Arthonia epipolytropa Hafellner & Grube and Arthonia subclemens Hafellner, Grube & Muggia are described as new to science. Both are specific parasites of Lecanora polytropa s. lat., but of differing pathogenicity and of very different appearance. Whereas the clearly parasitic Arthonia epipolytropa with its agglomerated ascomata is presently known with certainty from a number of localities along the arch of the Alps (Austria, Italy, Switzerland), other parts of Europe (Norway, Albania) and northern America (USA), the less harmful A. subclemens with its isolated sunken ascomata is currently known only from a small number of localities in the Eastern Alps (Austria, Italy) and various mountain ranges in southern Europe (Spain, North Macedonia, Greece). The species are compared with other Arthonia species known from Lecanora or one of its recently segregated genera. A key to the fungi regularly found on Lecanora polytropa s. lat. is presented.

Recent direct numerical simulation studies of canonical shock–isotropic turbulence interactions (SITIs) in the highly compressible regime exhibit streamwise Reynolds stress amplification that is significantly higher in some cases than in previous studies; an explanation is offered based on a relatively high Mach number combined with significant dilatational energy in the incident flow. Some cases exhibit a loss of amplification that is associated with a highly perturbed shock structure as the flow parameters approach the threshold between the wrinkled and broken shock regimes. The shock structure perturbations due to the highly compressible incident turbulence match those proposed by Donzis (Phys. Fluids, vol. 24, 2012, 126101) relatively well, but due to the presence of thermodynamic fluctuations in addition to velocity fluctuations in the incident flow, we propose a generalized parametrization based on the root-mean-square Mach number fluctuation in place of the turbulence Mach number. This is found to improve the collapse of the shock structure data, suggesting that the wrinkled–broken shock regime threshold determined previously for vortical turbulence (Donzis, Phys. Fluids, vol. 24, 2012, 126101; Larsson et al., J. Fluid Mech., vol. 717, 2013, pp. 293–321) can be applied to more general isotropic inflow fields using the proposed parametrization.

Linear interaction analysis (LIA) predicts that isotropic vortical turbulence interacting with a normal shock wave at Mach 2 or greater produces a post-shock Reynolds stress tensor whose transverse components $R_{22}$ and $R_{33}$ are greater than the streamwise component $R_{11}$. However, computational and experimental studies have consistently reported Reynolds stress tensors with $R_{11}>R_{22}$ in this regime. This discrepancy is primarily due to nonlinear terms which have been neglected in the linear analysis. However, if the effect of the nonlinear terms is to move the anisotropy from a state with $R_{22}>R_{11}$, through isotropy, to a state of qualitatively opposite anisotropy, this would seem contrary to the usual return-to-isotropy effect. Here, we explain the redistribution of energy between the transverse and streamwise Reynolds stresses by considering the wavelengths of the vortical waves emitted by the interaction. Our study shows that the transverse Reynolds stresses are concentrated at smaller length scales than the streamwise stress. In turn, the evolution of the modes associated with $R_{22}$ occurs on a faster time scale, and their energy is more quickly transferred away, allowing $R_{11}$ to dominate. The overall effect is that the global anisotropy quickly attains a state where $R_{11}>R_{22}$. Furthermore, a quantitative model is developed based on this understanding of the flow physics. The model uses LIA along with an eddy viscosity approximation for the nonlinear interactions in order to quantify the redistribution of energy between the transverse and streamwise Reynolds stresses. The model predicts anisotropy levels approximately matching those observed in direct numerical simulation data.

Si is a promising anode material for Li storage due to its high theoretical specific capacity surpassing 4200 Ah/kg. Si based anodes exhibit an extreme instability upon electrochemical incorporation of Li given the accompanied large volume expansion of about 400%. We show innovative anode assemblies composed of a forest of free standing Si nanowires conformally integrated on carbon meshes. The morphology of silicon nanowires allows a volume expansion and compression lowering strain incorporation. In this paper, we demonstrate the utilization of SiNW grown on top of a current collector made of a carbon fiber network. This leads to an increase of stability of Si with a remaining effective capacitance above 2000 Ah/kg(Si) after 225 full charge/discharge cycles. This is significantly better compared to previous results shown in literature. The anodes are fabricated by a simple and inexpensive method promising for a transfer into industrial integration.

Zeorin-containing red-fruited Cladonia species, the so-called C. coccifera group, are widespread terrestrial lichens which share most of their secondary substances but differ morphologically. The main objective of this study was to explore whether the current delimitation of these species is supported by molecular data. A total of 52 European and North American specimens of C. coccifera, C. deformis, C. diversa, and C. pleurota were examined. The internal transcribed spacer regions of the nuclear ribosomal DNA and the β-tubulin gene loci were sequenced for phylogenetic analyses. Traditional morphological species circumscriptions in zeorin-containing members of the C. coccifera group are not supported by molecular data. Cladonia coccifera, C. deformis, and C. pleurota were recovered as polyphyletic in both gene topologies; C. diversa formed a lineage in the ITS phylogeny but this was not statistically supported. We detected chemical patterns of the presence/absence of porphyrilic and/or isousnic acid which may help to characterize two lineages. Our results also show incongruence between the two molecular markers studied. Therefore, we focused on possible explanations of this phenomenon. Five major evolutionary mechanisms can potentially result in phylogenetic discordance between genes: presence of pseudogenes, horizontal gene transfer, gene paralogy, incomplete lineage sorting, and hybridization. These mechanisms are briefly discussed. We consider incomplete lineage sorting and/or hybridization to best explain the incongruence.

To test the phylogenetic position of phenotypically peculiar species in the Physciaceae we generated 47 new sequences (26 of nrITS region and 21 of mtSSU rDNA) from 19 crustose taxa of Physciaceae mainly from the genus Rinodina. Phylogenetic analysis confirmed the Buellia and Physcia groups. The analysis revealed a considerable variability of characters traditionally used for classification, especially in the delimitation of the genera Buellia and Rinodina. While ascus types agree well with the distinction of the Buellia and Physcia groups, none of the other traditional characters, including excipulum type and ascospore thickening, were consistent within subclades of the Physcia group. We suggest that both excipulum type and ascospore characters are rather dynamic in the evolution of Rinodina species and only appear consistent in morphologically more complex foliose and fruticose groups, which are characterized by thallus characters not present in the crustose groups. Two recent taxonomic changes are supported by molecular characters: Endohyalina insularis (syn. ‘Rinodina’ insularis) and Rinodina lindingeri (syn. ‘Buellia’ lindingeri). In addition Rinodina parvula (syn. ‘Buellia’ parvula) is reinstated. New records for Endohyalina brandii, E. diederichii, E. insularis and Rinodina albana are presented.

Fungi that are unrelated to the mycobiont species frequently colonize lichens. Some of these fungal colonists are described lichenicolous fungi, lichen parasites and pathogens that produce recognizable morphological characters, while others apparently produce no noticeable structures. Here we apply the single strand conformation polymorphism (SSCP) technique to directly assess the abundance of different fungi in lichens. Twenty-eight lichen thalli were chosen, some with and some without externally visible symptoms of parasite infection, and these were subjected to total DNA extraction. PCR was conducted with fungal-specific primers for the ITS region of ribosomal DNA. Single strands of the products were separated on native acrylamide gels. The majority of lichen specimens, both infected and those without symptoms, displayed more than one band in the stained gels. In one case, 14 bands were detected using SSCP. Some of these bands apparently represent other neighbouring lichens in the habitat, but many are apparently non-lichen-forming. Since few lichen-associated fungi have been cultured and sequenced, it is difficult to know if SSCP bands represent obligate lichenicolous fungi, other asymptomatic lichen parasites, or fungi not obligately associated with lichens, but our results indicate that large numbers of non-lichen-forming fungi commonly co-occur with lichens in nature. For specimens of the filamentous lichens Cystocoleus ebeneus and Racodium rupestre we used cloned sequences to compare the number of sequences obtained by the SSCP method to the number obtained by direct sequencing of thallus extracts, and we generally found that more sequences could be detected by SSCP than could be seen by direct sequencing.

Lichen-forming fungi are unique organisms, producing biologically active metabolites with a great variety of effects, including antibiotic, antimycobacterial, antiviral, anti-inflammatory, analgesic, antipyretic, antiproliferative and cytotoxic activities. However, only very limited numbers of lichen substances have been screened for their biological activities and their therapeutic potential in medicine. This is certainly due to the difficulties encountered in identification of the species, collection of bulk quantities, and the isolation of pure substances for structure determination and testing activity. Recently, possibilities for bypassing some of these former difficulties have arisen by the introduction of new techniques. This includes axenic cultivation for production of the genuine compounds or new ones, extraction of focused compounds, or synthesis of natural products or their derivatives for testing. Utilizing these new opportunities, the discovery of novel active metabolites, which could serve as lead compounds, is significantly facilitated. At the same time, the evolution of secondary metabolite patterns is studied using phylogenetic approaches. Yet, the genetic background of the complex chemical patterns is poorly understood. The scattered occurrence of some compounds suggests that their production evolved either in parallel or that ancient biosynthetic pathways are abandoned in many lineages. At least, studies on polyketide synthase genes from different lichen groups suggest a high level of gene paralogy. In this context, clades of orthologous polyketide synthase genes, which are often shared with distantly related non-lichenized fungi, can roughly be identified by their sequence similarity and their similar patterns of substitution rates. The functional assignment of paralogs is nevertheless difficult and reasonable only in a few cases. A global approach of the lichen metabolomic features appears to be essential in developing new and viable biotechnological processes which could afford suitable amounts of unique lichen compounds.

A phylogenetic study using large subunit ribosomal DNA sequence data of several species of Siphula, representing all phenotypically recognized species groups, suggests that Siphula is not monophyletic. One lineage, including the core group related to S. ceratites and the S. decumbens group, is placed with members of the Icmadophilaceae, whereas a second distinct lineage, comprising S. complanata, S. fragilis and their relatives, has evolved within the Coccotremataceae. To accommodate these species, the new genus Parasiphula is described as new to science. Parasiphula consists of species restricted to cool to cold latitudes of the Southern Hemisphere. The results show a remarkable case of parallel evolution of lineages that have lost sexual stages and propagate via thallus fragments.

A first assessment of paralogy in non-reducing polyketide synthases of Parmeliaceae is presented. Primers which are specific to the keto-acyl synthase domain were used to amplify gene fragments of putative non-reducing polyketide synthases from various representatives of the family. The corresponding sequences were analysed together with a selection of known polyketide synthase genes from other fungi, including lichenized fungi. The results suggest that genes from Parmeliaceae represent at least 6 paralogs. Their different positions in the tree partly correlate with the variable presence of spliceosomal introns at particular positions in the gene fragments. Because only one paralog could be unambiguously detected in each species by direct sequencing of PCR products with this approach, we tested the applicability of clade-specific primers, designed by using orthologous signature sequences. With these primers more paralogs could be detected from the same DNA extract in a number of species, but certain paralogs were consistently not amplified in these species. The paralog-specific primer approach can potentially be used for a rapid screening of PKS genes from a broader range of lichen fungi.

The family Porinaceae (Trichotheliales) is characterized by perithecial ascomata of ascohymenial origin. The phylogenetic position of this family in the system of ascomycetes has been uncertain and is investigated using mtSSU rDNA sequences. The dataset consists of lichenized representatives of major ascomycete lineages, including those that were previously suspected as relatives of Porinaceae, such as Pyrenulaceae. The dataset was subjected to a Bayesian phylogenetic analysis implementing a Metropolis Coupled Markov Chain Monte Carlo method. The analysis confirms previous classification of the apothecial Gomphillaceae near to Graphidaceae, and suggests that the pyrenocarpous Porinaceae are also close to Graphidaceae, Gyalectaceae, and Stictidaceae. The subclass Ostropomycetidae is here suggested to include the families Gomphillaceae, Gyalectaceae, Graphidaceae (incl. Thelotremataceae), Porinaceae, and Stictidaceae. A special type of hemiangiocarpous ontogeny of the ascomata is shared throughout the Ostropomycetidae, and the closed fruit bodies of Porinaceae are apparently a result of a neotenic ontogeny. This is associated with special hymenial characters: rather thin-walled narrow asci, and a different consistency of the hymenial gels.

A molecular phylogeny of the Lecanora rupicola group is presented, based on ITS sequence analyses. The study includes saxicolous and corticolous members of the Lecanora rupicola group as well as other Lecanora species with pruinose apothecia. A phylogenetic hypothesis for species in Lecanora s. lat. and various other genera in Lecanoraceae, based on an alignment-free distance estimation technique, shows that the Lecanora rupicola group forms a monophyletic clade within Lecanoraceae. Affinities to the core group of Lecanora are not well supported, likewise the monophyly of Lecanora s. str. with other species groups in Lecanora, such as the lobate taxa (and Rhizoplaca) is not supported. A more detailed analysis involving Lecanora species with pruinose apothecial discs was carried out with model-based Bayesian Markov chain Monte Carlo (B/MCMC) tree sampling. The results suggest the monophyly of the Lecanora species that are characterized by the presence of chromones. Corticolous as well as saxicolous species are included. Lepraria flavescens is closely related to the Lecanora swartzii subgroup, and the new name Lecanora rouxii nom. nov. is introduced for that species. Other Lecanora species with pruinose discs are not closely related to the Lecanora rupicola group.

Molecular sequence data of the nuclear ITS region was used to investigate the diversity of photobionts in Polish samples of Flavocetraria nivalis. The samples came both from alpine habitats, as well as from lowland localities near the coast. All green algal symbionts were identified as members of the Trebouxia simplex aggregate. These were compared with those of additional samples from Flavocetraria nivalis collected in different parts of Europe and also with photobionts assigned to T. simplex from other lichens. Within the T. simplex aggregate, the Trebouxia ITS sequences from F. nivalis formed four clades. In the Polish lowland populations only a single clade of T. simplex was detected which also occurs in Polish mountains, south Sweden and Austria. A further clade of T. simplex is present in F. nivalis from Polish mountains and is also known from F. nivalis further north in Scandinavia and Greenland, as well as from other lichens in Sweden, the Austrian Alps, and Antarctica.

The ketosynthase domains of putative polyketide synthase (PKS) genes from 15 species in the lichenized genus Lecanora as well as three representatives of other genera were amplified and sequenced using conserved primers. A phylogenetic analysis was carried out with the corresponding amino acid sequences, including those of non-lichenized fungi. The phylogenetic hypothesis places all PKS sequences from Lecanora and the other genera in a clade of PKSs that produce complex aromatic compounds. The PKSs from Lecanora are found in two distinct clades. One of these forms a monophyletic group with PKSs producing precursors of dihydroxy naphthalenes from non-lichenized species. This includes PKSs from the L. rupicola group and several other species which are not closely related. The other clade represents at least one functionally different protein and has no close relationships with known PKSs from other fungi. A comparison between an ITS phylogeny of the species with their DNA sequences of ketosynthase domains reveals similar PKS genes in certain closely related species. Coevolution was unapparent in other clades, suggesting the presence of paralogous genes.

Rimularia insularis forms an photosynthetic thallus on lichens of the Lecanora rupicola group. In the thalli of R. insularis, some hyphae of the host are detectable, and they are situated mainly in the basal part of the Rimularia's medulla. No Lecanora hyphae were present in the Rimularia's algal layer and they were indistinct in the upper parts of its medulla, from where we obtained clean ITS-sequences of Rimularia. Direct PCR from various sections of the algal layer detected only one photobiont genotype, although the algal cells could be assigned to two morphologically different types. Calcium deposits were found in the upper parts of the medulla, while abundant rock substrate fragments with different mineral compositions were present in the lower parts. Cavities and fissures in the rock below the infected thalli were filled by fungal cells, PCR analyses of such parts indicated that the Rimularia hyphae extend below the host, and into the rock.

This article reviews the current state of knowledge about the evolutionary history of lichenized ascomycetes within an integrated system of all ascomycetes. Substantial progress has been made since molecular techniques were applied to unravel evolutionary relationships. Molecular approaches detect how often the lichen symbiosis arose, test current classification concepts, and find the proper placement for species with uncertain relationships. Uncertainties in some evolutionary hypotheses still need to be resolved by studying further genes. The currently available phylogenetic trees show a number of convergent phenotypic developments in lichenized ascomycetes. The current classification of ascomycetes is reviewed in the light of recent molecular data.

The lichens Usnea florida and U. subfloridana have since long been recognised as distinct species. They show many similarities in morphology, but have different reproductive strategies. Usnea florida is always provided with many apothecia and produces no specialised asexual propagules. Usnea subfloridana has soralia, isidiomorphs and occasionally apothecia. Phylogenetic analyses based on continuous sequences of the ITS and LSU regions of the nuclear ribosomal DNA and the gene coding for β-tubulin, show that specimens of the two species form one monophyletic group of intermixed specimens, and not two groups corresponding to morphology, which would have been expected if two species were at hand. The ‘species pair’ concept in lichenology is discussed. Other Usnea species included in the study are: U. articulata, U. barbata, U. ceratina, U. filipendula, U. hirta, U. rigida and U. wasmuthii.

The new genus Coniarthonia is described to accommodate a group of species previously placed in Anhonia and Arthotheliwn. Crystallized red pigments that are distributed throughout hydrophobic ascomatal structures are characteristic of the new genus, which includes species with both muriform and transversely septate ascospores. Coniarthonia erythrocarpa, C. gregarina, C. pulchernma, C. pyrrhula and C. ivilmsiana are new combinations, and C. haematodea is new to science. Two subgroups are distinguished in the genus: the C. pyrrhula group, with larger ascospores, and the C. pulckcrruna group, which has comparatively small, one-septate ascospores. The reddish compounds are characterized by TLC. A key to the species is provided.