The genus Wetmoreana was studied using quantitative integrative taxonomy methods to resolve the genus delimitation and explore its taxonomy diversity at the species level. As a result, the genus ...Fulgogasparrea is synonymized with Wetmoreana, and the latter includes 15 formally described species, one subspecies, and three further, thus far undescribed species: W. appressa, W. awasthii comb. nov., W. bahiensis sp. nov., W. brachyloba comb. nov., W. brouardii, W. chapadensis comb. nov., W. circumlobata sp. nov., W. decipioides, W. intensa comb. nov., W. ochraceofulva comb. nov., W. rubra sp. nov., W. sliwae sp. nov., W. sliwae ssp. subparviloba subsp. nov., W. subnitida comb. nov., W. texana, and W. variegata sp. nov. Eleven of 19 examined taxa are newly placed within this genus or confirmed to belong to it. Two species, W. awasthii and W. intensa, are transferred to Wetmoreana without additional analysis but based on previous studies. The W. brouardii and W. ochraceofulva species complexes are discussed in detail. Additionally, Caloplaca muelleri and C. rubina var. evolutior are transferred to Squamulea, and the latter is elevated to the species rank.
Fungi evolved right on track Lucking, Robert; Huhndorf, Sabine; Pfister, Donald H ...
Mycologia,
11/2009, Letnik:
101, Številka:
6
Journal Article
Recenzirano
Odprti dostop
Dating of fungal divergences with molecular clocks thus far has yielded highly inconsistent results. The origin of fungi was estimated at between 660 million and up to 2.15 billion y ago, and the ...divergence of the two major lineages of higher fungi, Ascomycota and Basidiomycota, at between 390 million y and up to 1.5 billion y ago. Assuming that these inconsistencies stem from various causes, we reassessed the systematic placement of the most important fungal fossil, Paleopyrenomycites, and recalibrated internally unconstrained, published molecular clock trees by applying uniform calibration points. As a result the origin of fungi was re-estimated at between 760 million and 1.06 billion y ago and the origin of the Ascomycota at 500-650 million y ago. These dates are much more consistent than previous estimates, even if based on the same phylogenies and molecular clock trees, and they are also much better in line with the fossil record of fungi and plants and the ecological interdependence between filamentous fungi and land plants. Our results do not provide evidence to suggest the existence of ancient protolichens as an alternative to explain the ecology of early terrestrial fungi in the absence of land plants.
True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. ...Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
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•Large-scale molecular phylogenetic synthesis of the third largest class of fungi.•Based on a cumulative supermatrix approach of >1100 species representing all orders.•Up to ca. 8kb ...from four nuclear and one mitochondrial genes were included per species.•Comprehensive revision of classification including 74 taxonomic conclusions.•A new module “Hypha” of the Mesquite software is introduced.
The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, ‘Candelariomycetidae’). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module (“Hypha”) of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach.
The question of how many species of
there are has occasioned much speculation, with figures mostly posited from around half a million to 10 million, and in one extreme case even a sizable portion of ...the spectacular number of 1 trillion. Here we examine new evidence from various sources to derive an updated estimate of global fungal diversity. The rates and patterns in the description of new species from the 1750s show no sign of approaching an asymptote and even accelerated in the 2010s after the advent of molecular approaches to species delimitation. Species recognition studies of (semi-)cryptic species hidden in morpho-species complexes suggest a weighted average ratio of about an order of magnitude for the number of species recognized after and before such studies. New evidence also comes from extrapolations of plant:fungus ratios, with information now being generated from environmental sequence studies, including comparisons of molecular and fieldwork data from the same sites. We further draw attention to undescribed species awaiting discovery in biodiversity hot spots in the tropics, little-explored habitats (such as lichen-inhabiting fungi), and material in collections awaiting study. We conclude that the commonly cited estimate of 1.5 million species is conservative and that the actual range is properly estimated at 2.2 to 3.8 million. With 120,000 currently accepted species, it appears that at best just 8%, and in the worst case scenario just 3%, are named so far. Improved estimates hinge particularly on reliable statistical and phylogenetic approaches to analyze the rapidly increasing amount of environmental sequence data.
The history of assigning ranks to fungi, as well as the relative importance of using divergence time estimates is reviewed. The paper pays tribute to the major mycological players, and especially to ...David Hawksworth on his 70th birthday and his contribution to fungal ranking in
Systema Ascomycetum
from 1982 to 1998. Following the conclusion of the latter series, the ranking continued with the
Outlines of Ascomycota
in 2007 and 2010 and more recently with specific classes in ‘Towards an outline of Sordariomycetes’ and ‘Families of Dothideomycetes’. Earlier classifications based on phenotype were certainly more subjective; however, remarkably many of these old arrangements have stood the test of time. More recently, phylogenetic analyses have provided evidence towards a natural classification, resulting in significant changes in many lineages. The classification arrangements however, are still subjective and dependent on the taxa analysed, resulting in different taxonomic interpretations and schemes, particularly when it comes to ranking. Thus, what have been considered as genera by some, have been introduced as families by others. More recently, estimation of divergence times using molecular clock methods have been used as objective evidence for higher ranking of taxa. A divergence period (i.e. 200–300 MYA) can be used as a criterion to infer when a group of related taxa evolved and what rank they should be given. We compiled data on divergence times for various higher ranking taxa in the Kingdom Fungi. The kingdom evolved 1000–1600 MYA (Stenian–Calymmian), while the presently accepted phyla evolved between 358 and 541 MYA (Devonian–Cambrian). Divergence times for subphyla are generally between 358 and 485 MYA (Devonian–Ordovician), those of classes 145–358 MYA (Jurassic–Carboniferous), subclasses 66–358 MYA (Cretaceous–Carboniferous), orders 23–252 MYA (Paleogene–Triassic), families 2.8–145 MYA (Neogene–Cretaceous), and genera 2.8–66 MYA (Neogene–Paleogene). Thus, there are wide discrepancies in the times different taxa diverged. We provide an overview over Ascomycota, showing how application of temporal banding could affect the recognition of higher taxa at certain rank levels. We then use Sordariomycetes as an example where we use divergence times to provide additional evidence to stabilize ranking of taxa below class level. We propose a series of evolutionary periods that could be used as a guide to determine the various higher ranks of fungi: phyla >550 MYA, subphyla 400–550 MYA; classes 300–400 MYA; subclasses 250–300 MYA, orders 150–250 MYA, and families 50–150 MYA. It is proposed that classification schemes and ranking of taxa should, where possible, incorporate a polyphasic approach including phylogeny, phenotype, and estimate of divergence times.
In the age of next-generation sequencing, the number of loci available for phylogenetic analyses has increased by orders of magnitude. But despite this dramatic increase in the amount of data, some ...phylogenomic studies have revealed rampant gene-tree discordance that can be caused by many historical processes, such as rapid diversification, gene duplication, or reticulate evolution. We used a target enrichment approach to sample 400 single-copy nuclear genes and estimate the phylogenetic relationships of 13 genera in the lichen-forming family Lobariaceae to address the effect of data type (nucleotides and amino acids) and phylogenetic reconstruction method (concatenation and species tree approaches). Furthermore, we examined datasets for evidence of historical processes, such as rapid diversification and reticulate evolution. We found incongruence associated with sequence data types (nucleotide vs. amino acid sequences) and with different methods of phylogenetic reconstruction (species tree vs. concatenation). The resulting phylogenetic trees provided evidence for rapid and reticulate evolution based on extremely short branches in the backbone of the phylogenies. The observed rapid and reticulate diversifications may explain conflicts among gene trees and the challenges to resolving evolutionary relationships. Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.
The following corrections and amendments are made to the 2016 classification of lichenized fungi published in the previous issue of this journal. Four families are added: Harpidiaceae (Pezizomycotina ...incertae sedis), with the two genera Euopsis and Harpidium; Pleomassariaceae (Pleosporales), with the genus Splanchonema; Squamarinaceae (Lecanorales), with the two genera Herteliana (moved from Ramalinaceae) and Squamarina (moved from Stereocaulaceae); and Trichosphaeriaceae (Sordariomycetes: Trichosphaeriales), with the genus Cresporhaphis. The following previously overlooked genera are also added: Allophoron (Pezizomycotina incertae sedis), Cresporhaphis (Trichosphaeriaceae), Gabura (Arctomiaceae), Julella (Trypetheliaceae), Knightiella (Icmadophilaceae), Porpidinia (Lecideaceae), Protoroccella (Roccellaceae), Psoromidium (Pannariaceae) and Tremotylium (Arthoniales incertae sedis). The classification is adjusted for four genera: Asteroporum (moved from Pezizomycotina incertae sedis to Dothideomycetes incertae sedis), Eremastrella (moved from Psoraceae to Lecideaceae), Hosseusia (moved from Pannariaceae to Lecanoromycetes incertae sedis) and Joergensenia (moved from Lecanorales incertae sedis to Pannariaceae). Further, the following overlooked generic synonyms are listed: Buscalionia (= Marcelaria nom. cons. prop.), Degeliella (= Psoromaria), Dirinastrum (= Buellia), Gymnographa (= Phaeographis), Kroswia (= Fuscopannaria), Marfloraea (= Lepra), Medusulina (= Fissurina), and Phaeographina (= Pliariona); the genus Anapyrenium is discussed as a potential synonym of Thelomma. Species numbers are adjusted for nine genera: Austrella (Pannariaceae; 3 spp.), Icmadophila (Icmadophilaceae; 5 spp.), Lepidocollema (Pannariaceae; 23 spp.), Massalongia (Massalongiaceae; 6 spp.), Parmeliella (Pannariaceae; 70 spp.), Psoromidium (Pannariaceae; 1 spp.), Pyrgillus (Pyrenulaceae; 7 spp.), Siphula (Icmadophilaceae; 17 spp.) and Synarthonia (Arthoniales incertae sedis; 5 spp.). The fossil lichen Honeggeriella (complexa) is validated by adding MycoBank registration numbers, the validity of the genus name Pallidogramme (Graphidaceae) is discussed and confirmed, and the authorship of the name Thallinocarpon (Lichinaceae) is clarified. Several genera are (continued to be) considered non-lichenized, namely Chaenothecopsis (Eurotiomycetes: Mycocaliciales: Sphinctrinaceae), Limboria (newly lectotypified with L. constellata; Pezizomycotina incertae sedis), Naetrocymbe (Dothideomycetes: Pleosporales: Naetrocymbaceae), and Obryzum (Dothideomycetes incertae sedis: Obryzaceae); the status of the genus Pleurotrema (Dothideomycetes incertae sedis: Pleurotremataceae) is also discussed. Seven genera are corrected to have molecular data available: Adelolecia, Aspiciliopsis, Aspilidea, Crocodia, Parasiphula, Vezdaea and Xylopsora. With these corrections, the number of lichenized species is now tabulated at 19,409 and the number of fungal genera, families, and orders including lichens at 1,002, 119, and 40, respectively.
It is now a decade since The International Commission on the Taxonomy of Fungi (ICTF) produced an overview of requirements and best practices for describing a new fungal species. In the meantime the ...International Code of Nomenclature for algae, fungi, and plants (ICNafp) has changed from its former name (the International Code of Botanical Nomenclature) and introduced new formal requirements for valid publication of species scientific names, including the separation of provisions specific to Fungi and organisms treated as fungi in a new Chapter F. Equally transformative have been changes in the data collection, data dissemination, and analytical tools available to mycologists. This paper provides an updated and expanded discussion of current publication requirements along with best practices for the description of new fungal species and publication of new names and for improving accessibility of their associated metadata that have developed over the last 10 years. Additionally, we provide: (1) model papers for different fungal groups and circumstances; (2) a checklist to simplify meeting (i) the requirements of the ICNafp to ensure the effective, valid and legitimate publication of names of new taxa, and (ii) minimally accepted standards for description; and, (3) templates for preparing standardized species descriptions.
A revised classification for the emended family
Graphidaceae
is proposed, based on recent phylogenetic studies, including the finding that three previously separated families (
Asterothyriaceae
,
...Gomphillaceae
,
Thelotremataceae
) are nested within
Graphidaceae
and in part polyphyletic. The family comprises three major clades which are here delimited as subfamilies
Fissurinoideae
,
Gomphilloideae
, and
Graphidoideae
. The latter is composed of three major clades which are formally delimited as tribes
Graphideae
,
Ocellularieae
, and
Thelotremateae
. In addition, three new genera are described to accommodate the
Ocellularia clandestina
(
Clandestinotrema
) group, the
Ocellularia cruentata
group
(Cruentotrema)
and
Myriotrema pycnoporellum
(
Pycnotrema
). Keys are provided for the species placed in the new genera.
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