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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., (© 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.)

The species delimitation in fungi is currently in flux. A growing body of evidence shows that the morphology-based species circumscription underestimates the number of existing species. The large and ever growing number of DNA sequence data of fungi makes it possible to use these to identify potential cases of hidden species, which then need to be studied with extensive taxon samplings. We used Parmeliaceae, one of the largest families of lichenized fungi as a model. Intra- and interspecific distances derived from maximum-likelihood phylogenetic trees inferred from 491 nuclear ITS rDNA sequences were examined for five major clades of parmelioid lichens. The intra- and interspecific distances were well separated in most cases allowing the calculation of a threshold, with exceptions of highly deviating distances in a few cases. These situations are shown to be taxa in which the current delimitation needs revision. Thus the analysis of the distance distributions is shown to be a powerful tool for identifying species complexes., (Copyright 2010 Elsevier Inc. All rights reserved.)

A phylogenetic and taxonomic study of the Physconia distorta morphotype complex was undertaken using ITS nu-rDNA as a molecular marker to re-evaluate this group. The analysis incorporated several samples of European P. distorta and also of American and European populations, recently named as P. americana. The phylogenetic analysis revealed that P. distorta and the European population of P. americana form two monophyletic and partially sympatric species and that both are distinct from the American species P. americana. Because differences in upper cortex anatomy had been used in establishing P. americana as distinct from P. distorta, the anatomy of the upper cortex was restudied in all three of these taxa, and notable differences were revealed. Our study confirmed that the upper cortex of P. distorta is prosoplectenchymatous with thick hyphal cell walls and narrow lumina, and that American specimens of P. americana have a typical paraplectenchymatous upper cortex. The cortex anatomy of both of these looks essentially the same in both longitudinal and transverse sections. Conversely, the European specimens that have been called P. americana are different from both of these. The cells of the upper cortex are rather thin walled, and in transverse lobe sections the cortex closely resembles a paraplectenchyma. However, in longitudinal lobe sections these thin walled cells can be seen to be elongate and ramified, obviously hyphal in nature, and better meeting the criteria of a prosoplectenchyma. The results confirmed the evolutionary pattern and taxonomic assessment of the anatomy of the upper cortex in the genus Physconia and revealed a common undescribed species (P. thorstenii sp. nov.) that can be added to the North African and Southern Euro-Asiatic lichen flora.

Tropical regions harbor rich biodiversity but are relatively poorly explored, especially in lesser known taxonomic groups, such as lichenized fungi. In addition, the identification of species is complicated by frequent occurrence of cryptic species and the plasticity of phenotypic features traditionally used to identify species. Here, we aim to explore species diversity and provide tools for accurate sample identification of the genus Parmotrema from rainforests in Thailand. We gathered a three-locus DNA sequence data set and this was analysed in phylogenetic and DNA barcode frameworks. While some morpho-species were recovered as monophyletic, others did not form monophyletic groups. Our study unmasked cryptic lineages in Parmotrema species distributed in the tropics and show that phenotype-based sample identification may underestimate species diversity in this group of lichens. Further, genetic distances based on ITS DNA sequences (i.e. DNA barcode approach) were shown to be a valuable tool for sample identification. In addition, our study highlights the need for taxonomic reexamination of the following phenotypically delimited species: P. corniculans, P. crinitum, P. haitiense, P. maclayanum, P. perlatum and P. subtinctorium. [ABSTRACT FROM AUTHOR]

Hypotrachyna is a speciose genus of primarily tropical and oceanic lichen-forming fungi. It includes species with distinct distribution patterns, such as pantropical, restricted and disjunct species. We used a dataset of mitochondrial SSU, nuclear ITS and LSU ribosomal DNA from 89 specimens to study the historical biogeography of the genus. We employed Bayesian and maximum likelihood approaches for phylogenetic analyses, a likelihood-based approach to ancestral area estimation, and a Bayesian approach to estimate divergence times of major lineages within the genus based on molecular evolutionary rates for ITS and a secondary calibration point at the Hypotrachyna clade – Parmeliopsis split. Our analyses suggest that the genus might have originated in the Neotropics during the Eocene and that the split of major lineages happened primarily during the Eocene and Oligocene. The major diversification within those clades is estimated to have occurred during the Miocene. Pantropical species distributions are explained by long-distance dispersal. A number of currently accepted species were found to be non-monophyletic, illustrating that the delimitation of species in the genus needs attention. [ABSTRACT FROM AUTHOR]

Recently, the number of cryptic species known has increased considerably, showing that species diversity has in many cases been underestimated in the past. Parmelia sulcata is a widely distributed species and one of the most common taxa in temperate Europe. The first intra-specific molecular studies on P. sulcata showed an unexpectedly high genetic variability. In the present work, we study the biodiversity of this taxon including specimens from four continents and using three molecular markers (nuITS, nuIGS rDNA, and partial β-tubulin gene). Two monophyletic groups of P. sulcata were encountered; one of these is epitypified as P. sulcata s. str and the other one is segregated as the new cryptic species P. encryptata sp. nov. Issues surrounding the lectotypification of Parmelia sulcata have also been elucidated. [ABSTRACT FROM AUTHOR]

Parmelina tiliacea is a common, widely distributed species in south-western Europe, easily identifiable by morphology and much used as an air pollution bioindicator in many regions. A molecular phylogenetic survey of samples from many geographical areas, using Maximum Parsimony and Bayesian inference of nuITS and mtLSU rDNA regions, revealed a group of samples geographically restricted to a small region of the Iberian Peninsula and genetically separated from the other P. tiliacea specimens studied. These samples are morphologically indistinguishable from P. tiliacea, apart from subtle anatomical characters in the ascomata (hyphae of the exciple and ascospore width), which are frequently absent. Although geographically different, the two taxa occupy similar habitats and are even sympatric in some areas, indicating that they do not exchange genetic material. This previously overlooked, and apparently endemic lineage, is described as P. cryptotiliacea sp. nov., and the name Lichen tiliaceus is epitypified by a sequenced specimen to fix the application of Parmelina tiliacea to the widespread genotype. A second unexpected result was the discovery that the morphologically distinct P. pastillifera was nested within P. tiliacea. These two cases stress the need to use molecular tools to elucidate species concepts even within widespread morphologically well-characterized macrolichens. Such investigations are necessary to improve our understanding and estimation of biodiversity, and to facilitate the development of sound biodiversity conservation strategies for lichens. [ABSTRACT FROM AUTHOR]

Abstract: The phylogenetic position of Trypetheliaceae was studied using partial sequences of the mtSSU and nuLSU rDNA of 100 and 110 ascomycetes, respectively, including 48 newly obtained sequences. Our analysis confirms Trypetheliaceae as monophyletic and places the family in Dothideomycetes. Pyrenulaceae, which were previously classified with Trypetheliaceae in Pyrenulales or Melanommatales, are supported as belonging to Chaetothyriomycetes. Monophyly of Pyrenulales, including Trypetheliaceae is rejected using three independent test methods. Monophyly of Arthopyreniaceae plus Trypetheliaceae, the two families including lichen-forming fungi in Dothideomycetes, is also rejected, as well as a placement of Trypetheliaceae in Pleosporales (incl. Melanommatales). [Copyright &y& Elsevier]

The phylogenetic position of the European crustose pioneer lichen Moelleropsis (Biatora) humida (Kullhem) Coppins & P. M. Jørg. is studied using partial sequences of the mitochondrial SSU and nuclear LSU rDNA of 64 ascomycetes, including sequences of all known species of Arctomiaceae. The analysis places M. humida in the Arctomiaceae with strong support as sister to the Tasmanian genus Wawea. The genus Arctomia is monophyletic and sister-group to the Wawea+Moelleropsis humida clade. The new genus Gregorella is described to accommodate Moelleropsis humida and the new combination Gregorella humida (Kullhem) Lumbsch is proposed. The ontogeny of the ascomata of Gregorella humida is similar to that of other Arctomiaceae, in that the generative tissue is formed on a thallus outgrowth. The Arctomiaceae did not cluster with the bulk of cyanobacterial lichens in the Lecanorales suborder Peltigerineae (or Peltigerales), but is part of Ostropomycetidae. The closest relative of Arctomiaceae could not be identified, since the relationships of major clades within Ostropomycetidae lacked support. [ABSTRACT FROM AUTHOR]