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Using the genus Casearia, we assessed the status of nested singletons: individual specimens corresponding to accepted species but in molecular trees appearing nested within clades of closely related species. Normally, such cases would be left undecided, while on the other hand, timely taxonomic decisions are required. We argue that morphological, chorological, and ecological data can be informative to illuminate patterns of speciation. Their use can provide a first step in testing taxon concepts at species level. We focused on five cases of nested singletons in trees of the genus Casearia. We employed PCA and cluster analysis to assess phenotypic differentiation. Using geocoordinates, we calculated niche space differentiation based on 19 bioclim variables, by means of PCA and niche equivalency and similarity tests and generated dot maps. We found that the singletons were morphologically distinctive in two of the five cases (Casearia selloana and C. manausensis), relatively distinctive in two other cases (C. zizyphoides and C. mariquitensis), and partially overlapping in the last case (C. grandiflora). For two cases (C. mariquitensis and C. selloana), ecological niche space was broadly overlapping, in two cases it was found broadly nested (C. grandiflora and C. zizyphoides), and in one case narrowly nested (C. manausensis), but in no case niche differentiation was observed. Niche overlap, similarity and equivalency showed corresponding patterns. Given these data, one would interpret C. selloana and C. manausensis as presumably well‐distinguished taxa, their narrow distribution ranges suggesting recently emerging lineages. The other three cases are not clearcut. Morphological data would suggest particularly C. grandiflora conspecific with C. arborea, but differences in the distribution are intriguing. Our approach would reject the notion of potential synonymy based on nested phylogenetic placement for at least two of the five cases. The other case also shows no complete lack of differentiation which would support synonymy. [ABSTRACT FROM AUTHOR]

We propose that a qualitative trait approach based on more detailed nuanced traits may reveal previously overlooked patterns, especially when combined with phylogenetic perspectives. By sampling epiphytic lichens and using a functional approach based on nuanced qualitative traits, such as a much greater resolution over photobiont identity, type of cortex, and chemical compounds, we evaluated the effects of environmental filtering and phylogenetic constraints on community assembly along a natural succession of Atlantic rainforest. We found changes in taxonomic, functional, and phylogenetic composition, structure, and diversity. Functional traits such as photobiont genera, type of cortex, reproductive structures, propagule size, and protection strategies showed strong responses to succession. Mature forests with a closed canopy impose strong environment filtering that is reflected in lichen species turnover, limiting diversity, but also holding different functional and phylogenetic composition. The use of a nuanced qualitative trait approach may overcome some of the limitations of using this type of traits and shows the importance of often‐overlooked key lichen functional traits, including the presence of carbon‐concentrating mechanisms in photobionts and cortex properties. Furthermore, this is the first study showing how patterns of phylogenetic assembly along forest succession structure lichen communities. [ABSTRACT FROM AUTHOR]

High Andean forests harbor a remarkably high biodiversity and play a key role in providing vital ecosystem services for neighboring cities and settlements. However, they are among the most fragmented and threatened ecosystems in the neotropics. To preserve their unique biodiversity, a deeper understanding of the effects of anthropogenic perturbations on them is urgently needed. Here, we characterized the plant communities of high Andean forest remnants in the hinterland of Bogotá in 32 0.04 ha plots. We assessed the woody vegetation and sampled the understory and epiphytic cover. We gathered data on compositional and structural parameters and compiled a broad array of variables related to anthropogenic disturbance, ranging from local to landscape‐wide metrics. We also assessed phylogenetic diversity and functional diversity. We employed nonmetric multidimensional scaling (NMDS) to select meaningful variables in a first step of the analysis. Then, we performed partial redundancy analysis (pRDA) and generalized linear models (GLMs) in order to test how selected environmental and anthropogenic variables are affecting the composition, diversity, and aboveground biomass of these forests. Identified woody vegetation and understory layer communities were characterized by differences in elevation, temperature, and relative humidity, but were also related to different levels of human influence. We found that the increase of human‐related disturbance resulted in less phylogenetic diversity and in the phylogenetic clustering of the woody vegetation and in lower aboveground biomass (AGB) values. As to the understory, disturbance was associated with a higher diversity, jointly with a higher phylogenetic dispersion. The most relevant disturbance predictors identified here were as follows: edge effect, proximity of cattle, minimum fragment age, and median patch size. Interestingly, AGB was efficiently predicted by the proportion of late successional species. We therefore recommend the use of AGB and abundance of late successional species as indicators of human disturbance on high Andean forests. [ABSTRACT FROM AUTHOR]

Premise of the study: This study elucidates the phylogenetic position of a unique taxon of Graphidaceae occurring on rock in coastal desert areas, assessing its importance for our understanding of the evolution of the largest family of tropical lichenized fungi. Methods: We used maximum likelihood and Bayesian approaches to reconstruct a three-gene phylogeny of Graphidaceae and a Bayesian molecular clock approach to estimate divergence dates for major clades, as well as Bayesian ancestral ecogeography state analysis. Key results: The new genus Redonographa represents a new subfamily, Redonographoideae, sister to subfamily Graphidoideae. Redonographa is exclusively saxicolous and restricted to the American Pacific coast from California to central Chile, including Galapagos. It contains four species: Redonographa chilensis comb. nov., R. saxiseda comb. nov., R. saxorum comb. nov., an R. galapagoensis sp. nov. The genus Gymnographopsis, with a similar ecogeography but differing in excipular carbonization and chemistry, is also included in Redonographoideae, with the species G. chilena from Chile and G. latispora from So Africa. Molecular clock analysis indicates that Redonographoideae diverged from Graphidoideae about 132 million years ago (Ma) in the Early Cretaceous. Conclusions: The divergence date for subfamilies Redonographoideae and Graphidoideae coincides with the early breakup of Gondwana and ancient origin of the Atacama Desert. However, the common ancestor of Redonographoideae plus Graphidoideae was reconstructed to be tropical-epiphytic. Thus, even if Redonographoideae is subtropical-saxicolous, the hypothesis that Graphidoideae evolved from a subtropical-saxicolous ancestor is not supported. [ABSTRACT FROM AUTHOR]

In this paper, an extended molecular phylogeny was generated for the Ocellularia clade, which includes about half of the species that were previously separated in the family Thelotremataceae. Three genes (mtSSU, nuLSU, RPB2), from a total of 270 OTUs with 136 ingroup species, were sequenced to evaluate whether the core genera, Ocellularia and Myriotrema, form monophyletic clades or split into several lineages. Further, we tested the usefulness of phenotypic characters for circumscrib-ing monophyletic groups. Besides a maximum likelihood analysis, we incorporated the novel method of morphology-based 'phylogenetic binning', which allowed us to weight the morphological characters in those taxa with molecular data available and then predict the phylogenetic classification for over 200 additional species for which no molecular data are currently available. Our results showed that the large genera Myriotrema, Ocellularia, and Stegobolus are polyphyletic. For some of the previously unrecognized lineages, older generic names are available (Rhabdodiscus, Ocellis, Stigmagora, Antrocarpum, Macropyrenium). Some previously separated genera, such as Ampliotrema and Gyrotrema, were found to be nested within a large clade currently recognized as Ocellularia s.l. For this clade, no meaningful generic subdivision could be established based on the available data, and we proposed to recognize distinct subclades at the subgenus level. One new genus, Composi-trema, was also discovered, and a second new genus, Glaucotrema, is established for the Myriotrema glaucophaenum group. Further, the genus Rhabdodiscus is reinstated formally. We found a high level of homoplasy (parallel evolution) of phenotype characters previously used for classification purposes, such as excipular carbonization, columella morphology, and ascospore size, septation, and pigmentation. Secondary chemistry, on the other hand, was remarkably uniform in most clades. Some clades also exhibit a high level of disparity of ascoma morphology. Thus, the very distinctive Gyrotrema-type apothecia occur in a clade nested within and genetically very similar to Ocellularia s.str. [ABSTRACT FROM AUTHOR]

The fungal order Ostropales is unique in Ascomycota for including both lichen-forming and non-lichenized species and species with optional nutritional strategies depending on substrate. To address the phylogenetic relationships within the order, we assembled a dataset of 78 ostropalean species, including all major clades and 23 taxa that are only optionally lichenized or non-licl1ienized. The analyses are based on sequences of the mtSSU and nuLSU rDNA and the protein-coding gene RPB2. A close relationship of Graphidaceae and Gomphillaceae is suggested with the latter possibly nested within Graphidaceac. Odontotremataceae is composed of two distantly related groups. Coenogoniaceae and Porinaceae are sister taxa, and their relation to Gyalectaceae is unresolved. Gyalecta is paraphyletic with Belonia and Pachyphiale nested within. A polyphyletic Belonia indicates that perithecloid ascomata evolved more than once in Gyalectaceae. The new family Sagiolechiaceae is proposed to aLcommodate Rhexophiale and Sagiolechia and Solorinellaceae is reinstated distinct from Gomphillaceae. Belonia and Pachyphiale are reduced to synonymy with Gyalecta. The distribution of phenotypical character states is discussed with selected character states mapped onto a phylogenetic tree. A special focus is given on lifestyles. Our phylogeny suggests that there is more plasticity in the evolution of life-styles in these fungi than was previously assumed. [ABSTRACT FROM AUTHOR]

Phylogenetic diversity of lichen photobionts is low compared to that of fungal counterparts. Most lichen fungi are thought to be associated with just four photobiont genera, among them the cyanobacteria Nosioc and Scytoneina, two of the most important nitrogen fixers in humid ecosystems. Although many Nostoc photobionts have been identified using isolated cultures and sequences, the identity of Scytoneina photobionts has never been confirmed by culturing or sequencing. We investigated the phylogenetic placement of presumed Scytonema photobionts and unicellular morphotypes previously assigned to Chroococcus, from tropical Dictyonerna, Acantholichen, Coccocarpia, and Stereocaulon lichens. While we confirm that filamentous and unicellular photobiont morphotypes belong to a single dade, this dade does not cluster with Scytonema but represents a novel, previously unrecognized, highly diverse, exclusively lichenized lineage, for which the name Rhizonerna is available. The phylogenetic structure observed in this novel lineage suggests absence of coevolution with associated mycobionts at the species or dade level. Instead, highly efficient photobiont strains appear to have evolved through photobiont sharing between unrelated, but ecologically similar, coexisting lineages of lichenized fungi ("lichen guilds"), via the selection of particular photobiont strains through and subsequent horizontal transfer among unrelated mycobionts, a phenomenon not unlike crop domestication. [ABSTRACT FROM AUTHOR]

Aim To analyse the historical biogeography of the lichen genus Chroodiscus using a phenotype-based phylogeny in the context of continental drift and evolution of tropical rain forest vegetation. Location All tropical regions (Central and South America, Africa, India, Southeast Asia, north-east Australia). Methods We performed a phenotype-based phylogenetic analysis and ancestral character state reconstruction of 14 species of the lichen genus Chroodiscus, usingpaup* andmesquite; dispersal–vicariance analysis (DIVA) and dispersal–extinction–cladogenesis (DEC) modelling to trace the geographical origin of individual clades; and ordination and clustering by means ofpc-ord, based on a novel similarity index, to visualize the biogeographical relationships of floristic regions in which Chroodiscus occurs. Results The 14 species of Chroodiscus show distinctive distribution patterns, with one pantropical and one amphi-Pacific taxon and 12 species each restricted to a single continent. The genus comprises four clades. DIVA and DEC modelling suggest a South American origin of Chroodiscus in the mid to late Cretaceous (120–100 Ma), with subsequent expansion through a South American–African–Indian–Southeast Asian–Australian dispersal route and late diversification of the argillaceus clade in Southeast Asia. Based on the abundance of extant taxa, the probability of speciation events in Chroodiscus is shown to be extremely low. Slow dispersal of foliicolous rain forest understorey lichens is consistent with estimated phylogenetic ages of individual species and with average lengths of biological species intervals in fungi (10–20 Myr). Main conclusions The present-day distribution of Chroodiscus can be explained by vicariance and mid-distance dispersal through the interconnection or proximity of continental shelves, without the need for recent, trans-oceanic long-distance dispersal. Phylogenetic reconstruction and age estimation for Chroodiscus are consistent with the ‘biotic ferry’ hypothesis: a South American origin and subsequent eastward expansion through Africa towards Southeast Asia and north-eastern Australia via the Indian subcontinent. The present-day pantropical distributions of many clades and species of foliicolous lichens might thus be explained by eastward expansion through continental drift, along with the evolution of modern rain forests starting 120 Ma, rather than by the existence of a hypothetical continuous area of pre-modern rain forest spanning South America, Africa and Southeast Asia during the mid and late Cretaceous. [ABSTRACT FROM AUTHOR]

A chart is presented that list the proposal to conserve the name Phaeographis, with a conserved type, against Creographa, Ectographis, Flegographa, Hymenodecton, Platygramma, and Pyrographa, along with notes on the names Graphina and Phaeographina.

The recent uptake of the name Sclerophytonomyces Cif. & Tomas. sets a precedent for the potential use of 215 alternative generic names established by Ciferri and Tomaselli for lichen-forming fungi. It is generally believed that the intention of these authors was an alternative nomenclature for lichenized mycobionts, assuming that lichen names covered the entire symbiosis and were thus nomenclaturally incorrect. However, being aware of Art. 76 in the Stockholm Code ("… names given to lichens shall be considered as applying to their fungal components"; Art. 13 in subsequent Codes), the original idea of Ciferri and Tomaselli was not to replace these names, but to introduce a dual nomenclature that permitted separate naming of isolated fungal cultures, which appeared very different from the corresponding lichen mycobionts. Since Art. 76 did not allow such a dual nomenclature, the authors presented Proposal 46 to amend the Code, but at the same time published their new names separately. The names are conceptually illegitimate, but according to Art. 52.1, legitimacy is formally tied to the identity of the type specimens as governed by Art. 10.1. No type specimens were cited, yet the names are validly published since types were not required for valid publication of names prior to 1958. This has led to inconsistent interpretations of their use, and at least five generic names threaten more recently introduced generic names (Adelolecia, Allocetraria, Caleniopsis, Parmelina, Poeltinula), with about 100 species, many of which are widely distributed and well-known. About 75 of the 215 generic names were thought to be potentially available for use, because their presumed types are not types of previously published names of lichen genera. However, the species names cited as types of the 203 generic names published in the original paper lacked Latin diagnoses and so have no status under the Code, so the generic names are automatically typified under Art. 10.2 and 10.3 based on their diagnoses, which by use of the phrase "Ut in …" make direct reference to previously established generic names, and are thus formally illegitimate. Only three generic names are available for use because they are based on species with validly published names that are not the types of names of previously established genera of lichenized fungi: Coenomycogonium (based on Coenogonium interpositum), Dictyonematotnyces (based on Dictyonema sericeum), and Mycocoenogonium (based on Coenogonium curvulum). However, these names are younger taxonomic synonyms of Coenogonium and Dictyonema, respectively. [ABSTRACT FROM AUTHOR]

The new basidiolichen Multiclavula ichthyiformis Nelsen, Lücking, Umaña, Trest & Will-Wolf is described from Costa Rica. The new species differs from other species of Multiclavula in having a basidiocarp with tomentose stipe and flattened lamina with nonamphigenous hymenium. Molecular sequence data (ITS) confirmed its placement within Multiclavula in the Clavulinaceae (Cantharellales, Agaricomycetes). The new lichen was discovered in a Central American paramo remnant, illustrating the importance of biotic inventories of fungi and lichens to increase our knowledge of the diversity of these groups in endangered tropical ecosystems. The new species was found as part of the TICOLICHEN project in Costa Rica. [ABSTRACT FROM AUTHOR]

Summary • Suppositions about lichen reproductive strategies were investigated and elusive early stages of lichen ontogeny documented in a foliicolous lichen community. • Plastic coverslips attached to supportive netting were placed among foliicolous lichen communities within a neotropical lowland forest. The germination and development of diverse lichen propagules colonizing the coverslips were studied with light microscopy. • Foliicolous lichens were observed to begin development from lichenized vegetative propagules, aposymbiotic fungal spores, fungal spores dispersed together with attached phycobionts, and diahyphae. Aposymbiotically dispersed spores and diahyphae were capable of associating with compatible phycobionts encountered upon the substratum, following germination. • Many developing thalli produced characteristic structures (discoid isidia, thalline setae, pycnidia, etc.) which permitted their recognition as typical members of the foliicolous lichen community. Thalline setae in Tricharia were produced upon the prothallus, and subsequently incorporated into the thallus proper by advance of the lichenized thallus margin. Tricharia and other members of the Gomphillaceae showed a distinctive organization of symbionts in thallus growth, whereby the unicellular green phycobiont cells were positioned at the tips of advancing fascicles of mycobiont hyphae. In Coenogonium sp., branching filaments of the phycobiont Trentepohlia grew along prothallic paths initiated by the mycobiont. [ABSTRACT FROM AUTHOR]