| 1. |
- Fedorenko, Natalya, et al.
(författare)
-
A phylogenetic analysis of xanthorioid lichens (Teloschistaceae, Ascomycota) based on ITS and mtSSU sequences
- 2009
-
Ingår i: Bibliotheca Lichenologica. Diversity of Lichenology - Anniversary Volume.. - 1436-1698. ; 100, s. 49-84
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- A phylogenetic analysis of xanthorioid lichens of the lichen family Teloschistaceae, based on ITS rDNA and mtSSU sequences, is presented. The data set includes 201 specimens representing 50 species, covering the xanthorioid lichen group, which resulted in 183 new sequences. Five well-supported groups were recognized in the MP analysis: 1) Seirophora, 2) the Xanthoria s. str.-Xanthodactylon group, 3) the Xanthoria candelaria group, 4) Rusavskia, and 5) the Xanthomendoza group. In addition, two of the five groups included seven well-supported subgroups: 2a) the Xanthoria parietina group, 2b) Jackelixia, 2c) the Xanthodactylon flammeum group, 5a) Oxneria, 5b) the Xanthomendoza novozelandica group, 5c) the X. mendozae group, and 5d) the X. poeltii group. The groups are circumscribed, and alternative ways to treat the taxonomy of xanthorioid lichens, based on the presented phylogeny, are discussed. Representatives of the genera Caloplaca, Fulgensia and Teloschistes, related with xanthorioid lichens, are included in the phylogenetic tree and their status is briefly discussed. Three new genera, i. e., Jackelixia, Ovealmbornia and Xanthokarrooa are described and 15 new combinations are proposed.
|
|
| 2. |
- Fedorenko, Nataliya M., et al.
(författare)
-
Molecular phylogeny of xanthorioid lichens (Teloschistaceae, Ascomycota), with notes on their morphology.
- 2012
-
Ingår i: Systematics, biodiversity and ecology of lichens. Bibliotheca Lichenologica.. - 1436-1698. ; 108, s. 45-64
-
Bokkapitel (refereegranskat)abstract
- Five new monophyletic groups of xanthorioid lichens have been identified by phylogenetic analyses using nuclear ITS and 18S and mitochondrial 12 mt and 23 mt sequences. As a consequence, the following new genera are described: Gallowayella, Jesmurraya, Honeggeria, Massjukiella and Martinjahnsia. New combinations for 26 species are proposed: Gallowayella aphrodites, G. borealis, G. concinna, G. coppinsii, G. fulva, G. hasseana, G. hermonii, G. montana, G. galericulata, G. gallowayi, G. oregana, G. poeltii, G. sogdiana, G. tibellii, G. weberi, G. wetmorei, Honeggeria rosmarieae, Jesmurraya novozelandica, Massjukiella alaskana, M. candelaria, M. kaernefeltii, M. nowakii, M. polycarpa, M. ucrainica, M. ucrainica ssp. marginata and Martinjahnsia resendei.
|
|
| 3. |
- Gaya, Ester, et al.
(författare)
-
Implementing a cumulative supermatrix approach for a comprehensive phylogenetic study of the Teloschistales (Pezizomycotina, Ascomycota)
- 2012
-
Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1095-9513 .- 1055-7903. ; 63:2, s. 374-387
-
Tidskriftsartikel (refereegranskat)abstract
- The resolution of the phylogenetic relationships within the order Teloschistales (Ascomycota, lichen-forming-fungi), with nearly 2000 known species and outstanding phenotypic diversity, has been hindered by the limitation in the resolving power that single-locus or two-locus phylogenetic studies have provided to date. In this context, an extensive taxon sampling within the Teloschistales with more loci (especially nuclear protein-coding genes) was needed to confront the current taxonomic delimitations and to understand evolutionary trends within this order. Comprehensive maximum likelihood and Bayesian analyses were performed based on seven loci using a cumulative supermatrix approach, including protein-coding genes RPB1 and RPB2 in addition to nuclear and mitochondrial ribosomal RNA-coding genes. We included 167 taxa representing 12 of the 15 genera recognized within the currently accepted Teloschistineae, 22 of the 43 genera within the Physciineae, 49 genera of the closely related orders Lecanorales, Lecideales, and Peltigerales, and the dubiously placed family Brigantiaeaceae and genus Sipmaniella. Although the progressive addition of taxa (cumulative supermatrix approach) with increasing amounts of missing data did not dramatically affect the loss of support and resolution, the monophyly of the Teloschistales in the current sense was inconsistent, depending on the loci-taxa combination analyzed. Therefore, we propose a new, but provisional, classification for the re-circumscribed orders Caliciales and Teloschistales (previously referred to as Physciineae and Teloschistineae, respectively). We report here that the family Brigantiaeaceae, previously regarded as incertae sedis within the subclass Lecanoromycetidae, and Sipmaniella, are members of the Teloschistales in a strict sense. Within this order, one lineage led to the diversification of the mostly epiphytic crustose Brigantiaeaceae and Letrouitiaceae, with a circumpacific center of diversity and found mostly in the tropics. The other main lineage led to another epiphytic crustose family, mostly tropical, and with an Australasian center of diversity the Megalosporaceae - which is sister to the mainly rock-inhabiting, cosmopolitan, and species rich Teloschistaceae, with a diversity of growth habits ranging from crustose to fruticose. Our results confirm the use of a cumulative supermatrix approach as a viable method to generate comprehensive phylogenies summarizing relationships of taxa with multi-locus to single locus data. (C) 2012 Elsevier Inc. All rights reserved.
|
|
| 4. |
- Hognabba, Filip, et al.
(författare)
-
Phylogenetic position of the crustose Stereocaulon species
- 2014
-
Ingår i: The Lichenologist. - 0024-2829 .- 1096-1135. ; 46:1, s. 103-114
-
Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic relationships of Stereocaulon with emphasis on the crustose taxa were studied based on nuclear ribosomal ITS1-5.8S-ITS2 and partial beta-tubulin sequences. The placement of four of the six crustose species currently included in the genus has previously been confirmed based on molecular data. It has, however, remained unresolved whether the crustose growth form is a plesiomorphic or apomorphic feature within Stereocaulon, due to contradictory placements of the crustose species in earlier studies. The aim of this study was to clarify the position of the crustose species by including additional data, especially of S. nivale and S. plicatile, which have not been included in previous analyses. The inclusion of S. plicatile in the genus is of particular interest as it is the only species in the genus with submurifrom to muriform ascospores. Altogether 37 specimens representing 31 species of the ingroup, including all the crustose Stereocaulon species, were incorporated in the analyses. Conventional, as well as direct optimization parsimony, maximum likelihood and Bayesian analyses were performed. The results show that the crustose species do not form a monophyletic entity and that the crustose growth form is a plesiomorphic feature within Stereocaulon. The crustose S. nivale and S. plicatile are nested within the genus and their inclusion in Stereocaulon is thereby confirmed. The nested position of S. plicatile indicates that the submuriform to muriform spore type has been gained independently within the genus. Here, S. plicatile is also reported for the first time from Scandinavia.
|
|
| 5. |
- Högnabba, Filip, et al.
(författare)
-
Evolution of cyanobacterial symbioses in Ascomycota.
- 2009
-
Ingår i: Biodiversity and Ecology of lichens. Liber Amicorum Harrie Sipman. Bibliotheca Lichenologica. - 1436-1698. - 9783443580780 ; 99, s. 163-184
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Two fifths of the species in Ascomycota are lichen-forming, of which 10% and 3-4% have cyanobacteria as the primary and secondary photobionts respectively. To study the evolution of cyanobacterial symbioses, the phylogenetic relationships within the Ascomycota have been reconstructed. Phylogenetic analyses were made using direct optimization of nuclear SSU and LSU rDNA sequences under the parsimony optimality criterion. Our results indicate repeated evolution of the mutualistic assemblages between fungi and cyanobacteria. The stability of the cyanobacterial symbioses and the effects of photobiont alteration on the evolution of ascomycetes are discussed, as is the taxonomy of some cyanobacterial lichen taxa, and some future perspectives on the evolution of these ecologically important assemblages.
|
|
| 6. |
- Högnabba, Filip, et al.
(författare)
-
Phylogenetic relationships and evolution of photobiont associations in the Lobariaceae (Peltigerales, Lecanoromycetes, Ascomycota)
- 2009
-
Ingår i: Bibliotheca Lichenologica. Diversity of Lichenology - Anniversary Volume.. - 1436-1698. ; 100, s. 157-187
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Phylogenetic relationships of the family Lobariaceae (Lecanoromycetes, Ascomycota) were reconstructed using direct optimization of nuclear ITS and LSU, and mitochondrial SSU rDNA sequences. Delimitations of the genera currently included in the family were investigated. Relationships of austral temperate taxa occurring in New Zealand, Australia and southern South America were studied in detail. Finally, we studied the evolution of the symbiotic associations found in the family which proved to be monophyletic. Sticta, with the exception of S. oroborealis, but including Dendriscocaulon dendroides, was found to be monophyletic while the genera Lobaria and Pseudocyphellaria turned out to be non-monophyletic. The status of Lobariella, and Lobarina as independent genera was not supported. Relationships of southern temperate Sticta species indicate a common Gondwanan ancestor. In rest of the family, species from the austral temperate zone group together with more widespread species. The ancestor of the Lobariaceae was associated with cyanobacteria. Green algal photobionts have subsequently been acquired repeatedly, but also repeatedly lost within the family. The acquisition of green algae has not resulted in a complete loss of the cyanobacterial photobiont. The cyanobacterial symbioses therefore seem to be more stable than those with green algae.
|
|
| 7. |
- Kondratyuk, Sergey Y., et al.
(författare)
-
Phylogenetic analysis of lichen-forming fungi of the family Teloschistaceae (Ascomycota) after nuclear and mitochondrial DNA sequences.
- 2013
-
Ingår i: Molecular phylogeny and recent taxonomy of terrestrial spore plant.. - 9789660013322 ; , s. 7-57
-
Bokkapitel (refereegranskat)abstract
- Results of molecular phylogenetic analysis after nuclear (18S LSU, ITS1/ITS2), mitochondrial (12S and 23S SSU) and chloroplast DNA of lichen-forming fungi, symbiotic and terrestrial algae as well as microscopic filamentous fungi obtained for the first time in Ukraine are compared with recent data on morphology, anatomy and biochemical characters. Taxonomical treatment of several groups of lichen-forming fungi, i.e. families Teloschistaceae and Physciaceae as well as symbiotic algae of the Trebouxiophyceae and terrestrial algae of the Myrmeciaceae and Klebsormidiaceae as well as original keys for identification of spore plants mentioned are provided. For botanists, mycologists, phycologists, ecologists, tutors and students of biological, agricultural and forestry faculties of universities.
|
|
| 8. |
- Lohtander, Katileena, et al.
(författare)
-
New entities in Physcia aipolia-P-caesia group (Physciaceae, Ascomycetes) : an analysis based on mtSSU, ITS, group I intron and betatubulin sequences
- 2009
-
Ingår i: Annales Botanici Fennici. - 0003-3847 .- 1797-2442. ; 46:1, s. 43-53
-
Tidskriftsartikel (refereegranskat)abstract
- We have revisited the phylogenetic evaluation of the Physcia aipolia-P. caesia lichen group (sect. Caesiae; Physciaceae, Lecanorales) in order to investigate whether new sequence data and extensive sampling can help us to understand the phylogenetic relationships in that group. We combined partial mtSSU DNA data with two previously used nuclear gene regions (betatubulin, ITS) and a group I intron. We also compared the resulting phylogenies with chemical and morphological characters. Altogether 52 specimens of the P. aipolia-P. caesia group were analysed. Direct optimization of the molecular data revealed several well-supported groups. Our results essentially agreed with those of the earlier studies, and we were able to confirm the independent taxonomic status of some controversial morphotaxa. We also discovered at least two distinct clades that potentially represent species new to science. A new nomenclatural combination, Physcia alnophila (Vain.) Loht., Moberg, Myllys & Tehler, is proposed.
|
|
| 9. |
- Miadlikowska, Jolanta, et al.
(författare)
-
A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.
- 2014
-
Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1095-9513 .- 1055-7903. ; 79:Online 18 April 2014, s. 132-168
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 10. |
- Schoch, Conrad L., et al.
(författare)
-
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
- 2014
-
Ingår i: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21
-
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.
|
|
| 11. |
- Sohrabi, Mohammad, et al.
(författare)
-
Aspicilia rogeri sp. nov. (Megasporaceae), and other allied vagrant species in North America
- 2011
-
Ingår i: The Bryologist. - : American Bryological and Lichenological Society. - 0007-2745 .- 1938-4378. ; 114:1, s. 178-189
-
Tidskriftsartikel (refereegranskat)abstract
- A short revision of the vagrant Aspicilia species of North America is presented based on morphological, molecular and ecological data. Vagrant Aspicilia are common lichens throughout the steppes of the western United States and in southwestern parts of Canada. Species delimitation of these lichens is difficult because of the paucity of morphological characters and large degree of variation. Inferences from nuITSrDNA sequences reveals that the North American specimens of A. fruticulosa are not most closely related to their Eurasian populations but instead share a unique ancestor with A. hispida. The specimens of A. fruticulosa from the New World are hereby recognized as a distinct species, A. rogeri. Its differentiation from the similar A. fruticulosa and A. hispida is discussed. The exclusion of A. fruticulosa from the N. American checklist is proposed temporarily.
|
|
| 12. |
- Thell, Arne, et al.
(författare)
-
Phylogeny of the cetrarioid core (Parmeliaceae) based on five genetic markers
- 2009
-
Ingår i: Lichenologist. - 0024-2829. ; 41:5, s. 489-511
-
Tidskriftsartikel (refereegranskat)abstract
- Fourteen genera belong to a monophyletic core of cetrarioid lichens, Ahtiana, Allocetraria, Arctocetraria, Cetraria, Cetrariella, Cetreliopsis, Flavocetraria, Kaernefeltia, Masonhalea, Nephromopsis, Tuckermanella, Tuckermannopsis, Usnocetraria and Vulpicida. A total of 71 samples representing 65 species (of 90 worldwide) and all type species of the genera are included in phylogentic analyses based on a complete ITS matrix and incomplete sets of group I intron, β-tubulin, GAPDH and mtSSU sequences. Eleven of the species included in the study are analysed phylogenetically for the first time, and of the 178 sequences, 67 are newly constructed. Two phylogenetic trees, one based solely on the complete ITS-matrix and a second based on total information, are similar, but not entirely identical. About half of the species are gathered in a strongly supported clade composed of the genera Allocetraria, Cetraria s. str., Cetrariella and Vulpicida. Arctocetraria, Cetreliopsis, Kaernefeltia and Tuckermanella are monophyletic genera, whereas Cetraria, Flavocetraria and Tuckermannopsis are polyphyletic. The taxonomy in current use is compared with the phylogenetic results, and future, probable or potential adjustments to the phylogeny are discussed. The single non-DNA character with a strong correlation to phylogeny based on DNA-sequences is conidial shape. The secondary chemistry of the poorly known species Cetraria annae is analyzed for the first time; the cortex contains usnic acid and atranorin, whereas isonephrosterinic, nephrosterinic, lichesterinic, protolichesterinic and squamatic acids occur in the medulla. Notes on the anatomy of Cetraria annae and Flavocetraria minuscula are also provided.
|
|
| 13. |
- Zamora, Juan Carlos, et al.
(författare)
-
Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
-
Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
-
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.
|
|
