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We present a novel identification tool called PhyloKey , based on the method of morphology-based, phylogenetic binning developed within the software package RAxML. This method takes a reference data set of species for which both molecular and morphological data are available, computes a molecular reference tree, maps the morphological characters on the tree, and computes weights based on their level of consistency versus homoplasy using maximum likelihood (ML) and maximum parsimony (MP). Additional units for which only morphological data are known are then binned onto the reference tree, calculating bootstrap support values for alternative placements. This approach is modified here to work as an identification tool which uses the same character coding approach as interactive keys. However, rather than identifying individual samples through a progressive filtering process when entering or selecting characters, query samples are binned in batch mode to all possible alternative species in the tree, with each placement receiving a bootstrap support adding to 100% for all alternative placements. In addition to the fact that, after scoring a character matrix, a large number of specimens can be identified at once in short time, all possible alternative identifications are immediately apparent and can be evaluated based on their bootstrap support values. We illustrate this approach using the basidiolichen genus Cora , which was recently shown to contain hundreds of species. We also demonstrate how the PhyloKey approach can aid the restudying of herbarium samples, adding further value to these collections and contributing with large quantitative data matrices to 'non-molecular museomics'. Our analysis showed that PhyloKey identifies species correctly with as low as 50% of the characters sampled, depending on the nature of the reference tree and the character weighting scheme. Overall, a molecular reference tree worked best, but a randomized reference tree gave more consistent results, whereas a morphological reference tree performed less well. Surprisingly, even character weighting gave the best results, followed by parsimony weighting and then maximum likelihood weighting. [ABSTRACT FROM AUTHOR]

This study re-examined the status of species of Diorygma Eshw. known from the Western Ghats using an integrative taxonomy approach that includes morphological and chemical data, as well as multigene phylogenetic analyses. Prior to this work, the two species D. karnatakense and D. dandeliense were distinguished primarily on lirellae morphology (branching pattern) and the number of ascospores per ascus. Our study of the morphology, chemistry and molecular phylogeny (mtSSU, LSU and RPB 2) of freshly collected samples and re-examination of type material suggests that both names should be synonymized. Consequently, D. karnatakense is accepted as the correct name, with D. dandeliense as a newly proposed synonym. Phylogenetically, D. karnatakense is allied to D. antillarum and D. hieroglyphicum. [ABSTRACT FROM AUTHOR]

The taxonomy of the genus Sticta in Hawaii is reassessed, based on a separately published molecular phylogeny using the fungal barcoding marker ITS. Based on Magnusson and Zahlbruckner's treatment from 1943 and Magnusson's catalogue from 1955, seven species of Sticta and three infraspecific taxa had been reported from the archipelago, all widespread except the putative endemic S. plumbicolor. Here we provide a taxonomic treatment of 13 taxa, 12 species and one subspecies, distinguished in a previous phylogenetic analysis: S. acyphellata, S. andina, S. antoniana, S. emmanueliana, S. flynnii, S. fuliginosa, S. hawaiiensis, S. limbata, S. plumbicolor, S. scabrosa subsp. hawaiiensis, S. smithii, S. tomentosa and S. waikamoi. All taxa are described, discussed and illustrated and a dichotomous key is presented. The implications of revised species taxonomies for studies in other fields such as ecology, ecophysiology, biogeography, biochemistry, and applications such as environmental monitoring are discussed. We also propose a protocol to use Sticta lichens to monitor the environmental health of Hawaiian ecosystems. [ABSTRACT FROM AUTHOR]

Recently collected specimens of the crustose lichen Melaspilea demissa from south-eastern USA have been compared with those of Melaspilea spp. previously determined from North America. A review of both the historical and contemporary treatments of this species is provided. A lectotype was selected from the type collection of M. demissa in FH and is here proposed as it best matches incomplete citations in the original treatment. We also discuss the nomenclatural and taxonomic status of the name Opegrapha cymbiformis var. deformis (considered a synonym of M. gibberulosa). North American specimens of M. gibberulosa were found to be misidentifications, as were specimens attributed to M. lentiginosula, M. mesophlebia and M. octomera. We therefore recommend that these species be removed from the North American lichen checklist. We also present a key to North American Melaspilea. [ABSTRACT FROM AUTHOR]

Belonia and Pachyphiale were recently shown to be nested within Gyalecta. Here, new combinations and names are introduced for species earlier classified in Belonia: Gyalecta calcicola (Walt. Watson) Baloch & Lücking comb. nov., G. herculina (Rehm) Baloch, Lumbsch & Wedin comb. nov., G. incarnata (Th. Fr. & Graewe) Baloch & Lücking comb. nov., G. lumbrispora (Etayo) Baloch & Lücking comb. nov., G. lyngei Baloch & Lücking nom. nov. (for Belonia arctica Lynge), G. mediterranea (Nav.-Ros. & Llimona) Baloch & Lücking comb. nov., G. nidarosiensis (Kindt) Baloch & Lücking comb. nov., G. pellucida (Coppins & Malcolm) Baloch & Lücking comb. nov., G. russula (Körb. ex Nyl.) Baloch, Lumbsch & Wedin comb. nov., G. uncinata (P. M. McCarthy & Kantvilas) Baloch & Lücking comb. nov., and G. vezdana (Malcolm & Coppins) Baloch & Lücking comb. nov.; and for species earlier placed in Pachyphiale: Gyalecta arbuti (Bagl.) Baloch & Lücking comb. nov., G. gyalizella (Nyl.) Baloch & Lücking comb. nov., G. himalayensis (Vězda & Poelt) Baloch & Lücking comb. nov., and G. ophiospora (Bagl.) Baloch & Lücking comb. nov. [ABSTRACT FROM PUBLISHER]

As part of a phylogenetic and taxonomic revision of the lichenized genus Sticta in Colombia, six new species with apotheciate thalli but lacking vegetative propagules are described: Sticta atroandensis Moncada & Lücking sp. nov., S. brevior Moncada & Lücking sp. nov., S. lumbschiana Moncada & Lücking sp. nov., S. macrocyphellata Moncada & Coca sp. nov., S. parahumboldtii Moncada & Lücking sp. nov., and S. pseudohumboldtii Moncada & Lücking sp. nov. The last two are related to S. humboldtii but phylogenetically distinct and differ in details of cyphellae morphology and spot reactions. Sticta atroandensis is similar to S. andensis but has a dark lower tomentum, whereas S. brevior belongs in the S. kunthii group, being characterized by mainly laminal apothecia with tomentose margins and a rather stout thallus. Both S. lumbschiana and S. macrocyphellata form part of the S. dilatata group and can be characterized by their lobe surface structure and cyphellae anatomy. Keys to species of the S. dilatata and S. humboldtii groups are presented. [ABSTRACT FROM PUBLISHER]

As part of an ongoing inventory of the lichenized mycota of the Caxiuanã National Forest, at Ferreira Penna Research Station in the Brazilian Amazon, two species of lichenized fungi are described as new and four new combinations are introduced: Ampliotrema megalostoma (Müll. Arg.) M. Cáceres & Lücking comb. nov., Graphis brachylirellata M. Cáceres & Lücking sp. nov., Malmidea leucogranifera M. Cáceres & Lücking sp. nov., Ocellularia conformalis (Kremp.) M. Cáceres & Lücking comb. nov., Redingeria microspora (Zahlbr.) M. Cáceres & Lücking comb. nov., and Sarcographa megistocarpa (Leight.) M. Cáceres & Lücking comb. nov. [ABSTRACT FROM AUTHOR]

Three new species of Chapsa in the family Graphidaceae are described from tropical Asia. Chapsa mastersonii Rivas Plata, Lumbsch & Lücking from the Philippines is characterized by large apothecia with thickly white-pruinose discs, large, muriform, non-amyloid ascospores, and the stictic acid chemosyndrome. Chapsa wijeyaratniana Weerakon, Lumbsch & Lücking from Sri Lanka has apothecia similar to the preceding species but forms an ecorticate thallus with maculiform to capitate soralia, has small, submuriform ascospores, and lacks secondary substances. Chapsa wolseleyana Weerakon, Lumbsch & Lücking forms apothecia with red to pinkish or purplish red discs and large, muriform ascospores becoming pale brown. [ABSTRACT FROM AUTHOR]

In the course of an ongoing systematic and taxonomic revision of the lichen family Graphidaceae (including Thelotremataceae), we present world-wide keys to the currently accepted thelotremoid genera and species, excluding the columellate taxa and their relatives of the Ocellularia- Myriotrema-Stegobolus clade (Melanotrema, Myriotrema, Ocellularia, Ocellularia clandestina group, Redingeria, Stegobolus), which will be treated in a forthcoming paper. The keys include all genera and species with chroodiscoid, lepadinoid, and topeliopsidoid apothecia and other taxa featuring periphysoids or fibrils, and their relatives. Taxa keyed out to genus and species level are Acanthotrema, Chapsa, Chroodiscus, Diploschistes, Fibrillithecis, Gyrotrema, Leptotrema, Leucodecton, Melanotopelia, the 'Ocellularia' cruentata group, Pseudoramonia, Reimnitzia, Schizotrema, Thelotrema, Topeliopsis and Wirthiotrema. Over 260 species are treated, including a few yet unnamed taxa. The following taxonomic and nomenclatural novelties are introduced: Acanthotrema frischii Lücking sp. nov., Chapsa aggregata (Hale) Sipman & Lücking comb. nov., C. albida (Nyl.) Lücking & Sipman comb. nov.; C. albomaculata (Sipman) Sipman & Lücking comb. nov., C. boninensis (Tat. Matsumoto) Rivas Plata & Mangold comb. nov., C. elabens (Müll. Arg.) Rivas Plata&Mangold comb. nov., C. imperfecta (Hale) Rivas Plata & Lücking comb. nov., C. laceratula (Müll. Arg.) Rivas Plata & Lücking comb. nov., C. magnifica (Berk. & Broome) Rivas Plata & Lücking comb. nov., C. meghalayensis (Patw. & Nagarkar) Lumbsch & Divakar comb. nov., C. meridensis (Kalb & Frisch) Lücking, Lumbsch & Rivas Plata comb. nov., C. mirabilis (Zahlbr.) Lücking comb. nov., C. neei (Hale) Mangold & Lücking comb. nov., C. paralbida (Riddle) Rivas Plata & Lücking comb. nov., C. pseudoexanthismocarpa (Patw. & C. R. Kulk.) Rivas Plata & Lücking comb. nov., C. pulvereodisca (Hale) Rivas Plata & Mangold comb. nov., C. scabiomarginata (Hale) Rivas Plata & Lücking comb. nov., C. waasii (Hale) Sipman & Lücking comb. nov., Fibrillithecis argentea (Müll. Arg.) Rivas Plata & Lücking comb. nov., F. carneodisca (Hale) Rivas Plata & Lücking comb. nov., F. confusa Lücking, Kalb & Rivas Plata spec. nov., F. diminita (Hale) Rivas Plata & Lücking comb. nov., F. eximia (R. C. Harris) Rivas Plata & Lücking comb. nov., F. fissurata (Nagarkar & Hale) Rivas Plata & Lücking comb. nov., F. gibbosa (H. Magn.) Rivas Plata & Lücking comb. nov., Leucodecton desquamescens (Vain.) Lücking comb. nov., L. oxysporum (Redinger) Lücking comb. nov., Schizotrema cryptotrema (Nyl.) Rivas Plata & Mangold comb. nov., Thelotrema patwardhanii (Hale) Rivas Plata & Mangold comb. nov., Topeliopsis guaiquinimae (Sipman) Rivas Plata & Mangold comb. nov., and T. tuberculifera (Vain.) Rivas Plata & Mangold comb. nov. Using the examples of Fibrillithecis halei s. lat., Leucodecton compunctellum s. lat., and Thelotrema monosporum s. lat., we show how difficult species complexes can be flexibly treated in a key, allowing for either a broad concept or the distinction of several individual taxa. [ABSTRACT FROM AUTHOR]

Chapsa rubropruinosa Messuti & Codesal collected in Argentina is described as new to science. The species is characterized by a thin thallus, apothecia with a pigmented disc, and transversely septate, hyaline, non-amyloid to faintly amyloid ascospores with thin cell walls. Chapsa minor is recorded for the first time from South America. The new combination Topeliopsis lomatiae (Messuti, Lumbsch & Ve?zda) Messuti & Mangold is proposed. [ABSTRACT FROM AUTHOR]

The species-level taxonomy of the genus Graphis sensu Staiger was revised using numerical taxonomy and cladistic techniques. In its current circumscription, Graphis includes more than 300 species and is characterized by lirellae with well-developed, carbonized labia usually concealing the disc and usually hyaline, I+ blue-violet, transversely septate to muriform ascospores. The study analyzed the importance of morphological, anatomical, and chemical characters for taxonomic purposes in the genus, both at species level and at the level of species groups and lineages. A phenotype-based cladistic analysis, combined with a novel method to estimate the degree of character state homoplasies prior to a cladogram, as well as a species ordination using non-metric multidimensional scaling (NMS), was performed to assess the delimitation of potentially natural groups within the genus. Contrary to previous views, the most important character complex characterizing potentially natural groups in the genus Graphis is lirellae morphology, whereas labia striation, excipulum carbonization, ascospore features, and secondary chemistry, vary greatly even in closely related species. Based on these findings, Wirth and Hale's concept of 'sporomorphs' is emended to generally characterize morphologically similar species that differ in a single character, such as labia striation ('labiomorph'), excipulum carbonization ('excipulomorph'), hymenium inspersion ('inspersomorph'), ascospore size and septation ('sporomorph') and secondary chemistry ('chemomorph'). [ABSTRACT FROM AUTHOR]

A corticolous Graphis discovered in the southern part of Venezuela is described as new to science. The new species, Graphis breussii sp. nov., is characterized by rather large, prominent lirellae with striate labia and apically thin complete thalline cover, a completely carbonized exciple, four submuriform ascospores per ascus, and norstictic acid; it belongs in the Graphis acharii group. [ABSTRACT FROM AUTHOR]

One new species and 71 new records are reported from Thailand. Coenogonium disciforme sp. nov. is distinguished by its disc-shaped, shortly stipitate isidia, which leave perfectly circular holes, almost like punched holes, when detached. [ABSTRACT FROM AUTHOR]

A new species, Chrysothrix septemseptata, is described from India. It is characterized by 7-septate ascospores, which is unique within the genus. It is currently known only from the Sundarbans Biosphere Reserve, where it grows in mangrove plantations. [ABSTRACT FROM AUTHOR]