| 1. |
- Ariyawansa, Hiran A., et al.
(author)
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Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa
- 2015
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In: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 75, s. 27-274
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Journal article (peer-reviewed)abstract
- This paper is a compilation of notes on 142 fungal taxa, including five new families, 20 new genera, and 100 new species, representing a wide taxonomic and geographic range. The new families, Ascocylindricaceae, Caryosporaceae and Wicklowiaceae (Ascomycota) are introduced based on their distinct lineages and unique morphology. The new Dothideomycete genera Pseudomassariosphaeria (Amniculicolaceae), Heracleicola, Neodidymella and P s e u d o m i c ros p h a e r i o p s i s ( D id y m e l l a c e a e ) , P s e u d o p i t h o m y c e s ( D i d y m o s p h a e r i a c e a e ) , Brunneoclavispora, Neolophiostoma and Sulcosporium (Halotthiaceae), Lophiohelichrysum (Lophiostomataceae), G a l l i i c o l a , Popul o c re s c e n t i a a nd Va g i c o l a (Phaeosphaeriaceae), Ascocylindrica (Ascocylindricaceae), E l o n g a t o p e d i c e l l a t a ( R o u s s o e l l a c e a e ) , Pseudoasteromassaria (Latoruaceae) and Pseudomonodictys (Macrodiplodiopsidaceae) are introduced. The newly described species of Dothideomycetes (Ascomycota) are Pseudomassariosphaeria bromicola (Amniculicolaceae), Flammeascoma lignicola (Anteagloniaceae), Ascocylindrica marina (Ascocylindricaceae) , Lembosia xyliae (Asterinaceae), Diplodia crataegicola and Diplodia galiicola ( B o t r yosphae r i a cea e ) , Caryospor a aquat i c a (Caryosporaceae), Heracleicola premilcurensis and Neodi dymell a thai landi cum (Didymellaceae) , Pseudopithomyces palmicola (Didymosphaeriaceae), Floricola viticola (Floricolaceae), Brunneoclavispora bambusae, Neolophiostoma pigmentatum and Sulcosporium thailandica (Halotthiaceae), Pseudoasteromassaria fagi (Latoruaceae), Keissleriella dactylidicola (Lentitheciaceae), Lophiohelichrysum helichrysi (Lophiostomataceae), Aquasubmersa japonica (Lophiotremataceae) , Pseudomonodictys tectonae (Macrodiplodiopsidaceae), Microthyrium buxicola and Tumidispora shoreae (Microthyriaceae), Alloleptosphaeria clematidis, Allophaeosphaer i a c y t i s i , Allophaeosphae r i a subcylindrospora, Dematiopleospora luzulae, Entodesmium artemisiae, Galiicola pseudophaeosphaeria, Loratospora(Basidiomycota) are introduced together with a new genus Neoantrodiella (Neoantrodiellaceae), here based on both morphology coupled with molecular data. In the class Agaricomycetes, Agaricus pseudolangei, Agaricus haematinus, Agaricus atrodiscus and Agaricus exilissimus (Agaricaceae) , Amanita m e l l e i a l b a , Amanita pseudosychnopyramis and Amanita subparvipantherina (Amanitaceae), Entoloma calabrum, Cora barbulata, Dictyonema gomezianum and Inocybe granulosa (Inocybaceae), Xerocomellus sarnarii (Boletaceae), Cantharellus eucalyptorum, Cantharellus nigrescens, Cantharellus tricolor and Cantharellus variabilicolor (Cantharellaceae), Cortinarius alboamarescens, Cortinarius brunneoalbus, Cortinarius ochroamarus, Cortinarius putorius and Cortinarius seidlii (Cortinariaceae), Hymenochaete micropora and Hymenochaete subporioides (Hymenochaetaceae), Xylodon ramicida (Schizoporaceae), Colospora andalasii (Polyporaceae), Russula guangxiensis and Russula hakkae (Russulaceae), Tremella dirinariae, Tremella graphidis and Tremella pyrenulae (Tremellaceae) are introduced. Four new combinations Neoantrodiella gypsea, Neoantrodiella thujae (Neoantrodiellaceae), Punctulariopsis cremeoalbida, Punctulariopsis efibulata (Punctulariaceae) are also introduced here for the division Basidiomycota. Furthermore Absidia caatinguensis, Absidia koreana and Gongronella koreana (Cunninghamellaceae), Mortierella pisiformis and Mortierella formosana (Mortierellaceae) are newly introduced in the Zygomycota, while Neocallimastix cameroonii and Piromyces irregularis (Neocallimastigaceae) ar e i n t roduced i n the Neocallimastigomycota. Reference specimens or changes in classification and notes are provided for Alternaria ethzedia, Cucurbitaria ephedricola, Austropleospora, Austropleospora archidendri, Byssosphaeria rhodomphala, Lophiostoma caulium, Pseudopithomyces maydicus, Massariosphaeria, Neomassariosphaeria and Pestalotiopsis montellica.
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| 2. |
- Jayasiri, Subashini C., et al.
(author)
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The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts
- 2015
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In: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 74:1, s. 3-18
-
Journal article (peer-reviewed)abstract
- Taxonomic names are key links between various databases that store information on different organisms. Several global fungal nomenclural and taxonomic databases (notably Index Fungorum, Species Fungorum and MycoBank) can be sourced to find taxonomic details about fungi, while DNA sequence data can be sourced from NCBI, EBI and UNITE databases. Although the sequence data may be linked to a name, the quality of the metadata is variable and generally there is no corresponding link to images, descriptions or herbarium material. There is generally no way to establish the accuracy of the names in these genomic databases, other than whether the submission is from a reputable source. To tackle this problem, a new database (FacesofFungi), accessible at www.facesoffungi.org (FoF) has been established. This fungal database allows deposition of taxonomic data, phenotypic details and other useful data, which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database will also allow access to comprehensive metadata including descriptions of voucher and type specimens. This database is user-friendly, providing links and easy access between taxonomic ranks, with the classification system based primarily on molecular data (from the literature and via updated web-based phylogenetic trees), and to a lesser extent on morphological data when molecular data are unavailable. In FoF species are not only linked to the closest phylogenetic representatives, but also relevant data is provided, wherever available, on various applied aspects, such as ecological, industrial, quarantine and chemical uses. The data include the three main fungal groups (Ascomycota, Basidiomycota, Basal fungi) and fungus-like organisms. The FoF webpage is an output funded by the Mushroom Research Foundation which is an NGO with seven directors with mycological expertise. The webpage has 76 curators, and with the help of these specialists, FoF will provide an updated natural classification of the fungi, with illustrated accounts of species linked to molecular data. The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups. The structure and use of the database is then explained. We would like to invite all mycologists to contribute to these web pages.
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| 3. |
- Zamora, Juan Carlos, et al.
(author)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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In: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Journal article (peer-reviewed)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 4. |
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| 5. |
- Crespo, Ana, et al.
(author)
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Phylogenetic generic classification of parmelioid lichens (Parmeliaceae,Ascomycota) based on molecular, morphological and chemical evidence.
- 2010
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In: Taxon. - : John Wiley & Sons. - 0040-0262 .- 1996-8175. ; 59:6, s. 1735-1753
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Journal article (peer-reviewed)abstract
- Parmelioid lichens are a diverse and ubiquitous group of foliose lichens. Generic delimitation in parmelioid lichens has been in a state of flux since the late 1960s with the segregation of the large, heterogeneous genus Parmelia into numerous smaller genera. Recent molecular phylogenetic studies have demonstrated that some of these new genera were monophyletic, some were not, and others, previously believed to be unrelated, fell within single monophyletic groups, indicating the need for a revision of the generic delimitations. This study aims to give an overview of current knowledge of the major clades of all parmelioid lichens. For this, we assembled a dataset of 762 specimens, including 31 of 33 currently accepted parmelioid genera (and 63 of 84 accepted genera of Parmeliaceae). We performed maximum likelihood and Bayesian analyses of combined datasets including two, three and four loci. Based on these phylogenies and the correlation of morphological and chemical characters that characterize monophyletic groups, we accept 27 genera within nine main clades. We re-circumscribe several genera and reduce Parmelaria to synonymy with Parmotrema. Emodomelanelia Divakar & A. Crespo is described as a new genus (type: E. masonii). Nipponoparmelia (Kurok.) K.H. Moon, Y. Ohmura & Kashiw. ex A. Crespo & al. is elevated to generic rank and 15 new combinations are proposed (in the genera Flavoparmelia, Parmotrema, Myelochroa, Melanelixia and Nipponoparmelia). A short discussion of the accepted genera is provided and remaining challenges and areas requiring additional taxon sampling are identified.
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| 6. |
- Crespo, Ana, et al.
(author)
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Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene
- 2007
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In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 44:2, s. 812-824
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Journal article (peer-reviewed)abstract
- Parmeliaceae is the largest family of lichen-forming fungi with more than 2000 species and includes taxa with different growth forms. Morphology was widely employed to distinguish groups within this large, cosmopolitan family. In this study we test these morphology-based groupings using DNA sequence data from three nuclear and one mitochondrial marker from 1.20 taxa that include 59 genera and represent the morphological and chemical diversity in this lineage. Parmeliaceae is strongly supported as monophyletic and six well-supported main clades can be distinguished within the family. The relationships among them remain unresolved. The clades largely agree with the morphology-based groupings and only the placement of four of the genera studied is rejected by molecular data, while four other genera belong to clades previously unrecognised. The classification of these previously misplaced genera, however, has already been questioned by some authors based on morphological evidence. These results support morphological characters as important for the identification of monophyletic clades within Parmeliaceae.
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| 7. |
- Divakar, Pradeep K., et al.
(author)
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Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi
- 2015
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In: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 208:4, s. 1217-1226
-
Journal article (peer-reviewed)abstract
- We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes.
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| 8. |
- Grewe, F., et al.
(author)
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Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota)
- 2020
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In: IMA Fungus. - : Springer Science and Business Media LLC. - 2210-6340 .- 2210-6359. ; 11
-
Journal article (peer-reviewed)abstract
- Parmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenated-based Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow.
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| 9. |
- Kärnefelt, Ingvar, et al.
(author)
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Chemical evolution in the cetrarioid lichens.
- 1993
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In: Phytochemistry of lichenized ascomycetes - a festschrift in honour of Siegfried Huneck. Bibliotheca Lichenologica. - 1436-1698. ; 53, s. 115-127
-
Book chapter (peer-reviewed)abstract
- Abstract is not available
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| 10. |
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| 11. |
- Lumbsch, H. Thorsten, et al.
(author)
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One hundred new species of lichenized fungi: a signature of undiscovered global diversity
- 2011
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In: Phytotaxa. - 1179-3163. ; 18, s. 1-127
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Journal article (peer-reviewed)abstract
- The number of undescribed species of lichenized fungi has been estimated at roughly 10,000. Describing and cataloging these would take the existing number of taxonomists several decades; however, the support for taxonomy is in decline worldwide. In this paper we emphasize the dire need for taxonomic expertise in lichenology. We bring together 103 colleagues from institutions worldwide to describe a total of 100 new species of lichenized fungi, representing a wide taxonomic and geographic range. The newly described species are: Acarospora flavisparsa, A. janae, Aderkomyces thailandicus, Amandinea maritima, Ampliotrema cocosense, Anomomorpha lecanorina, A. tuberculata, Aspicilia mansourii, Bacidina sorediata, Badimia multiseptata, B. vezdana, Biatora epirotica, Buellia sulphurica, Bunodophoron pinnatum, Byssoloma spinulosum, Calopadia cinereopruinosa, C. editae, Caloplaca brownlieae, C. decipioides, C. digitaurea, C. magnussoniana, C. mereschkowskiana, C. yorkensis, Calvitimela uniseptata, Chapsa microspora, C. psoromica, C. rubropulveracea, C. thallotrema, Chiodecton pustuliferum, Cladonia mongkolsukii, Clypeopyrenis porinoides, Coccocarpia delicatula, Coenogonium flammeum, Cresponea ancistrosporelloides, Crocynia microphyllina, Dictyonema hernandezii, D. hirsutum, Diorygma microsporum, D. sticticum, Echinoplaca pernambucensis, E. schizidiifera, Eremithallus marusae, Everniastrum constictovexans, Fellhanera borbonica, Fibrillithecis sprucei, Fissurina astroisidiata, F. nigrolabiata, F. subcomparimuralis, Graphis caribica, G. cerradensis, G. itatiaiensis, G. marusa, Gyalideopsis chicaque, Gyrotrema papillatum, Harpidium gavilaniae, Hypogymnia amplexa, Hypotrachyna guatemalensis, H. indica, H. lueckingii, H. paracitrella, H. paraphyscioides, H. parasinuosa, Icmadophila eucalypti, Krogia microphylla, Lecanora mugambii, L. printzenii, L. xanthoplumosella, Lecidea lygommella, Lecidella greenii, Lempholemma corticola, Lepraria sekikaica, Lobariella sipmanii, Megalospora austropacifica, M. galapagoensis, Menegazzia endocrocea, Myriotrema endoflavescens, Ocellularia albobullata, O. vizcayensis, Ochrolechia insularis, Opegrapha viridipruinosa, Pannaria phyllidiata, Parmelia asiatica, Pertusaria conspersa, Phlyctis psoromica, Placopsis imshaugii, Platismatia wheeleri, Porina huainamdungensis, Ramalina hyrcana, R. stoffersii, Relicina colombiana, Rhizocarpon diploschistidina, Sticta venosa, Sagenidiopsis isidiata, Tapellaria albomarginata, Thelotrema fijiense, Tricharia nigriuncinata, Usnea galapagona, U. pallidocarpa, Verrucaria rhizicola, and Xanthomendoza rosmarieae. In addition, three new combinations are proposed: Fibrillithecis dehiscens, Lobariella botryoides, and Lobariella pallida.
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| 12. |
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| 13. |
- Miadlikowska, Jolanta, et al.
(author)
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A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.
- 2014
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In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1095-9513 .- 1055-7903. ; 79:Online 18 April 2014, s. 132-168
-
Journal article (peer-reviewed)abstract
- 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 635 newly generated and 3307 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.
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| 14. |
- Nelsen, Matthew P., et al.
(author)
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A reappraisal of Masonhalea (Parmeliaceae, Lecanorales) based on molecular and morphological data.
- 2013
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In: Lichenologist. - 0024-2829. ; 45:6, s. 729-738
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Journal article (peer-reviewed)abstract
- Previous studies have identified a close relationship between the monospecific Masonhalea richardsonii and Tuckermannopsis inermis. However, formal taxonomic changes were postponed until existing sequence data could be confirmed. Here we validate these data and discuss the transfer of T. inermis to Masonhalea (made by Lumbsch et al. in Thell & Moberg 2011), consider the morphological, anatomical and biogeographic similarities and differences between these two taxa. The two Masonhalea species both produce lateral apothecia, marginal pycnidia, a layer of cortical tissue beneath the pycnidial wall and bacillariform conidia.
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| 15. |
- Nelsen, Matthew P., et al.
(author)
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The cetrarioid core group revisited (Lecanorales: Parmeliaceae)
- 2011
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In: Lichenologist. - 0024-2829. ; 43:6, s. 537-551
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Journal article (peer-reviewed)abstract
- The cetrarioid core group has been the focus of numerous taxonomic and phylogenetic studies in recent years, yet the phylogenetic resolution and support among these clades remains unclear. Here we use four commonly employed loci to estimate if their use increases phylogenetic resolution and support. The present study largely confirms the topologies of previous studies, but with increased support. Approximately half of the genera in the cetrarioid core were not monophyletic. Melanelia sorediella was clustered within Cetrariella, and the combination Cetrariella sorediella (Lettau) V. J. Rico & A. Thell comb. nov. is made. Additionally, the genus Flavocetrariella was supported as part of Nephromopsis and is considered to be a synonym of the latter. Finally, a comparison of genetic distances shows that the maximum intrageneric genetic distance encompassed by many cetrarioid genera is lower than that of many other genera in Parmeliaceae.
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| 16. |
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| 17. |
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| 18. |
- Poengsungnoen, Vasun, et al.
(author)
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Phylogenetic analysis reveals two morphologically unique new species in the genera Astrochapsa and Nitidochapsa (lichenized Ascomycota Graphidaceae)
- 2014
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In: Phytotaxa. - : Magnolia Press. - 1179-3163 .- 1179-3155. ; 189, s. 268-281
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Journal article (peer-reviewed)abstract
- Graphidaceae is the largest family of tropical crustose lichens, with nearly 2,400 known species, and exhibits a large diversity of ascoma morphologies. Ascomata that open by triangular marginal lobules that become recurved to form geaster-like fruiting bodies, so-called chroodiscoid ascomata, were recently shown to have evolved independently several times within the family. A special type of such ascomata is the gyrotremoid form in which the hymenium and excipulum are organized in concentric rings. In the present study, we address the phylogenetic position of two chroodiscoid species collected in Thailand that form aggregate or gyrotremoid, chroodiscoid ascomata, using a molecular phylogeny of nuclear LSU and mitochondrial SSU rDNA sequences of 92 Graphidaceae. Our morphological, chemical and phylogenetic analyses show that one species is an undescribed species in the genus Astrochapsa, here newly described as A. kalbii Poengsungnoen, Lücking & Lumbsch, with a unique, gyrotremoid ascoma morphology. The second species belongs in the recently established genus Nitidochapsa, which is a close relative of Ocellularia, and is here described as new species N. siamensis Poengsungnoen, Lücking & Lumbsch. Based on these findings, three further new combinations are proposed in the genus Nitidochapsa, viz. N. aggregata (Hale) Poengsungnoen, Lücking & Lumbsch, N. phlyctidea (Vain.) Lücking & Lumbsch, and N. stictoides (Leight.) Tehler, Lücking & Lumbsch. A key to all five species is presented.
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| 19. |
- Schoch, Conrad L., et al.
(author)
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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
- 2014
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In: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21
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Journal article (peer-reviewed)abstract
- DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
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| 20. |
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| 21. |
- Thell, Arne, et al.
(author)
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A review of the lichen family Parmeliaceae - history, phylogeny and current taxonomy.
- 2012
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In: Nordic Journal of Botany. - : Wiley. - 0107-055X. ; 30:6, s. 641-664
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Journal article (peer-reviewed)abstract
- The largest family of lichen-forming fungi, the Parmeliaceae, is reviewed. It includes 79 genera in current use and ca 2726 species, a large majority of which belong to one of five main clades: the parmelioid, cetrarioid, usneoid, alectorioid and hypogymnioid. However, 21 genera are positioned outside these clades, and four genera in current use still lack DNA- data. The family has been shown to be monophyletic and the generic classification is relatively well-settled compared with other lecanoralean families. Each clade and its genera are presented here with the latest results from phylogenetic analyses and current taxonomy. In addition, a historical outline of the family and its most prominent researchers is provided.
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| 22. |
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| 23. |
- Zhao, Xin, et al.
(author)
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Towards a revised generic classification of lecanoroid lichens (Lecanoraceae, Ascomycota) based on molecular, morphological and chemical evidence
- 2016
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In: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 78:1, s. 293-304
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Journal article (peer-reviewed)abstract
- The phylogenetic relationship of lecanoroid lichens is studied using two data sets: 1) a 2-locus data set including 251 OTUs representing 150 species, and 2) a 6-locus data set with 82 OTUs representing 53 species. The genus Lecanora as currently circumscribed is shown to be highly polyphyletic and several genera, including Adelolecia, Arctopeltis, Bryonora, Carbonea, Frutidella, Lecidella, Miriquidica, Palicella, Protoparmeliopsis, Pyrrhospora, and Rhizoplaca are nested within Lecanora sensu lato. A core group of Lecanora is supported as monophyletic and includes species of the L. carpinea, L. rupicola, and L. subcarnea groups, and a core group of the L. subfusca group. Three monophyletic clades that are well supported in our analyses and well characterized by phenotypical characters are accepted here: 1) Myriolecis to accommodate the Lecanora dispersa group and Arctopeltis; 2) Protoparmeliopsis for the L. muralis group; and 3) Rhizoplaca is emended to include three placodioid taxa previously classified in Lecanora (L. novomexicana. L. opiniconensis, L. phaedrophthalma), whereas R. aspidophora and R. peltata are excluded from Rhizoplaca. The latter is transferred into Protoparmeliopsis. Lecidella is strongly supported as a monophyletic group. Our studies indicate the presence of additional clades of species currently placed in Lecanora sensu lato that warrant taxonomic recognition but additional data will be necessary before the circumscription of these entities is fully understood. 37 new combinations are proposed into the genera Myriolecis (30), Protoparmeliopsis (2), and Rhizoplaca (5).
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