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Asexual species with vegetative propagation of both symbiont partners (soredia) in lichens may harbor lower species diversity because they may indeed represent evolutionary dead ends or clones. In this study we aim to critically examine species boundaries in the sorediate lichen forming fungi Parmotrema reticulatum-Parmotrema pseudoreticulatum complex applying coalescent-based approaches and other recently developed DNA-based methods. To this end, we gathered 180 samples from Africa, Asia, Australasia, Europe, North and South America and generated sequences of internal transcribed spacer of nuclear ribosomal DNA (ITS) and DNA replication licensing factor MCM7 (MCM7). The dataset was analysed using different approaches such as traditional phylogeny-maximum likelihood and Bayesian-genetic distances, automatic barcode gap discovery and coalescent-based methods-PTP, GMYC, spedeSTEM and *Beast-in order to test congruence among results. Additionally, the divergence times were also estimated to elucidate diversification events. Delimitations inferred from the different analyses are comparable with only minor differences, and following a conservative approach we propose that the sampled specimens of the P. reticulatum-P. pseudoreticulatum complex belong to at least eight distinct species-level lineages. Seven are currently classified under P. reticulatum and one as P. pseudoreticulatum. In this work we discuss one of only few examples of cryptic species that have so far been found in sorediate reproducing lichen forming fungi. Additionally our estimates suggest a recent origin of the species complex-during the Miocene. Consequently, the wide distribution of several of the cryptic species has to be explained by intercontinental long-distance dispersal events.

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.)

Premise of the Study: In spite of the recent advances in generic and species circumscriptions and in recognizing species diversity in lichen-forming fungi, the timing of speciation and the factors that promote diversification in lichens remain largely unexplored. We used brown parmelioids as a model to assess the timing of divergence and explore the impact of geological and climatic events on lineage divergence and diversification in lichenized fungi. Additionally, to clarify the phylogenetic position of the species currently placed in Melanelia disjuncta group, we evaluated the taxonomic status and phylogenetic relationships within Parmeliaceae. •, Methods: Phylogenetic relationships and divergence time estimates were inferred from a four-loci data set. Alternative hypotheses were tested using Shimodaira-Hasegawa and expected likelihood weights tests. •, Key Results: The M. disjuncta group forms a strongly supported, monophyletic lineage independent from Melanelia s.s. The M. disjuncta clade arose ca. 23.1 million years ago (Ma). Our results suggest that most of the lineages within the clade diversified during the Miocene (17.6 to 11.2 Ma). The split of other brown parmelioids, such as Emodomelanelia-Melanelixia occurred ca. 41.70 Ma, and the radiation of Melanelixia began during the Eocene-Oligocene transition (ca. 33.75 Ma). •, Conclusions: Montanelia is described here as a new genus to accommodate species of the Melanelia disjuncta group. Further, the study indicates that the current species delimitation within the newly described genus requires revision. We provide evidence of lineage divergence of Montanelia at the Oligocene-Miocene boundary. Our results indicate that the diversification during Miocene would have happened during major mountain uplifts.

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).

We used a genetic distance approach in conjunction with molecular phylogeny to establish species boundaries and detect cryptic lineages in the Parmotrema reticulatum – P. pseudoreticulatum complex. The phylogeny of specimens from a broad geographic distribution was reconstructed from the internal transcribed spacer region. Pairwise genetic distances were calculated and compared to an intraspecific range defined for the parmelioid lichens to circumscribe species-level groups. Our results showed that P. reticulatum and P. pseudoreticulatum are polyphyletic, being comprised of at least seven well-supported lineages. In contrast, the genetic distance approach revealed ten cryptic lineages within the P. reticulatum – P. pseudoreticulatum complex. Neither morphology nor geography was conclusive in attempting to corroborate these genetic lineages. However FST indices suggest significant genetic differentiation between these lineages. Our results suggest that the morphology-based circumscriptions underestimated species in Parmotrema and that, in some cases, genetic distances may be used as an additional tool to determine species boundaries in morphologically cryptic species complexes. The most significant contribution of the present study is the application of a fast and accurate method to identify problematic groups and candidate species using the ITS locus with a genetic distances approach. [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]

This study focuses on European Usnea species with sorediate shrubby thalli, with the aim to evaluate the morphological and chemical separation of species in the light of molecular data. Twenty-two Usnea species, including widely distributed taxa such as U. diplotypus, U. fulvoreagens, U. glabrescens, U. lapponica, U. subfloridana, U. substerilis and U. wasmuthii, were included in the study using Bayesian and maximum parsimony analyses of nuclear ITS and beta-tubulin sequences. The analyses showed that: 1) most taxa that are morphologically well delimited are also distinct by means of molecular characters, 2) shrubby taxa in the section Usnea that are difficult to determine by traditional characters form a group of closely related but still genetically distinct entities, except U. diplotypus and U. substerilis which appear to be polyphyletic. The branch lengths differed largely between two parts of the ITS tree (sections Usnea and Ceratinae). Usnea intermedia is proposed as the sexually reproducing counterpart for the sorediate U. lapponica. Additionally, some new chemotypes of Usnea species were determined. [ABSTRACT FROM AUTHOR]

Two asexual reproductive strategies of the common lichen Pseudevernia furfuracea are described. Although the species propagates mainly by isidia, some specimens also show the development of soralia. Morphological, chemical and molecular analyses were performed on three such sorediate specimens from the Canary Islands, Morocco and Turkey. Maximum parsimony, maximum likelihood and Bayesian analyses indicate that: a) sorediate samples represent only a morphological variant of the reproductive mode and b) the separation of taxa (at species level or below) on the basis of their containing either olivetoric acid or physodic and oxyphysodic acids is not appropriate. In addition, a phylogenetic reconstruction of the genus Pseudevernia is presented for the first time. The tree shows two sister monophyletic clades, one containing American species (P. intensa, P. cladonia, P. consocians), and the second encompassing the P. furfuracea samples (including sorediate specimens). The biological and taxonomic significance of soralia in sorediate samples is discussed. [ABSTRACT FROM AUTHOR]

Abstract: 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 &y& Elsevier]