| 1. |
- Divakar, Pradeep K., et al.
(författare)
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Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi
- 2015
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 208:4, s. 1217-1226
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Tidskriftsartikel (refereegranskat)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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| 2. |
- Crespo, Ana, et al.
(författare)
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Phylogenetic generic classification of parmelioid lichens (Parmeliaceae,Ascomycota) based on molecular, morphological and chemical evidence.
- 2010
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Ingår i: Taxon. - : John Wiley & Sons. - 0040-0262 .- 1996-8175. ; 59:6, s. 1735-1753
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Tidskriftsartikel (refereegranskat)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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| 3. |
- Schoch, Conrad L., et al.
(författare)
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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
- 2014
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Ingår i: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21
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Tidskriftsartikel (refereegranskat)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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| 4. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)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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| 5. |
- Alstrup, Vagn, et al.
(författare)
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Lichens from Tanzania and Kenya III : Macrolichens and calicioid lichens
- 2010
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Ingår i: Cryptogamie Mycologie. - 0181-1584 .- 1776-100X. ; 31:3, s. 333-351
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Tidskriftsartikel (refereegranskat)abstract
- 156 species of macrolichens and calicioid lichens are reported from Tanzania and Kenya. 28 species are new for Tanzania and 2 for Kenya. New for Africa are Hypotrachyna novella, H. physcioides, Melanelia panniformis, Physcidia squamulosa, and Xanthoparmelia microspora.
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| 6. |
- Crespo, Ana, et al.
(författare)
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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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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 44:2, s. 812-824
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Tidskriftsartikel (refereegranskat)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. |
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| 8. |
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| 9. |
- Thell, Arne, et al.
(författare)
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A review of the lichen family Parmeliaceae - history, phylogeny and current taxonomy.
- 2012
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Ingår i: Nordic Journal of Botany. - : Wiley. - 0107-055X. ; 30:6, s. 641-664
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Tidskriftsartikel (refereegranskat)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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| 10. |
- Zhao, Xin, et al.
(författare)
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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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Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 78:1, s. 293-304
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Tidskriftsartikel (refereegranskat)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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