High-level classification of the Fungi and a tool for evolutionary ecological analyses

High-throughput sequencing studies generate vast amounts of taxonomic data. Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone. We propose an updated phylum-and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative. Based on phylogenies and divergence time estimates, we adopt phylum rank to Aphelidiomycota, Basidiobolomycota, Calcarisporiellomycota, Glomeromycota, Entomophthoromycota, Entorrhizomycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota and Olpidiomycota. We accept nine subkingdoms to accommodate these 18 phyla. We consider the kingdom Nucleariae (phyla Nuclearida and Fonticulida) as a sister group to the Fungi. We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework, using this or any other classification system. We provide an example of testing evolutionary ecological hypotheses based on a global soil fungal data set.Peer reviewe

Inventory and review of the Mio–Pleistocene São Jorge flora (Madeira Island, Portugal): palaeoecological and biogeographical implications

The occurrence of plant fossils on Madeira Island has been known since the mid-nineteenth century. Charles Lyell and George Hartung discovered a leaf bed rich in Lauraceae and fern fossils at S~ao Jorge in 1854. The determinations were controversial but a full review was never performed. Here we propose possible geological settings for the fossiliferous outcrop, and present an inventory and a systematic review of the surviving specimens of the S~ao Jorge macroflora. The S~ao Jorge leaf bed no longer outcrops due to a landslide in 1865. It was possible to establish the two alternative volcano stratigraphical settings in the sedimentary intercalations from the Middle Volcanic Complex, ranging in age from 7 to 1.8 Ma. The descriptions of Heer (1857), Bunbury (1859) and Hartung & Mayer (1864) are reviewed based on 82 surviving specimens. From the initial 37 taxa, we recognize only 20: Osmunda sp., Pteridium aquilinum, Asplenium cf. onopteris, aff. Asplenium, cf. Polystichum, cf. Davallia, Woodwardia radicans, Filicopsida gen. et sp. indet. 1 and 2, Ocotea foetens, Salix sp., Erica arborea, cf. Vaccinium, Rubus sp, cf. Myrtus, Magnoliopsida gen. et sp. indet. 1 to 3, Liliopsida gen. et sp. indet. 1. Magnoliopsida gen. et sp. indet. 4 is based on one previously undescribed flower or fruit. The floristic composition of the S~ao Jorge fossils resembles the current floristic association of temperate stink laurel (Ocotea foetens) forest, suggesting a warm and humid palaeoclimate and indicating that laurel forests were present in Macaronesia at least since the Gelasian, a time when the palaeotropical geofloral elements were almost extinct in Europe.info:eu-repo/semantics/publishedVersio

A taxonomic backbone for the global synthesis of species diversity in the angiosperm order Caryophyllales

The Caryophyllales constitute a major lineage of flowering plants with approximately 12500 species in 39 families. A taxonomic backbone at the genus level is provided that reflects the current state of knowledge and accepts 749 genera for the order. A detailed review of the literature of the past two decades shows that enormous progress has been made in understanding overall phylogenetic relationships in Caryophyllales. The process of re-circumscribing families in order to be monophyletic appears to be largely complete and has led to the recognition of eight new families (Anacampserotaceae, Kewaceae, Limeaceae, Lophiocarpaceae, Macarthuriaceae, Microteaceae, Montiaceae and Talinaceae), while the phylogenetic evaluation of generic concepts is still well underway. As a result of this, the number of genera has increased by more than ten percent in comparison to the last complete treatments in the Families and genera of vascular plants” series. A checklist with all currently accepted genus names in Caryophyllales, as well as nomenclatural references, type names and synonymy is presented. Notes indicate how extensively the respective genera have been studied in a phylogenetic context. The most diverse families at the generic level are Cactaceae and Aizoaceae, but 28 families comprise only one to six genera. This synopsis represents a first step towards the aim of creating a global synthesis of the species diversity in the angiosperm order Caryophyllales integrating the work of numerous specialists around the world

Notes for genera: basal clades of Fungi (including Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota)

Compared to the higher fungi (Dikarya), taxonomic and evolutionary studies on the basal clades of fungi are fewer in number. Thus, the generic boundaries and higher ranks in the basal clades of fungi are poorly known. Recent DNA based taxonomic studies have provided reliable and accurate information. It is therefore necessary to compile all available information since basal clades genera lack updated checklists or outlines. Recently, Tedersoo et al. (MycoKeys 13:1--20, 2016) accepted Aphelidiomycota and Rozellomycota in Fungal clade. Thus, we regard both these phyla as members in Kingdom Fungi. We accept 16 phyla in basal clades viz. Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota. Thus, 611 genera in 153 families, 43 orders and 18 classes are provided with details of classification, synonyms, life modes, distribution, recent literature and genomic data. Moreover, Catenariaceae Couch is proposed to be conserved, Cladochytriales Mozl.-Standr. is emended and the family Nephridiophagaceae is introduced

(276–279) Proposals to provide for registration of new names and nomenclatural acts

The Melbourne Congress of 2011 authorized a Special Committee on Registration of Algal and Plant Names (including fossils), which was established the following year (Wilson in Taxon 61: 878–879. 2012). Its explicit mandate was “to consider what would be involved in registering algal and plant names (including fossils), using a procedure analogous to that for fungal names agreed upon in Melbourne and included in the Code as Art. 42”, but expectations at the Nomenclature Section in Melbourne went farther than that. There was the hope that registration systems for at least some of the main groups would soon be set up, to be used and tested on a voluntary basis and, if found to be generally accepted, would persuade the subsequent Congress in Shenzhen, in 2017, to declare registration of new names an additional requirement for valid publication. The Melbourne Congress also approved mandatory registration of nomenclatural novelties in fungi, starting on 1 Jan 2013. The new Art. 42 of the Code (McNeill & al. in Regnum Veg. 154. 2012) requires authors to register any fungal nomenclatural novelty, prior to publication, with a recognized repository, whereupon they are provided with a unique identifier for each name, to be included in the protologue along with other Code-mandated information. Years before registration became mandatory, mycologists had been encouraged, often prompted by journal editors, to register their nomenclatural novelties prior to publication. Most complied. Consequently, when mandatory registration was proposed, it had strong support from the mycological community. There are currently three recognized repositories for fungal names. They vary somewhat in how they operate, but they share records of their registered novelties as soon as publication has been effected. One consequence of implementing mandatory registration is that locating new fungal names and combinations and associated protologue information is much simpler now than it was before. This makes it easier to incorporate the information into taxonomic studies and to update taxonomic treatments, inventories, and indices. A corollary is that, no matter what publication outlet an author chooses, the name cannot fail to be noticed. The positive experience in mycology makes extension of the registration concept to plants and algae a compelling idea. That experience shows that the best way to make mandatory registration of nomenclatural novelties palatable to botanists and phycologists is the establishment of trial registration at repositories with a history of involvement in and commitment to the indexing of names. Trial registration enables users to acquaint themselves with registration procedures, make suggestions on how they might be improved, and appreciate, by personal experience, the benefits of registration. Unfortunately, the task of establishing such repositories proved to be more complex and time-consuming than had been foreseen. Substantial progress has been made in the establishment of such centres (Barkworth & al., in this issue, pp. 670–672) but the Committee is not in a position to make firm proposals to regulate registration procedures, even less to make registration mandatory from a concrete future date. Nevertheless, the Committee sees it as imperative that the Shenzhen Congress be offered the opportunity to move forward with registration without having to wait six more years. In this spirit, we offer the proposals below. Proposal (276) would declare registration an ongoing concern of the botanical, mycological, and phycological community and provide the basic structure for making it possible. Proposal (277) and Prop. (278) would, in addition, define a flexible framework within which a system of voluntary registration could be developed for various categories of organisms. Proposal (279) would provide for future mandatory registration in a way that does not depend on the six-year intervals between International Botanical Congresses. Presentation of each proposal is followed by a summary of the support received from members of the Committee.Fil: Barkworth, Mary E.. State University of Utah; Estados UnidosFil: Watson, Mark. Royal Botanic Gardens; Reino UnidoFil: Barrie, Fred R.. Missouri Botanical Garden; Estados Unidos. Field Museum Of Natural History; Estados UnidosFil: Belyaeva, Irina V.. Royal Botanic Gardens; Reino UnidoFil: Chung, Richard C. K.. Forest Research Institute ; MalasiaFil: Dasková, Jirina. Národní Muzeum; República ChecaFil: Davidse, Gerrit. Missouri Botanical Garden; Estados UnidosFil: Dönmez, Ali A.. Hacettepe Üniversitesi; TurquíaFil: Doweld, Alexander B.. National Institute Of Carpology; RusiaFil: Dressler, Stefan. Senckenberg Forschungsinstitut Und Naturmuseum; AlemaniaFil: Flann, Christina. Naturalis Biodiversity Center; Países BajosFil: Gandhi, Kanchi. Harvard University; Estados UnidosFil: Geltman, Dmitry. Russian Academy of Science; RusiaFil: Glen, Hugh F.. Forest Hills; SudáfricaFil: Greuter, Werner. Freie Universität Berlin; AlemaniaFil: Head, Martin J.. Brock University; CanadáFil: Jahn, Regine. Freie Universität Berlin; AlemaniaFil: Janarthanam, Malapati K.. Goa University; IndiaFil: Katinas, Liliana. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División de Plantas Vasculares; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Kirk, Paul M.. Royal Botanic Gardens; Reino UnidoFil: Klazenga, Niels. Royal Botanic Gardens Victoria; AustraliaFil: Kusber, Wolf-Henning. Freie Universität Berlin; AlemaniaFil: Kvacek, Jirí. Národní Muzeum; República ChecaFil: Malécot, Valéry. Universite D'angers; FranciaFil: Mann, David G.. Royal Botanic Gardens; Reino UnidoFil: Marhold, Karol. Charles University; República ChecaFil: Nagamasu, Hidetoshi. Kyoto University; JapónFil: Nicolson, Nicky. Royal Botanic Gardens; Reino UnidoFil: Paton, Alan. Royal Botanic Gardens; Reino UnidoFil: Patterson, David J.. The University Of Sydney; AustraliaFil: Price, Michelle J.. Conservatoire et Jardin botaniques de la Ville de Genève; SuizaFil: van Reine, Willem F Prud' Homme. Naturalis Biodiversity Center; Países BajosFil: Schneider, Craig W.. Trinity College Hartford; Estados UnidosFil: Sennikov, Alexander. Russian Academy Of Sciences; RusiaFil: Smith, Gideon F.. Nelson Mandela Metropolitan University; Sudáfrica. Universidad de Coimbra; PortugalFil: Stevens, Peter F.. Missouri Botanical Garden; Estados Unidos. University of Missouri; Estados UnidosFil: Yang, Zhu-Liang. Kunming Institute Of Botany Chinese Academy Of Sciences; ChinaFil: Zhang, Xian-Chun. Chinese Academy of Sciences; República de ChinaFil: Zuccarello, Giuseppe C.. Victoria University Of Wellington; Nueva Zeland

Morphology, Ultrastructure, and Molecular Phylogeny of Rozella multimorpha, a New Species in Cryptomycota

Increasing numbers of sequences of basal fungi from environmental DNA studies are being deposited in public databases. Many of these sequences remain unclassified below the phylum level because sequence information from identified species is sparse. Lack of basic biological knowledge due to a dearth of identified species is extreme in Cryptomycota, a new phylum widespread in the environment and phylogenetically basal within the fungal lineage. Consequently, we are attempting to fill gaps in the knowledge of Rozella, the best‐known genus in this lineage. Rozella is a genus of unwalled, holocarpic, endobiotic parasites of hosts including Chytridiomycota, Blastocladiomycota, Oomycota, Basidiomycota, and a green alga, with most species descriptions based on morphology and host specificity. We found a Rozella parasitizing a Pythium host that was a saprobe on spruce pollen bait placed with an aquatic sample. We characterized the parasite with light microscopy, TEM of its zoospores and sporangia, and its 18S/28S rDNA. Comparison with other Rozella species indicates that the new isolate differs morphologically, ultrastructurally, and genetically from Rozella species for which we have data. Features of the zoospore also differ from those of previously studied species. Herein we describe the Rozella as a new species, R. multimorpha.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142496/1/jeu12452-sup-0002-FigS2-S3.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142496/2/jeu12452.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142496/3/jeu12452_am.pd

Glucosinolate Diversity in Bretschneidera sinensis

The glucosinolate (GL) profile in several plant parts (leaf, branch, bark, root, and fruit) of Bretschneidera sinensis from three geographical regions of the People's Republic of China was established for the first time by HPLC. During this investigation, benzyl GL (1), 4-hydroxybenzyl GL (2), 2-hydroxy-2-methylpropyl GL (3), and 4-methoxybenzyl GL (4) were identified. In addition, one new GL, 3-hydroxy-4-methoxybenzyl GL (5), was isolated in a minor amount from the fruit and characterized by spectroscopic data interpretation. Furthermore, traces of 4-hydroxy-3-methoxyphenylacetonitrile were detected by GC-MS analysis in the fruits, thus confirming the presence of the regioisomeric 4-hydroxy-3-methoxybenzyl GL (6). GLs 1-5 were also quantified for the first time by HPLC in the various plant organs