The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. ...Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third‐party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web‐based sequence management system in UNITE.
The use of different sources of evidence has been recommended in order to conduct species delimitation analyses to solve taxonomic issues. In this study, we use a maximum likelihood framework to ...combine morphological and molecular traits to study the case of Xylodon australis (Hymenochaetales, Basidiomycota) using the locate.yeti function from the phytools R package. Xylodon australis has been considered a single species distributed across Australia, New Zealand and Patagonia. Multi-locus phylogenetic analyses were conducted to unmask the actual diversity under X. australis as well as the kinship relations respect their relatives. To assess the taxonomic position of each clade, locate.yeti function was used to locate in a molecular phylogeny the X. australis type material for which no molecular data was available using morphological continuous traits. Two different species were distinguished under the X. australis name, one from Australia-New Zealand and other from Patagonia. In addition, a close relationship with Xylodon lenis, a species from the South East of Asia, was confirmed for the Patagonian clade. We discuss the implications of our results for the biogeographical history of this genus and we evaluate the potential of this method to be used with historical collections for which molecular data is not available.
Species distribution models based on environmental predictors are useful to explain a species geographic range. For many groups of organisms, including fungi, the increase in occurrence data sets has ...generalized their use. However, fungal species are not always easy to distinguish, and taxonomy of many groups is not completely settled. This study explores the effect of taxonomic uncertainty in databases used for modeling fungal distributions. We analyze distribution models for three morphospecies from the corticioid genus Xylodon (Hymenochaetales, Basidiomycota), comparing models based on species names on vouchers specimens with models derived from species identified by DNA barcode. Differences in the contribution of predictors driving the distribution of each modeled taxon and the extent of their ranges were studied. Records under Xylodon paradoxus, X. flaviporus, and X. raduloides were obtained from fungarium collections and GenBank repository. Two grouping criteria were used: (a) specimens were grouped by their collection or sequence voucher names and (b) specimens were grouped following molecular identification using ITS sequences through barcoding gap species recognition (BGSR). Climatic, geographic, and biotic variables were used to predict the potential distribution of each taxon through MaxEnt algorithm. From the three morphospecies selected according to voucher names, up to 19 species candidates were detected using BGSR. Climatic variables were the most important predictors in distribution models made from names on voucher specimens, but their importance decreased when BGSR was applied. In general, the extent of species distributions was more restricted for taxa under BGSR. Our results show that taxonomic uncertainty has a strong effect in Xylodon species distribution models. Misleading results can be obtained when cryptic species or identification errors mask the actual diversity of the presence records. Preserved specimens in natural history collections offer the possibility to assess whether the species name on labels matches the current species recognition criteria.
This study explores the effect of taxonomic uncertainty in databases used for modeling fungal distributions, comparing models based on species names on voucher specimens with models derived from species identified by DNA barcode. Our results show that taxonomic uncertainty has a strong effect in fungal species distribution models producing misleading results when cryptic species or identification errors mask the actual diversity of the presence records.
In the framework of a research project on corticioid fungi (Basidiomycota) from Cape Verde, we collected several specimens provisionally assigned to
Coniophora
sp. On the basis of morphological and ...molecular analyses, we identified these specimens as
C. eremophila
Lindsey & Gilb. These records extend the geographical distribution of this species by approximately 8,800 km in a straight line west to east, from its previously known North American locality and 8,700 km southwest to northeast from the other known locality in Chile. The pres-ence of the genus
Coniophora
is reported for the first time in the Cape Verde Archipelago.
Schizoporaparadoxa
, current name
Xylodonparadoxus
, is a white-rot fungus with certain useful biotechnological properties. The representative genome of
Schizoporaparadoxa
strain KUC8140 was ...published in 2015 as part of the 1000 Fungal Genomes Project. Multilocus phylogenetic analyses, based on three nuclear regions (ITS, LSU and
rpb
2), confirmed a misidentification of
S.paradoxa
strain KUC8140 which should be identified as
Xylodonovisporus
. This wrong identification explains the unexpected geographical distribution of
S.paradoxa
, since this species has a European distribution, whereas the strain KUC8140 was recorded from Korea, Eastern Asia.
Hypochnicium is a genus of corticioid, wood-inhabiting fungi in the Polyporales with a worldwide distribution. The genus has been characterized by the nature of the spores; they are thick-walled, ...smooth or ornamented, and cyanophilous. Nine new ITS nrDNA sequences from species of this genus were aligned with 32 sequences from GenBank, and phylogenetic analyses were performed. Six clades were determined within the genus; one contains taxa with smooth spores, and the other three with ornamented spores. Hypochnicium versatum must be included in Gloeohypochnicium, and the new combination Gloeohypochnicium versatum is proposed. Two new species, Hypochnicium michelii from Spain and Hypochnicium guineensis from Equatorial Guinea, are described.
In this study, the taxonomic diversity of the
species complex (
,
) is examined. Specimens were studied using an integrative taxonomic approach that includes molecular phylogenetic and morphological ...analyses, and environmental niche comparisons. Four different species were found inside the
complex, with a biogeographic distribution pattern bound by geographic regions: Europe, North America, Patagonia, and Australia-New Zealand. Molecular, morphological, and environmental evidences delimit two lineages within this complex: a Northern Hemisphere clade with longer basidiospores and wider ranges in temperature and precipitation tolerance, and a Southern Hemisphere clade with smaller and more spherical basidiospores, and an isothermal and more humid climate preference. The integrative taxonomic approach used in this study demonstrates congruence between data sets and shows how morphological and environmental characteristics contribute to the differentiation of fungal species complexes. By combining various sources of taxonomic information, three new species are described:
,
and
.
The genus Hydnophlebia includes two species of wood-inhabiting fungi, Hydnophlebia chrysorhizon and Hydnophlebia omnivora . Both are characterized by cream to reddish-orange, resupinate basidiome, ...with hydnoid hymenophore, margin with strands, a monomitic hyphal system, tubular to ventricose cystidia and elliptical spores. In this paper, a taxonomic study of Hydnophlebia , using morphology and molecular analyses of large subunit nuclear ribosomal DNA (LSU) and the internal transcribed spacer nrDNA operon (ITS), is reported. Three new species, Hydnophlebia canariensis , H. gorgonea and H. meloi , from the Macaronesia bioregion (Canary Islands and Cape Verde Archipelago), are described.
Amylostereum laevigatum has been reported from Japan growing on Cryptomeria japonica and Chamaecyparis obtusa. Using morphological and molecular data (internal transcribed spacer (ITS) nrDNA and rpb2 ...markers), we demonstrate that some specimens under A. laevigatum from Japan belong to A. orientale, a species described from China. Amylostereum orientale differs from A. laevigatum mainly in having smaller basidiospores. This is the first citation of A. orientale in Japan.
•Molecular analyses, ITS nrDNA and rpb2, allow separation of Amylostereum species.•ITS sequences confirm Amylostereum laevigatum from Japan as A. orientale.•Amylostereum orientale is distributed in Japan.•Spore size allows separation of Amylostereum orientale and A. laevigatum.
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