings in molecular systematics and gene function.
... Another important limitation is that RPB2, which has demonstrated to be one of the best markers for Aspergillus, and in our study, it was able to identify seven isolates, is not currently available for all ex-type species. In contrast, ITS, BenA and CaM, although less discriminatory, are available to a greater number of species.Another difficulty in identifying cryptic species is the fact that the taxonomy is being continuously updated with new modifications due to the new criteria for fungal nomenclature,69 synonymisations50,70 and new species being constantly described in the current literature.6,8,12,16,[27][28][29]50,55,57,60,62 For example, among the species reported in the isolates of this study, three of them (A. ...
Background
In the last few decades there has been an emergence of cryptic Aspergillus as agents of human infections due to the increase of immunocompromised population and to the improvement of identification tools.
Methods
Continuing our study on Aspergillus isolates from clinical origin deposited in a mycological reference center in the USA, we selected 37 isolates belonging to less common sections of the genus, to study their species diversity and detect cryptic species by using a polyphasic approach.
Results
From this set of isolates, a total of 16 species were identified; the most frequent being A. calidoustus (48.6%, section Usti), A. terreus (13.5%, section Terrei), and A. nidulans (5.7%, section Nidulantes). The remaining isolates corresponded to 13 species of rare or cryptic Aspergillus, i.e. A. europaeus (section Cremei); A. iizukae, A. micronesiensis, A. spelaeus (section Flavipedes); A. pachycristatus, A. quadrilineatus, A. spinulosporus, A. unguis (section Nidulantes); A. alabamensis, A. carneus, A. hortai (section Terrei), A. granulosus (section Usti); and the new species A. suttoniae (section Flavipedes), which is described here.
Conclusions
Correct identification of cryptic species is crucial to reveal new potential pathogens, gather accurate epidemiological data, and to choose an appropriate treatment.
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... In addition, because type material for F. ambrosium was not designated (Gadd & Loos 1947), or appears to have been lost (Nirenberg 1990), a line-drawing of a clavate conidium of the species from Gadd & Loos (1947) was selected as the lectotype. Furthermore, an epitype was prepared from an authentic strain of this species to stabilize its taxonomy, according to the International Code of Nomenclature for algae, fungi and plants (ICN, the Melbourne Code;McNeill et al. 2012). ...
Fusarium oligoseptatum sp. nov. was isolated from the invasive Asian ambrosia beetle Euwallacea validis (Coleoptera, Scolytinae, Xyleborini) and from the galleries that females had constructed in dying Ailanthus altissima (tree-of-heaven) symptomatic for Verticillium wilt in south-central Pennsylvania, USA. This ambrosia fungus was cultivated by Euwallacea validis as the primary source of nutrition together with a second symbiont, Raffaelea subfusca . Female beetles transport their fungal symbionts within and from their natal galleries in paired pre-oral mycangia. Fusarium oligoseptatum was distinguished phenotypically from the 11 other known members of the Ambrosia Fusarium Clade (AFC) by uniquely producing mostly 1-2 septate clavate sporodochial conidia that were swollen apically. Phylogenetic analysis of multilocus DNA sequence data resolved F. oligoseptatum as a genealogically exclusive species-level lineage but evolutionary relationships with other members of the AFC were unresolved. Published studies have shown that F. oligoseptatum can be identified via phylogenetic analysis of multilocus DNA sequence data or a PCR multiplex assay employing species-specific oligonucleotide primers. In addition, to provide nomenclatural stability, an epitype was prepared from an authentic strain of F. ambrosium that was originally isolated from a gallery constructed in Chinese tea (Camellia sinensis ) by E. fornicatus in India, together with its lectotypification based on a published illustration.
... Setosphaeria differs from Trichometasphaeria by the production of non-clypeate ascomata which can be erumpent or superficial and produce larger ascospores (Leonard & Suggs 1974). Recently, Rossman et al. (2015) recommend to use the name Exserohilum over Setosphaeria according to Article 57.2 of the International Code of Nomenclature for algae, fungi and plants (McNeill et al. 2012). MycoBank currently lists 38 taxa in Exserohilum, most of which are associated with diseases of grasses (Sivanesan 1984(Sivanesan , 1987, although a few have been described from other substrates such as river sediments (Sivanesan et al. 1993), soil (Guiraud et al. 1997, Steiman et al. 2000, grains (El Shafie 1980), the palm tree Borassus flabel lifer (Subramanian 1956), plant debris (Castañeda-Ruiz et al. 1995), and humans (McGinnis et al. 1986, Padhye et al. 1986). ...
Exserohilum includes a number of plant pathogenic, saprobic and clinically relevant fungi. Some of these species are of great importance in human activities, but the genus has never been revised in a phylogenetic framework. In this study, we revise Exserohilum based on available ex-type cultures from worldwide collections, observation of the holotypes and/or protologues, and additional isolates from diverse substrates and geographical origins. Based on nine nuclear loci, i.e., ITS, LSU, act, tub2, cam, gapdh, his, tef1 and rpb2, as well as phenotypic data, the genus and species boundaries are assessed for Exserohilum. Three species, i.e., E. novae-zelandiae, E. paspali and E. sorghicola, are excluded from the genus and reallocated in Sporidesmiella and Curvularia, respectively, whereas E. heteropogonicola and E. inaequale are confirmed as members of Curvularia. Exserohilum rostratum is revealed as conspecific with species previously described in Exserohilum such as E. antillanum, E. gedarefense, E. leptochloae, E. longirostratum, E. macginnisii and E. prolatum. Additionally, E. curvatum is revealed as synonym of E. holmii, and E. fusiforme of E. oryzicola. A total of 11 Exserohilum phylogenetic species are described, illustrated and discussed, including one novel taxon, E. corniculatum. The placements of 15 other doubtful species are discussed, and E. elongatum is validated.
... The prevalence of DNA sequence comparisons prompted the abolition of a nearly 150-year-old practice to use different names for some sexual and asexual morphological forms in Fungi. The latest version of the International Code of Nomenclature for algae, fungi and plants (ICN) was ratified in Melbourne 2011 and effectively ended this dual naming system (16). This means that often long standing names have to be merged so that related sexual and asexual morphs can be placed in a single genus. ...
The ITS (nuclear ribosomal internal transcribed spacer) RefSeq database at the National Center for Biotechnology Information (NCBI) is dedicated to the clear association between name, specimen and sequence data. This database is focused on sequences obtained from type material stored in public collections. While the initial ITS sequence curation effort together with numerous fungal taxonomy experts attempted to cover as many orders as possible, we extended our latest focus to the family and genus ranks. We focused on Trichoderma for several reasons, mainly because the asexual and sexual synonyms were well documented, and a list of proposed names and type material were recently proposed and published. In this case study the recent taxonomic information was applied to do a complete taxonomic audit for the genus Trichoderma in the NCBI Taxonomy database. A name status report is available here: https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi. As a result, the ITS RefSeq Targeted Loci database at NCBI has been augmented with more sequences from type and verified material from Trichoderma species. Additionally, to aid in the cross referencing of data from single loci and genomes we have collected a list of quality records of the RPB2 gene obtained from type material in GenBank that could help validate future submissions. During the process of curation misidentified genomes were discovered, and sequence records from type material were found hidden under previous classifications. Source metadata curation, although more cumbersome, proved to be useful as confirmation of the type material designation.
Database URL:http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353
... were examined after mixing in every possible pair on dilute V8, YCBAS and YCBY, but no asci or signs of conjugation were observed. The novel species are thus assigned to the genus Wickerhamiella according to the new rules of the Melbourne Code (McNeill et al. 2012), but with the mention f.a. (forma asexualis), as proposed by Lachance (2012). ...
Flowers offer favourable microenvironments for yeast growth, and are increasingly recognised as a rich source of novel yeast species. Independent surveys of yeasts associated with flowers and pollinators in South Africa led to the discovery of 38 strains of two new species. Physiological profiles and analysis of the internal transcribed spacer and the D1/D2 domains of the large subunit rRNA gene showed that they represent two novel species that belong to the Wickerhamiella clade. We describe the species as Wickerhamiella nectarea f.a. sp. nov. (type strain EBDCdVSA11–1T, CBS 14162T, NRRL Y-63791T) and W. natalensis f.a. sp. nov. (type strain EBDCdVSA7–1T, CBS 14161T, NRRL Y-63790T). We extend the known range of flower-associated Wickerhamiella species to South Africa and discuss the ecology and phylogenetic relationships of the clade in relation to its host species and biogeography. Examination of growth characteristics supports that the Wickerhamiella clade exhibits a high degree of evolutionary lability, and that specialisation to different niches may occur rapidly. We review the current status of floral yeast biodiversity and nectar as a reservoir of species diversity, and the importance of pollinators and biogeography. In addition, 18 species formerly assigned to the genus Candida are reassigned formally to the genus Wickerhamiella.
... Species are named and described according to a collection of rules called the codes of nomenclature. There are five: one for animals (Ride et al. 1999), one for plants, fungi, and algae (McNeill et al. 2012), one for cultivated plants (Brickell et al. 2016), one for bacteria (Lapage et al. 1992), and one for viruses (King 2011). This may seem overly complicated, but, these rules attempt to: (1) prevent taxonomists from applying the same name to two different species; (2) mandate that original descriptions are published in such a way that they are widely available; and (3) ground taxonomic descriptions in physical reality by requiring specimens. ...
Biodiversity informatics, the application of informatics techniques to biodiversity data, is rooted in physical objects and nomenclatural codes. Through two user stories, one from wildlife conservation and another from agriculture, we demonstrate the importance and process of biodiversity informatics. We discuss the importance and integration of taxonomic names, identification tools, species distributions, phylogenetic trees, traits, associations, the literature, ontologies, controlled vocabularies, standards, and genomics. Despite the plethora of resources, a seamless, biodiversity question and answer engine is still out of reach. The largest impediment to our user stories is the lack of cross-disciplinary infrastructure and the digitized and standardized data to support services. Satisfying our user stories will require additional investment in infrastructure and data that will be a challenge to manage and sustain. This chapter discusses the basic biodiversity informatics concepts that are at the heart of our user stories, and will be the basis of the user stories of the future as society rushes to cope with global environmental change.
... It is important to highlight the large number of reported taxa that could not be studied because of the lack of living cultures and consequently considered uncertain species. Given the usefulness and importance of combining morphological data with molecular phylogenetic studies to adhere to the requirements of the ICN (McNeill et al. 2012), it is crucial for the progress of science to encourage all authors of fungal names to deposit live material in international culture collections for future studies. ...
The taxonomy of the synnematous genera Cephalotrichum, Doratomyces and Trichurus, and other related genera Gamsia, Wardomyces and Wardomycopsis, has been controversial and relies mainly on morphological criteria. These are microascaceous saprobic fungi mostly found in air and soil and with a worldwide distribution. In order to clarify their taxonomy and to delineate generic boundaries within the Microascaceae, we studied 57 isolates that include clinical, environmental and all the available ex-type strains of a large set of species by means of morphological, physiological and molecular phylogenetic analyses using DNA sequence data of four loci (the ITS region, and fragments of rDNA LSU, translation elongation factor 1-α and β-tubulin). The results demonstrate that Cephalotrichum, Doratomyces and Trichurus are congeneric and the genus Cephalotrichum is accepted here with Echinobotryum as a further synonym. The genera Acaulium and Fairmania, typified by A. albonigrescens and F. singularis, respectively, are distinct from Microascus and Scopulariopsis, Gamsia is distinct from Wardomyces, and Wardomycopsis is confirmed as a separate genus in the Microascaceae. Two new species of Cephalotrichum are described as C. brevistipitatum and C. hinnuleum. Nine new combinations are proposed, i.e. Acaulium acremonium, A. caviariforme, Cephalotrichum asperulum, C. columnare, C. cylindricum, C. dendrocephalum, C. gorgonifer, Gamsia columbina and Wardomyces giganteus. A neotype is designed for C. stemonitis. Lectotypes and epitypes are designated for A. acremonium, A. albonigrescens, C. gorgonifer, C. nanum and W. anomalus. Cephalotrichum cylindricum, C. microsporum, F. singularis and Gamsia columbina are also epitypified with new specimens. Descriptions of the phenotypic features and dichotomous keys for identification are provided for accepted species in the different genera.
... Thus the material in Rauh 63791a is excluded from type status, likewise HEID 602339, which obviously was taken from the same plant but at a different time, which is a violation of Art. 8.2. of the ICN, since this specimen comes from a different "gathering" (McNeill et al. 2011). The specimen in alcohol is not a type specimen since it bears no evidence showing when it was preserved and that Rauh considered it the type. ...
In the protologue to the new species Pitcairnia aureobrunnea (Rauh 1984) its discoverer Werner Rauh names as its type location “Peruvia septentrionalis, Dptm. San Martin, inter Tarapoto et Yurimaguas.“ This corresponds to a stretch of highway ca. 130 km long and is thus not a very precise specification of the locality where it was found. The Werner Rauh Heritage Project (WRHP), financed by the Klaus Tschira Foundation, made it possible to evaluate data from various sources and to determine the locus classicus more precisely. In addition the nine herbarium specimens of the gathering Rauh 53677 in HEID as well as other specimens of Pitcairnia aureobrunnea collected by Rauh were given a critical review in order to identify the types which Rauh focussed on. The individual data and results are presented in this article in appropriate brevity.
In the past 40 years, progress in GC‐MS and GC‐FID has lent the modern perfume industry powerful tools for determining raw ingredients in fragrances, which is still often manual and based on molecular markers thus subjective and unreliable due to variability and chromatographic challenges. This article presents an alternative approach by introducing the concept of chromatographic spectrum. This approach was evaluated on a commercial database containing molecular composition of 4106 perfumery ingredients and on real and simulated mixtures. Five hundred and seven out of 565 database ingredients classes were differentiated by their chromatographic spectrum against 164 with distinctive markers. The 5 ingredients of a real Eau de Cologne mixture were identified, and their proportions estimated with less than 12% relative error for 4 of them. The usefulness of chromatographic spectra in a deformulation support algorithm is discussed based on the deformulation of 210 simulated mixtures of 5, 10, and 15 ingredients. Chromatographic spectrum concept is introduced and used to deformulate an Eau de Cologne and simulated mixtures using a database containing 4106 perfumery ingredients.
Since 2009 Heidelberg Botanic Garden and Herbarium HEID have been working on the “Werner Rauh Heritage Project” (WRHP) dealing with the scientific heritage left behind by the German botanist Werner Rauh (1913–2000). From 2009 up until 2016 this work was funded by the foundation Klaus Tschira Stiftung. The cover of the January issue of Kakteen und andere Sukkulenten showed an Apocynacee from Madagascar. This was one of the many species first described by Rauh: Ceropegia simoneae Rauh. This article tries to explain how
difficult it may be to find out the Locus classicus (type location) of a species described by Rauh and to identify the actual type specimens.
Seit 2009 wird am Botanischen Garten Heidelberg und Herbarium HEID im Rahmen des «Werner Rauh Heritage Project» (WRHP), das von 2009 bis 2016 von der Klaus Tschira Stiftung gefördert wurde, der wissenschaftliche Nachlass des deutschen Botanikers Werner Rauh (1913–2000) aufgearbeitet. Das Titelbild der Januarausgabe 2013 von Kakteen und andere Sukkulenten lenkte die Aufmerksamkeit auf eine madagassische Apocynacee, die Rauh neben zahlreichen anderen Arten erstbeschrieben hatte: Ceropegia simoneae Rauh. In diesem Beitrag soll aufgezeigt werden, wie schwierig es mitunter ist, bei einer Rauh-Art den Locus classicus (Typfundort) herauszufinden und die tatsächlichen Typus-Belege zu identifizieren.
Ganoderma is a large, diverse and globally-distributed genus in the Basidiomycota that includes species causing a white rot form of wood decay on a variety of tree species. For the past century, many studies of Ganoderma in North America and other regions of the world have used the name G. lucidum sensu lato for any laccate (shiny or varnished) Ganoderma species growing on hardwood trees or substrates. Molecular studies have established that G. lucidum sensu stricto (Curtis) Karst is native to Europe and some parts of China. To determine the species of the laccate Ganoderma that are present in the United States, we studied over 500 collections from recently collected samples and herbarium specimens from hardwoods, conifers, and monocots. A multilocus phylogeny using ITS, tef1α, rpb1 and rpb2 revealed three well-supported clades, similar to previously reported findings. From the U.S. collections, thirteen taxa representing twelve species were identified,
Two new species in the Fusarium solani species complex (FSSC) are described and introduced. The new taxa are represented by German isolates CBS 142481 and CBS 142480 collected from commercial yard waste compost and vascular tissue of a wilting branch of hibiscus, respectively. The phylogenetic relationships of the collected strains to one another and within the FSSC were evaluated based on DNA sequences of 6 gene loci. Due to the limited sequence data available for reference strains in GenBank, however, a multi-gene phylogenetic analysis included partial sequences for the internal transcribed spacer region and intervening 5.8S nrRNA gene (ITS), translation elongation factor 1-alpha (tef1) and the RNA polymerase II second largest subunit (rpb2). Morphological and molecular phylogenetic data independently showed that these strains are distinct populations of the FSSC, nested within Clade 3. Thus, we introduce Fusarium stercicola and Fusarium witzenhausenense as novel species in the complex. In addition, 19 plant species of 7 legume genera were evaluated for their potential to host the newly described taxa. Eighteen plant species were successfully colonized, with 6 and 9 of these being symptomatic hosts for F. stercicola and F. witzenhausenense, respectively. As plants of the family Fabaceae are very distant to the originally sourced material from which the new taxa were recovered, our results suggest that F. stercicola and F. witzenhausenense are not host-specific and are ecologically fit to sustain stable populations in variety of habitats.
The genus Talaromyces constitutes an important group of molds with species that are mainly found in soil, indoor environments and food products. Traditionally, it has been considered, together with Eupenicillium, the teleomorphic state of Penicillium. However, the taxonomy of these fungi has changed considerably, and Talaromyces currently includes sexually and asexually reproducing species. In a previous study of the occurrence of penicillium-like fungi from clinical samples in the USA, we used the combined phylogeny of the internal transcribed spacer (ITS) region of the rDNA and β-tubulin (BenA) gene to identify 31 isolates of Talaromyces, 85 of Penicillium and two of Rasamsonia. However, seven isolates of Talaromyces were assigned to the corresponding sections but not to any particular species. In this study, we have resolved the taxonomy of these isolates through a multilocus sequence analysis of the ITS, fragments of the BenA, calmodulin (CaM), and RNA polymerase II second largest subunit (RPB2) genes, and a detailed phenotypic study. As a result, four new species are described and illustrated, ie Talaromyces alveolaris, T. georgiensis, T. minnesotensis and T. rapidus.
Dactylorhiza purpurella is a well known species, which is mainly distributed in the British Isles, Denmark and the southern part of Norway. The southeastern most area of its distribution is the Danish Wadden Sea Island of Rømø. This island is not far away from West-Frisian Island of Schiermonnikoog, where the species has occurred for more than twenty years, but where it has only been recognized since 2015.
Background and Aims The genetic and morphological consequences of natural selection and selective breeding are explored in the genus Abelia. The genus consists of ornamental shrubs endemic to China, which have been bred to create attractive and diverse cultivars.
Methods DNA fingerprinting (AFLP) and DNA sequence data are used to investigate the genetic diversity among 46 accessions of Abelia (22 natural taxa and 24 horticultural breeds). In the cultivated varieties these data are used to explore taxon boundaries, hybridisation and backcrossing. The genetic analysis dataset is also used to investigate morphological variation within natural species complexes and subsequently to inform a taxonomic treatment.
Key ResultsAbelia comprises five species: A. forrestii, A. schumannii, A. macrotera, A. uniflora and A. chinensis and has a total of 11 varieties. Abelia uniflora and A. macrotera do not occur in sympatry and are disjunctly distributed to the east and west of the A. chinensis distribution range. Abelia chinensis is widespread in eastern China and creates hybrids and introgressive taxa, including A. uniflora, along the contact zones with the previous taxa. Abelia `Maurice Foster' is a horticultural variety collected from wild stocks in Sichuan (China). Bayesian clustering methods (inferred in STRUCTURE based on AFLP data) indicate admixture between A. macrotera and A. schumannii in this variety. Hybridization probably occurred in the wild where these progenitor taxa co-occur and naturally form hybrids. AFLP results also reveal that a few diagnostic morphological characters such as sepal number or inflorescence structure were transferred between natural species and this is mirrored by taxa such as in Abelia `Saxon Gold' and A. forrestii.
Conclusions Studying both natural and cultivated species from the same group has helped understanding both differentiation mechanisms and how to improve cultivated plants in the future by studying which morphological characters are transferred between species and which taxa may already have arisen through hybridisation.
Molecular phylogenetic analyses of New Zealand rust fungi suggested that four taxa, Aecidium otagense on Clematis spp., Puccinia tiritea on Muehlenbeckia spp., Puccinia rhei-undulati sensu auct. NZ, non (Dietel) Hirats. f. on Rheum ×rhabarbarum, and an unidentified Puccinia species on Rumex sagittatus, are a single species. Morphological studies and multilocus molecular data, together with inoculation studies, confirmed this finding. This species is only the third heteroecious rust fungus known to be native to New Zealand.
Aspergillus is one of the economically most important fungal genera. Recently, the ICN adopted the single name nomenclature which has forced mycologists to choose one name for fungi (e.g. Aspergillus, Fusarium, Penicillium, etc.). Previously two proposals for the single name nomenclature in Aspergillus were presented: one attributes the name “Aspergillus” to clades comprising seven different teleomorphic names, by supporting the monophyly of this genus; the other proposes that Aspergillus is a non-monophyletic genus, by preserving the Aspergillus name only to species belonging to subgenus Circumdati and maintaining the sexual names in the other clades. The aim of our study was to test the monophyly of Aspergilli by two independent phylogenetic analyses using a multilocus phylogenetic approach. One test was run on the publicly available coding regions of six genes (RPB1, RPB2, Tsr1, Cct8, BenA, CaM), using 96 species of Penicillium, Aspergillus and related taxa. Bayesian (MrBayes) and Ultrafast Maximum Likelihood (IQ-Tree) and Rapid Maximum Likelihood (RaxML) analyses gave the same conclusion highly supporting the monophyly of Aspergillus. The other analyses were also performed by using publicly available data of the coding sequences of nine loci (18S rRNA, 5,8S rRNA, 28S rRNA (D1-D2), RPB1, RPB2, CaM, BenA, Tsr1, Cct8) of 204 different species. Both Bayesian (MrBayes) and Maximum Likelihood (RAxML) trees obtained by this second round of independent analyses strongly supported the monophyly of the genus Aspergillus. The stability test also confirmed the robustness of the results obtained. In conclusion, statistical analyses have rejected the hypothesis that the Aspergilli are non-monophyletic, and provided robust arguments that the genus is monophyletic and clearly separated from the monophyletic genus Penicillium. There is no phylogenetic evidence to split Aspergillus into several genera and the name Aspergillus can be used for all the species belonging to Aspergillus i.e. the clade comprising the subgenera Aspergillus, Circumdati, Fumigati, Nidulantes, section Cremei and certain species which were formerly part of the genera Phialosimplex and Polypaecilum. Section Cremei and the clade containing Polypaecilum and Phialosimplex are proposed as new subgenera of Aspergillus. The phylogenetic analysis also clearly shows that Aspergillus clavatoflavus and A. zonatus do not belong to the genus Aspergillus. Aspergillus clavatoflavus is therefore transferred to a new genus Aspergillago as Aspergillago clavatoflavus and A. zonatus was transferred to Penicilliopsis as P. zonata. The subgenera of Aspergillus share similar extrolite profiles indicating that the genus is one large genus from a chemotaxonomical point of view. Morphological and ecophysiological characteristics of the species also strongly indicate that Aspergillus is a polythetic class in phenotypic characters.
The Paleocene Eocene Thermal Maximum (PETM) is characterized by a transient group of nannoplankton, belonging to the genus Discoaster. Our investigation of expanded shelf sections provides unprecedented detail of the morphology and phylogeny of the transient Discoaster during the PETM and their relationship with environmental change. We observe a much larger range of morphological variation than previously documented suggesting that the taxa belonged to a plexus of highly gradational morphotypes rather than individual species. We propose that the plexus represents malformed ecophenotypes of a single species that migrated to a deep photic zone refuge during the height of PETM warming and eutrophication. Anomalously high rates of organic matter remineralization characterized these depths during the event and led to lower saturation levels, which caused malformation. The proposed mechanism explains the co-occurrence of malformed Discoaster with pristine species that grew in the upper photic zone; moreover, it illuminates why malformation is a rare phenomenon in the paleontological record.
Algae are very ancient living organisms. Their presence on earth came about some 3.5 billion years ago. They are considered “pioneer organisms” of outdoor environment, and it is actually possible to find different varieties of algae on the ground, in the air, in ice and even in anthropogenic elements such as the facades of buildings since they are able to survive through frequent freeze–thaw and dehydration cycles. The aesthetic quality and durability of an external building envelope could be seriously impaired by the development of algae which will colonise building materials whenever a suitable combination of humidity, warmth and light occurs. The fundamental role of water for algal growth is clear which, for several reasons, is found in large quantities on building facades. External sources of water here include rain, snow, ground moisture, airborne humidity and condensation of vapour from outdoor air. In addition to environmental conditions, the rate of stain development largely depends on the “bioreceptivity” of the material, that is, its aptitude to be biologically colonised which is related to the material properties that contribute to the anchorage and development of microorganisms. The facades of the buildings are then fertile substrates for the growth of algae.
Astrosphaeriella sensu lato is a common genus occurring on bamboo, palms and stout grasses. Species of Astrosphaeriella have been collected from various countries in tropical, subtropical or temperate regions. In Asia, species have been collected in Brunei, China, Indonesia, Japan, Philippines and Vietnam. There have been several morphological studies on Astrosphaeriella, but molecular work and phylogenetic analyses are generally lacking. Taxa included in Astrosphaeriella were characterized in three main groups 1) typical Astrosphaeriella species (sensu stricto) having carbonaceous, erumpent, conical ascostromata 2) atypical Astrosphaeriella species (sensu lato) having immersed, coriaceous ascostromata with short to long papilla and 3) lophiostoma-like species having immersed ascostromata with slit-like openings. Some of the latter Astrosphaeriella species, having slit-like openings, have been transferred to Fissuroma and Rimora in Aigialaceae. In this study five type specimens of Astrosphaeriella were loaned from herbaria worldwide and re-examined and are re-described and illustrated. Collections of Astrosphaeriella were also made in Thailand and morphologically examined. Pure cultures were obtained from single spores and used in molecular studies. The asexual morph was induced on sterile bamboo pieces placed on water agar. Phylogenetic analyses of combined LSU, SSU and TEF1 sequence data of astrosphaeriella-like species using Bayesian, Maximum parsimony (MP) and Randomized Accelerated Maximum Likelihood (RAxML) analyses were carried out. Phylogenetic analyses show that species of Astrosphaeriella can be distinguished in at least three families. Species of Astrosphaeriella
sensu stricto with erumpent, carbonaceous ascostromata, form a strongly supported clade with Pteridiospora species and a new family, Astrosphaeriellaceae, is introduced to accommodate these taxa. The genera are revised and Astrosphaeriella bambusae, A. neofusispora, A. neostellata, A. thailandica, A. thysanolaenae and Pteridiospora chiangraiensis are introduced as new species. Astrosphaeriella exorrhiza is reported on a dead stem of Thysanolaena maxima and is the first record for Thailand. Reference specimens for A. fusispora and A. tornata are designated to stabilize the taxonomy of Astrosphaeriella. The coelomycetous asexual morph of A. bambusae is reported and forms hyaline, globose to subglobose, aseptate conidia. Species of Astrosphaeriella
sensu lato with immersed, coriaceous ascostromata, with short to long papilla and striate ascospores, form a sister clade with Tetraplosphaeriaceae. The genus Pseudoastrosphaeriella is introduced to accommodate some of these taxa with three new species and three new combinations, viz. P. aequatoriensis, P. africana, P. bambusae, P. longicolla, P. papillata and P. thailandensis. A new family Pseudoastrosphaeriellaceae is introduced to accommodate this presently monotypic lineage comprising Pseudoastrosphaeriella. The asexual morph of P. thailandensis is described. Astrosphaeriella bakeriana forms a distinct clade basal to Aigialaceae. Astrosphaeriella bakeriana is excluded from Astrosphaeriella and a new genus Astrosphaeriellopsis, placed in Dothideomycetes genera incertae sedis, is introduced to accommodate this taxon. Fissuroma aggregata (Aigialaceae) is re-visited and is shown to be a cryptic species. Three new species of Fissuroma and a new combination are introduced based on morphology and phylogeny viz. F. bambusae, F. fissuristoma, F. neoaggregata and F. thailandicum. The asexual morph of Fissuroma bambusae is also reported.
A new species, Sonerila keralensis, from the Western Ghats of Kerala is described and illustrated. It is allied to S. rheedei differing by having a tuberous root stock, three to seven flowers, and petals with sparsely glandular-hairy margins.
Objectives : A precise and simple system of nomenclature was required to avoid error, ambiguity or confusion. Although medicinal plants must be produced or distributed based on a pharmacopoeia described origin including scientific name, the Korean Pharmacopoeia tenth edition (KP 10) had many names against the nomenclature. Therefore, this study aimed at searching correct scientific names for 241 plants in KP 10. Methods : Authoritative databases - The Plant List, International Plant Name Index, YList, Tropicos, eFloras, World Checklist of Selected Plant Families, The Global Compositae Checklist, The International Legume Database and Information Service, et al. - and previously performed researches, floras were cross-checked. Results : The arrangement of this list was designed for four cases, errors including illegitimate, nomenclatural synonyms, recommended names and decision reserved names. Consideration about the scientific names produced nine correct names for ten misspellings and illegitimate, and thirty-six correct names for forty-one nomenclatural synonyms. These results should be reflected in the next of KP 10. Separately, ten recommended names were also suggested for taxonomic synonyms which had been used indiscriminately due to diverse taxonomic opinions. In addition to those, decision reserved names were suggested for thirteen species which had been corridor of uncertainty. Then again, there was need to study about authorship, because KP 10 did not keep recommendations for author citations. Conclusions : Correction of scientific names for some medicinal plants which violated the International Code of Nomenclature would be useful to improve the accuracy of a Pharmacopoeia as the criterional materials.
The cellulase producing fungal strain Y-94, isolated in Japan and invalidly described as Acremonium cellulolyticus nom. nud. strain Y-94, seldom forms enteroarthric conidia under nutrient starvation conditions. Phylogenetic analysis using ITS1-5.8S-ITS2 and RNA polymerase II large subunit gene sequences revealed that strain Y-94 is closely related to Talaromyces, given that these Y-94 sequences showed 100% identity with those of Talaromyces pinophilus NBRC 100533(T) . By contrast, the identity between β-tubulin-encoding genes from strain Y-94 and T. pinophilus NBRC 100533(T) was 98.1%. Morphological and phenotypic differences between these strains in colony color, conidiphore formation, and cellulase productivity were observed. Together, these data indicate that strain Y-94 belongs to the genus Talaromyces. We propose that strain Y-94 is a new species, Talaromyces cellulolyticus, on the basis of morphology and molecular evidence. The ex-holotype is Y-94 (= FERM BP-5826, CBS 136886 [holotype] TNS-F-48752). This article is protected by copyright. All rights reserved.
The extant coccolithophore Tergestiella adriatica Kamptner, which had not been reported since its original description in 1940, was recently re-discovered in coastal-nearshore waters at Tomari, Tottori (Japan) and offshore Rovinj (Croatia). Morphological analysis shows that extant Tergestiella and the Mesozoic genus Cyclagelosphaera (Watznaueriaceae), thought to have been extinct since the early Eocene (~ 54 Ma), are virtually identical. Molecular phylogenetic study supports the inference that T. adriatica is a direct descendent of Cyclagelosphaera. It is therefore a remarkable example of a living fossil. Our documentation of patchy coastal distribution in living T. adriatica and records of rare occurrences of fossil Cyclagelosphaera in Oligocene-Miocene shallow water sediments, from the New Jersey shelf, suggest that Tergestiella/Cyclagelosphaera was restricted to nearshore environments during much of the Cenozoic. This restricted ecology explains the lack of fossil Tergestiella/Cyclagelosphaera recorded in open ocean sediments deposited during the last 54 myr.
Online edition available at http://www.iapt-taxon.org/nomen/main.php
Most haptophytes are unicellular, photosynthetic flagellates, although some have coccoid, colonial, amoeboid, or filamentous stages. Nearly all have a characteristic filamentous appendage, the haptonema, arising between the two flagella. The small subunit ribosomal RNA gene (l8S ribosomal DNA) from 18 haptophyte species has been sequenced, and the sequences aligned with those of more than 300 published and unpublished chlorophyll a + c algae. Phylogenies were constructed using maximum likelihood, neighbor-joining, and weighted maximum parsimony analyses. The high divergence (6%) be tween members of Pavlova and the remaining haptophytes supports the division of Haptophyta into two classes: Prymne siophyceae and Pavlovophyceae. Three major clades that correspond to known taxa within the Prymnesiophyceae were identified: one clade embraces Phaeocystis spp.; the second includes members of the genera Chrysochromulina, Prymnesium, and Imantonia; and the third includes coccolithophorid genera and the genus Isochrysis. Two other clades contain taxa whose sequences were derived from a gene clone library. These taxa are not strongly related to any of the cultured taxa included in this study. Based on 18S ribosomal DNA sequence data and available information on morphological structure and ultrastructure, we propose that the class Prymnesiophyceae be divided into four orders: Phaeocystales ord. nov., Prym nesiales, Isochrysidales, and Coccolithales. A total of 1-2% divergence at this level in the 18S ribosomal RNA gene analysis warrants a separation above the level of family. Within the Pavlovophyceae, a new genus is established, Rebecca J.e. Green gen. nov., into which Pavlova salina and Pavlova helicata are moved.
We present here a collection of light microscope, and comparative scanning electron microscope, images of extant coccolithophores, sampled from various oceanic locations, and also from cultured strains. This series of images is intended to provide students and researchers interested in extant coccolithophore biology with an accessible means of identifying the common coccolithophore species found in modern assemblages.
Patterns of diversifi cation and longevity in Paleogene coccolithophorids are analyzed by combining the temporal history of selected genera, families, and orders with the number of discrete morphospecies in them. The coccolithophorids underwent an abrupt mass extinction at the Cretaceous/Paleogene boundary, and a rapid (~1 m.y.- long) global turnover at the Paleocene/Eocene boundary. In contrast, they underwent a diachronous turnover at the Eocene/Oligocene boundary that spread over 6-7 m.y. at mid- and low-latitudes. The turnover included sequential extinctions and speciations of short-lived taxa, beginning slightly before 37 Ma, and losses of taxa that dominated mid- and low latitudes at 34.2 Ma and high latitudes at 32.3 Ma. It is also marked by a few evolutionary appearances, in particular, that of the Family Syracosphaeraceae, which is the most diversifi ed of the living coccolithophorids. Most importantly, the turnover resulted in a shift in the balance between families across several orders, such that families that dominated during the Eocene dwindled during the turnover, and, conversely, families that were little diversifi ed during the Eocene became dominant. Thus, members of Family Coccolithaceae and the genus Helio-discoaster typify Eocene communities; members of the Family Calcidiscaceae and the genus Eu-discoaster characterize Neogene communities. This shift was accompanied by a decrease in the robustness of coccoliths, suggesting that the Eocene/Oligocene event had a marked effect on the physiology of Eocene coccolithophorids. Bolide impacts and the emplacement of large basaltic provinces provide mechanisms to explain large biotic events. Such mechanisms, however, can be ruled out in the case of the Eocene/ Oligocene turnover, which was undoubtedly related to climatic cooling and glaciation. The fi ltering effect of environmental stress on late Eocene diversity remains to be explained.
The use of genomic data and the rise of phylogenomics have radically changed our view of the eukaryotic tree of life at a high taxonomic level by identifying 4-6 "supergroups." Yet, our understanding of the evolution of key innovations within each of these supergroups is limited because of poor species sampling relative to the massive diversity encompassed by each supergroup. Here we apply a multigene approach that incorporates a wide taxonomic diversity to infer the time line of the emergence of strategic evolutionary transitions in the haptophytes, a group of ecologically and biogeochemically significant marine protists that belong to the Chromalveolata supergroup. Four genes (SSU, LSU, tufA, and rbcL) were extensively analyzed under several Bayesian models to assess the robustness of the phylogeny, particularly with respect to 1) data partitioning; 2) the origin of the genes (host vs. endosymbiont); 3) across-site rate variation; and 4) across-lineage rate variation. We show with a relaxed clock analysis that the origin of haptophytes dates back to 824 million years ago (Ma) (95% highest probability density 1,031-637 Ma). Our dating results show that the ability to calcify evolved earlier than previously thought, between 329 and 291 Ma, in the Carboniferous period and that the transition from mixotrophy to autotrophy occurred during the same time period. Although these two transitions precede a habitat change of major diversities from coastal/neritic waters to the pelagic realm (291-243 Ma, around the Permian/Triassic boundary event), the emergence of calcification, full autotrophy, and oceanic lifestyle seem mutually independent.
Here we use phylogenomics with expressed sequence tag (EST) data from the ecologically important coccolithophore-forming alga Emiliania huxleyi and the plastid-lacking cryptophyte Goniomonas cf. pacifica to establish their phylogenetic positions in the eukaryotic tree. Haptophytes and cryptophytes are members of the putative eukaryotic supergroup Chromalveolata (chromists [cryptophytes, haptophytes, stramenopiles] and alveolates [apicomplexans, ciliates, and dinoflagellates]). The chromalveolates are postulated to be monophyletic on the basis of plastid pigmentation in photosynthetic members, plastid gene and genome relationships, nuclear "host" phylogenies of some chromalveolate lineages, unique gene duplication and replacements shared by these taxa, and the evolutionary history of components of the plastid import and translocation systems. However the phylogenetic position of cryptophytes and haptophytes and the monophyly of chromalveolates as a whole remain to be substantiated. Here we assess chromalveolate monophyly using a multigene dataset of nuclear genes that includes members of all 6 eukaryotic supergroups. An automated phylogenomics pipeline followed by targeted database searches was used to assemble a 16-protein dataset (6,735 aa) from 46 taxa for tree inference. Maximum likelihood and Bayesian analyses of these data support the monophyly of haptophytes and cryptophytes. This relationship is consistent with a gene replacement via horizontal gene transfer of plastid-encoded rpl36 that is uniquely shared by these taxa. The haptophytes + cryptophytes are sister to a clade that includes all other chromalveolates and, surprisingly, two members of the Rhizaria, Reticulomyxa filosa and Bigelowiella natans. The association of the two Rhizaria with chromalveolates is supported by the approximately unbiased (AU)-test and when the fastest evolving amino acid sites are removed from the 16-protein alignment.
A revised six-kingdom system of life is presented, down to the level of infraphylum. As in my 1983 system Bacteria are treated as a single kingdom, and eukaryotes are divided into only five kingdoms: Protozoa, Animalia, Fungi, Plantae and Chromista. Intermediate high level categories (superkingdom, subkingdom, branch, infrakingdom, superphylum, subphylum and infraphylum) are extensively used to avoid splitting organisms into an excessive number of kingdoms and phyla (60 only being recognized). The two 'zoological' kingdoms, Protozoa and Animalia, are subject to the International Code of Zoological Nomenclature, the kingdom Bacteria to the International Code of Bacteriological Nomenclature, and the three 'botanical' kingdoms (Plantae, Fungi, Chromista) to the International Code of Botanical Nomenclature. Circumscriptions of the kingdoms Bacteria and Plantae remain unchanged since Cavalier-Smith (1981). The kingdom Fungi is expanded by adding Microsporidia, because of protein sequence evidence that these amitochondrial intracellular parasites are related to conventional Fungi, not Protozoa. Fungi are subdivided into four phyla and 20 classes; fungal classification at the rank of subclass and above is comprehensively revised. The kingdoms Protozoa and Animalia are modified in the light of molecular phylogenetic evidence that Myxozoa are actually Animalia, not Protozoa, and that mesozoans are related to bilaterian animals. Animalia are divided into four subkingdoms: Radiata (phyla Porifera, Cnidaria, Placozoa, Ctenophora), Myxozoa, Mesozoa and Bilateria (bilateral animals: all other phyla). Several new higher level groupings are made in the animal kingdom including three new phyla: Acanthognatha (rotifers, acanthocephalans, gastrotrichs, gnathostomulids), Brachiozoa (brachiopods and phoronids) and Lobopoda (onychophorans and tardigrades), so only 23 animal phyla are recognized. Archezoa, here restricted to the phyla Metamonada and Trichozoa, are treated as a subkingdom within Protozoa, as in my 1983 six-kingdom system, not as a separate kingdom. The recently revised phylum Rhizopoda is modified further by adding more flagellates and removing some 'rhizopods' and is therefore renamed Cercozoa. The number of protozoan phyla is reduced by grouping Mycetozoa and Archamoebae (both now infraphyla) as a new subphylum Conosa within the phylum Amoebozoa alongside the subphylum Lobosa, which now includes both the traditional aerobic lobosean amoebae and Multicilia. Haplosporidia and the (formerly microsporidian) metchnikovellids are now both placed within the phylum Sporozoa. These changes make a total of only 13 currently recognized protozoan phyla, which are grouped into two subkingdoms: Archezoa and Neozoa; the latter is modified in circumscription by adding the Discicristata, a new infrakingdom comprising the phyla Percolozoa and Euglenozoa). These changes are discussed in relation to the principles of megasystematics, here defined as systematics that concentrates on the higher levels of classes, phyla, and kingdoms. These principles also make it desirable to rank Archaebacteria as an infrakingdom of the kingdom Bacteria, not as a separate kingdom. Archaebacteria are grouped with the infrakingdom Posibacteria to form a new subkingdom, Unibacteria, comprising all bacteria bounded by a single membrane. The bacterial subkingdom Negibacteria, with separate cytoplasmic and outer membranes, is subdivided into two infrakingdoms: Lipobacteria, which lack lipopolysaccharide and have only phospholipids in the outer membrane, and Glycobacteria, with lipopolysaccharides in the outer leaflet of the outer membrane and phospholipids in its inner leaflet. This primary grouping of the 10 bacterial phyla into subkingdoms is based on the number of cell-envelope membranes, whilst their subdivision into infrakingdoms emphasises their membrane chemistry; definition of the negibacterial phyla, five at least partly photosynthetic, relies chiefly on photosynthetic mechanism and cell-envelope structure and chemistry corroborated by ribosomal RNA phylogeny. The kingdoms Protozoa and Chromista are slightly changed in circumscription by transferring subphylum Opalinata (classes Opalinea, Proteromonadea, Blastocystea cl. nov.) from Protozoa into infrakingdom Heterokonta of the kingdom Chromista. Opalinata are grouped with the subphylum Pseudofungi and the zooflagellate Developayella elegans (in a new subphylum Bigyromonada) to form a new botanical phylum (Bigyra) of heterotrophs with a double ciliary transitional helix, making it necessary to abandon the phylum name Opalozoa, which formerly included Opalinata. The loss of ciliary retronemes in Opalinata is attributed to their evolution of gut commensalism. The nature of the ancestral chromist is discussed in the light of recent phylogenetic evidence.
Stephanocha nom. nov. (Silicoflagellata, Dictyochophyceae) is herein proposed as a replacement name for the illegitimate genus name Distephanus, which is a later homonym of Distephanus, a flowering plant. The old generic description is emended, with S. rotunda as the designated type, and new combinations are made for all bona fide silicoflagellate taxa previously assigned (including those tentatively assigned) to Distephanus, except most already transferred to Distephanopsis.
In the logically convoluted language of Art. 64 of ICBN a homonym (which is a botanical name with multiple typifications) is written about as two or more different names, one "legitimate" and the rest "illegitimate". A proposal referred to the Special Committee on Orthography by the Sydney Congress to eliminate the language of legitimacy/illegitimacy from a straightforward matter of the correct and incorrect use of a name is revised and presented again, since the Special Committee has neglected to deal with it. A further proposal is made to divorce the material on homonymy from the material on parahomonyms (confusingly similar names) and to stop the confusing practice of "treating as homonyms(!)" quite distinct validly published and heterotypic names which simply happen to have a similar orthography. Such names should both be retained unless there are pragmatic grounds for rejecting one of them, and when this is necessary existing strategies for nomenclatural conservation are perfectly adequate.
Silva, P. C: Report of the Committee for Algae: 1. – Taxon 42: 699–710. 1993. – ISSN 0040‐0262.
The previous Committee deferred 36 proposals to conserve family names to the present Committee (1987–1993). Seven, based on orthographic variants, were deemed unnecessary and have been withdrawn. Of the remaining 29 proposals 19 are recommended and 10 are not.
Nicolson, D. H.: Report on the status of proposals to conserve and/or reject names (nomina conservanda et rejicienda proposita) published by the end of 1992. — Taxon 42: 435–446. 1993. — ISSN 0040–0262.
Accounts for all botanical names proposed for conservation/rejection that were not acted upon by the XIV International Botanical Congress in 1987 (Berlin), and those proposed by the end of 1992.
This annotated index of 581 entries includes modern and fossil calcareous nannoplankton taxa of all levels, in addition to those appearing in the earlier index and supplements. Some 320 are new entries, 198 of which are valid and 122 invalid. The bibliography of 290 entries includes all references cited in the index to taxa, and additional publications concerning all phases of calcareous nannoplankton studies that have appeared since the previous indices.
The haptophyte algae (sometimes referred to as the prymnesiophyte algae) are cosmopolitan in their distribution and are particularly important in marine ecosystems. They form a significant component of the phytoplankon and may occasionally be the dominant organisms. In recent years there has been a marked increase in these algae, partly as a result of the occurence of a number of ichthyotoxic blooms in Scandinavian coastal waters, whose effects have been dramatic in terms of both the diversity of species affected and their economic impact. It is also now recognised that some members of the Haptophyta may affect our climate through the production of volatile sulphur compounds and through the effects that calcifying biomineralization may have on ocean/atmospheric carbon dioxide exchange. This is the first monograph on the Haptophyta, each chapter having been contributed by authors experienced in their subject. The topics covered include all major aspects of haptophyte biology, such as their structure, biochemistry, ecology, climatological and economic importance, fossil record, evolution and systematics.
Hamilton, C. W. & Reichard, S. H.: Current practice in the use of subspecies, variety, and forma in the classification of wild plants. — Taxon 41: 485–498. 1992. — ISSN 0040‐0262.
Infraspecific classification of plants continues to be practiced commonly by taxonomists: c. 8 % of species monographed in 26 major journals and series during the period 1987–1990 were subdivided. Of those, c. 42 % were divided into subspecies only, 52 % into varieties, 3 % into formae, and 3 % into taxa of more than one level. Subspecies and varieties are usually defined as requiring some integrity — geographic, ecologic, and/or phylogenetic — beyond the morphological. Despite some attempts to differentiate between subspecies and variety, they are largely equivalent in practice. European taxonomists tend to favor subspecies, whereas their counterparts in the United States usually employ variety. Formae usually are defined as lacking any extramorphological integrity. Given the general inconsistency of practice found, it is imperative that more authors state briefly their philosophy of infraspecific taxonomy so their classifications may be interpreted more clearly. Taxonomists collectively should promote greater standardization of infraspecific classification.
The coccolithophorids are a well-established group of unicellular algae whose bodies are covered by calcareous scales. They are usually assigned to the class Haptophyceae or Prymnesiophyceae, but we present arguments in favor of the name Coccolithophyceae. The taxonomic diversity within the coccolithophorids far exceeds that within the remaining members of the class. Molecular evidence shows phylogenetic closeness of coccolithophorids to certain haptophytes that do not form coccoliths, suggesting that the ability to produce calcareous scales has arisen only once and has been lost in some haptophytes. Electron microscopical detection of weak calcification in noncoccolithophorid haptophytes further supports the view that calcification is distributed throughout the class. Of three available names for the class, Coccolithophycea Rothmaler 1951 has priority over Prymnesiophyceae Casper ex Hibberd 1976 and Haptophyceae Christensen ex P.C. Silva 1980. We urge the use of the name Coccolithophyceae for this class.
A survey of the use of two common suffixes of generic names and species epithets in botanical nomenclature is provided and discrepancies in treatment, either in the form of the stem or in the gender, are demonstrated. The reasons for these discrepancies and their consequences are outlined and possible means of harmonization are indicated.
Members of the Haptophyta from British waters have been listed in a number of check-lists between 1953 and 1976 (Parke, 1953; Parke & Dixon, 1964, 1968, 1976), but there has been no attempt to draw the records together on a world-wide basis. However, a recent review of the classification system of the coccolithophorids included a check-list of all species thought to be extant from marine, coastal and freshwater habitats (Jordan & Kleijne, 1994). At the same time, two ambitious projects, the Encyclopaedia of Algal Genera (ed. B.C. Parker, in preparation) and the preparation of a CD-ROM retrieval system for information on algal and protist groups by the Expert-Centre for Taxonomic Identification (ETI), have required further collation of the available records (see Note 1), and, as a result, we have now extended the scheme of Jordan & Kleijne (1994) to include a global list of all extant haptophytes.(Received July 16 1993)(Accepted October 03 1993)
Symbioses between nitrogen (N)2–fixing prokaryotes and photosynthetic eukaryotes are important for nitrogen acquisition in N-limited environments. Recently,
a widely distributed planktonic uncultured nitrogen-fixing cyanobacterium (UCYN-A) was found to have unprecedented genome
reduction, including the lack of oxygen-evolving photosystem II and the tricarboxylic acid cycle, which suggested partnership
in a symbiosis. We showed that UCYN-A has a symbiotic association with a unicellular prymnesiophyte, closely related to calcifying
taxa present in the fossil record. The partnership is mutualistic, because the prymnesiophyte receives fixed N in exchange
for transferring fixed carbon to UCYN-A. This unusual partnership between a cyanobacterium and a unicellular alga is a model
for symbiosis and is analogous to plastid and organismal evolution, and if calcifying, may have important implications for
past and present oceanic N2 fixation.
Information on the internal structure of the Chrysophyceae is reviewed and some new data are presented. From these a model has been constructed which represents the combination of features constructed to be the basic pattern of cell structure in this group. A brief review is given of modern research, which demonstrates that the choanoflagellates should be removed not only from the Chrysophyccae but also from the plant kingdom. The organization of the Prymnesiophyceae classis nova (= Haptophyceae) is compared with that of the Chrysophyceae, and the relationship of both groups to the Xanthophyccae, Phaeophyceac anti Bacillariophyceae is considered. This leads to the conclusion that the Prymnesiophyceae must be considered as a class separate from the Chrysophyceae. Removal of the Prymnesiophyceae and choanoflagellates from the Chrysophyceae leaves a largely homogeneous and monophyletic group, though the family Pedinellaceae appears to have a unique organization and may be found to be separated from the Chrysophyccae by a phyletic distance at least as great as that between the remaining classes of heterokont algae. It is suggested that this family should occupy a more isolated position in the Chrysophyceae than at present, possibly in a separate order Pedinellales.
Traditional classification imposed a division into plant-like and animal-like forms on the unicellular eukaryotes, or protists; in a current view the protists are a diverse assemblage of plant-, animal- and fungus-like groups. Classification of these into phyla is difficult because of their relatively simple structure and limited geological record, but study of ultrastructure and other characteristics is providing new insight on protist classification. Possible classifications are discussed, and a summary classification of the living world into kingdoms (Monera, Protista, Fungi, Animalia, Plantae) and phyla is suggested. This classification also suggests groupings of phyla into superphyla and form-superphyla, and a broadened kingdom Protista (including green algae, oomycotes and slime molds but excluding red and brown algae). The classification thus seeks to offer a compromise between the protist and protoctist kingdoms of Whittaker and Margulis and to combine a full listing of phyla with grouping of these for synoptic treatment.
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The ICBN: Things you need to know -9
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Journal of Nannoplankton Research, 16(1): 6-7.
ICBN -Things you need to know index
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Flagellatae, Chlorophyceae, Coccosphaerales und Silicofl agellatae
- E Lemmermann
Lemmermann, E. 1908. Flagellatae, Chlorophyceae, Coccosphaerales und Silicofl agellatae. In: K. Brandt & C. Apstein
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Chrysophyta: defi nition and interpretation
- D J Hibberd
Hibberd, D.J. 1972. Chrysophyta: defi nition and interpretation.
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Natürliche Schöpfungs-Geschichte, Achte umgearbeitete und vermehrte Aufl age. Georg Reimer, Berlin
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Haeckel, E. 1889. Natürliche Schöpfungs-Geschichte, Achte
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Opinion 805 (Coccolithophorida): validated under the plenary powers
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Algen 1925-1927. Mit Nachträgen aus den Jahren 1914 bis 1924
- O C Schmidt
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Silicofl agellates (Dictyochophyceae)
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The ICBN: Things you need to know -8
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van Heck, S.E. 1993. The ICBN: Things you need to know -8.
INA Newsletter, 15(1): 8-9.
On the nature and use of the suffi x -ellus, -ella, -ellum in species-group names
- G C Steyskal
Steyskal, G.C. 1970. On the nature and use of the suffi x -ellus,
-ella, -ellum in species-group names. Journal of the Lepidopterist's Society, 24(1): 38-41.
Unravelling the algae: the past, present and future of algal molecular systematics
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Haptophyta. In: J. Lewis & J. Brodie (Eds). Unravelling the
algae: the past, present and future of algal molecular systematics. Systematics Association Special Volume, 75: 183-196.
Über Coccosphaera und einige neue Tintinniden im Plankton des nördlichen Atlantischen Oceans
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