Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits ...will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction.
Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfil diverse roles in the ecosystem, ...including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree and infer ages and broad patterns of speciation/extinction and morphological innovation in mushroom-forming fungi. Agaricomycetes started a rapid class-wide radiation in the Jurassic, coinciding with the spread of (sub)tropical coniferous forests and a warming climate. A possible mass extinction, several clade-specific adaptive radiations and morphological diversification of fruiting bodies followed during the Cretaceous and the Paleogene, convergently giving rise to the classic toadstool morphology, with a cap, stalk and gills (pileate-stipitate morphology). This morphology is associated with increased rates of lineage diversification, suggesting it represents a key innovation in the evolution of mushroom-forming fungi. The increase in mushroom diversity started during the Mesozoic-Cenozoic radiation event, an era of humid climate when terrestrial communities dominated by gymnosperms and reptiles were also expanding.
We report on the generation of a continuous-wave (CW) radially polarized beam with an Yb:Lu
2
O
3
polycrystalline ceramic disk in a thin-disk laser (TDL) oscillator. A circular grating-waveguide ...mirror (CGWM) with a high polarization discrimination given by a reflectivity difference between the two orthogonal polarization states of 44.6% was used as a polarization-selective cavity end-mirror. An output power of 175 W was achieved with an optical efficiency of 39.6%. A high degree of radial polarization of 96.2% and a beam propagation factor of
M
2
hor.
= 2.05 and
M
2
ver.
= 2.32 were measured at the maximum output power.
Species delimitation is one of the most fundamental processes in biology. Biodiversity undertakings, for instance, require explicit species concepts and criteria for species delimitation in order to ...be relevant and translatable. However, a perfect species concept does not exist for Fungi. Here, we review the species concepts commonly used in Basidiomycota, the second largest phylum of Fungi that contains some of the best known species of mushrooms, rusts, smuts, and jelly fungi. In general, best practice is to delimitate species, publish new taxa, and conduct taxonomic revisions based on as many independent lines of evidence as possible, that is, by applying a so-called unifying (or integrative) conceptual framework. However, the types of data used vary considerably from group to group. For this reason we discuss the different classes of Basidiomycota, and for each provide: (i) a general introduction with difficulties faced in species recognition, (ii) species concepts and methods for species delimitation, and (iii) community recommendations and conclusions.
Basidiomycota is one of the major phyla in the fungal tree of life. The outline of Basidiomycota provides essential taxonomic information for researchers and workers in mycology. In this study, we ...present a time-framed phylogenomic tree with 487 species of Basidiomycota from 127 families, 47 orders, 14 classes and four subphyla; we update the outline of Basidiomycota based on the phylogenomic relationships and the taxonomic studies since 2019; and we provide notes for each order and discuss the history, defining characteristics, evolution, justification of orders, problems, significance, and plates. Our phylogenomic analysis suggests that the subphyla diverged in a time range of 443–490 Myr (million years), classes in a time range of 312–412 Myr, and orders in a time range of 102–361 Myr. Families diverged in a time range of 50–289 Myr, 76–224 Myr, and 62–156 Myr in Agaricomycotina, Pucciniomycotina, and Ustilaginomycotina, respectively. Based on the phylogenomic relationships and divergence times, we propose a new suborder Mycenineae in Agaricales to accommodate Mycenaceae. In the current outline of Basidiomycota, there are four subphyla, 20 classes, 77 orders, 297 families, and 2134 genera accepted. When building a robust taxonomy of Basidiomycota in the genomic era, the generation of molecular phylogenetic data has become relatively easier. Finding phenotypical characters, especially those that can be applied for identification and classification, however, has become increasingly challenging.
Morphological and DNA data show that effused representatives of the Auriculariales (Basidiomycota) with sphaeropedunculate basidia belong to eleven genera of which seven are dealt with in this study. ...Among them, Myxarium is the largest genus containing 21 accepted species of which nine are reintroduced below and five are described as new. Protodontia is limited to three species only, P. subgelatinosa (the generic type) and two newly described species from Africa. Protoacia is a new monotypic genus for P. delicata, sp. nov., widely distributed on coniferous hosts in Eurasia. Myxariellum is erected for two new species with smooth hymenophore from northwestern North America while Gelacantha is introduced for G. pura, a new species with hydnoid hymenophore from Caucasus. Our data do not confirm the present synonymy of Sebacina sphaerospora with Tremella glaira, and these species are placed in two separate genera – Hydrophana, gen. nov., and Ofella, gen. nov., respectively. A key to European Myxarium and similar‐looking species is included.
We present the intracavity generation of beams with radial polarization at an average output power of 750 W and an optical efficiency of 43% from a continuous wave thin-disk laser. Circular grating ...waveguide output couplers (GWOC) were used to select the radial polarization. The sensitivity of the polarizing function of the GWOC with regards to the fabrication tolerances is also analysed in details with a particular emphasis on the effect of the duty cycle and the geometrical profile of the gratings. Furthermore, we present the conversion of femtosecond laser pulses from linear to azimuthal polarization using a nanograting-based polarization converter. Azimuthally polarized beams with an average power of up to 850 W, a pulse duration of 400 fs and a pulse repetition rate of 1 MHz were generated in this way with a conversion efficiency of >90%.
In the present paper, we select a neotype for
Tremella cerasi
and prove that it is conspecific with
Ditangium insigne
(the genus type of
Ditangium
). We argue that
Ditangium
should be restored as a ...correct genus for
T. cerasi
, while the currently used generic name
Craterocolla
is to be treated as its younger synonym. Morphological, ecological and genetic variability of
Ditangium cerasi
is discussed, and two other
Ditangium
species are described—
D. altaicum
, sp. nov. and
D. incarnatum
, comb. nov. In addition,
Exidia fulva
is combined in
Globulisebacina
.
Fungi play crucial roles in ecosystems and are among the species-richest organism groups on Earth. However, knowledge on their occurrence lags behind the data for animals and plants. Recent analyses ...of fungal occurrence data from Western, Central and Northern Europe provided important insights into response of fungi to global warming. The consequences of the global changes for biodiversity on a larger geographical scale are not yet understood. Landscapes of Eastern Europe and particularly of eastern Ukraine, with their specific geological history, vegetation and climate, can add substantially new information about fungal diversity in Europe.
We describe the dataset and provide a checklist of aphyllophoroid fungi (non-gilled macroscopic
) from eastern Ukraine sampled in 16 areas between 2007 and 2011. The dataset was managed on the PlutoF biodiversity workbench (http://dx.doi.org/10.15156/BIO/587471) and can also be accessed via Global Biodiversity Information Facility (GBIF, parts of datasets https://doi.org/10.15468/kuspj6 and https://doi.org/10.15468/h7qtfd). This dataset includes 3418 occurences, namely 2727 specimens and 691 observations of fructifications belonging to 349 species of fungi. With these data, the digitised CWU herbarium (V. N. Karazin Kharkiv National University, Ukraine) doubled in size A most detailed description of the substrate's properties and habitat for each record is provided. The specimen records are supplemented by 26 nuclear ribosomal DNA ITS sequences and six 28S sequences. Additionally, 287 photographs depicting diagnostic macro- and microscopic features of fungal fruitbodies as well as studied habitats are linked to the dataset. Most of the specimens have at least one mention in literature and relevant references are displayed as associated with specimen data. In total, 16 publication references are linked to the dataset. The dataset sheds new light on the fungal diversity of Eastern Europe. It is expected to complement other public sources of fungal occurrence information on continental and global levels in addressing macroecological and biogeographical questions.
BioDATA is an international project on developing skills in biodiversity data management and data publishing. Between 2018 and 2021, undergraduate and postgraduate students from Armenia, Belarus, ...Tajikistan, and Ukraine, have an opportunity to take part in the intensive courses to become certified professionals in biodiversity data management. They will gain practical skills and obtain appropriate knowledge on: international data standards (Darwin Core); data cleaning software, data publishing software such as the Integrated Publishing Toolkit (IPT), and preparation of data papers. Working with databases, creating datasets, managing data for statistical analyses and publishing research papers are essential for the everyday tasks of a modern biologist. At the same time, these skills are rarely taught in higher education. Most of the contemporary professionals in biodiversity have to gain these skills independently, through colleagues, or through supervision. In addition, all the participants familiarize themselves with one of the important international research data infrastructures such as the Global Biodiversity Information Facility (GBIF). The project is coordinated by the University of Oslo (Norway) and supported by the Global Biodiversity Information Facility (GBIF). The project is funded by the Norwegian Agency for International Cooperation and Quality Enhancement in Higher Education (DIKU).
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