Considerations and consequences of allowing DNA sequence data as types of fungal taxa

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.

Sharpening the species boundaries in the Cladonia mediterranea complex (Cladoniaceae, Ascomycota)

The complex Cladonia mediterranea belongs to the section Impexae and is formed by C. azorica, C. macaronesica and C.mediterranea. These species are basically distributed in the Mediterranean and Macaronesian Regions. In the present work the limits between the species of this complex are re-examined. To this end, the morphological characters were studied along with the secondary metabolites and the DNA sequences from three loci (ITS rDNA, IGS rDNA and rpb2). The morphological data were studied by principal component analysis (PCA), while the DNA sequences were analyzed using several approaches available to delimit species: genealogical concordance phylogenetic species recognition, species tree (BEAST* and spedeSTEM) and cohesion species recognition. In addition, the genealogical sorting index was used in order to assess the monophyly of the species. The different procedures used in our study turned out to be highly congruent with respect to the limits they establish, but these limits are not the ones separating the prior species. Either the morphological analysis or the different approaches to species delimitation indicate that C. mediterranea is a different species from C. macaronesica, while C. azorica and C. macaronesica, which are reduced to synonyms of C. portentosa, constitute a separate lineage.

Molecular systematics of the wood-inhabiting, lichen-forming genus Xylographa (Baeomycetales, Ostropomycetidae) with eight new species

The ascomycete genus Xylographa includes some of the most abundant species of wood-inhabiting lichenized fungi in boreal and temperate regions. It has never been monographed and little is known of its species diversity and evolutionary relationships. Based on a morphological and secondary metabolite-based assessment of material from North and South America, Europe and Asia, we generated a three-locus phylogeny based on sequences of the internal transcribed spacer, 28S nuclear rDNA and mitochondrial small subunit rDNA. We analyzed the data within the context of putatively related genera in the order Baeomycetales. Xylographa is a strongly supported monophyletic group closely related to Lithographa and Ptychographa, as well as rock-dwelling and lichenicolous species of Rimularia s.lat. The evolution of linearized ascomata in Xylographa appears to have enabled ascomata to grow laterally, and patterns of lateral growth are diagnostic. We recognize twenty species in Xylographa and provide a thorough revision of nomenclature. The following eight species are new: Xylographa bjoerkii T. Sprib., X. constricta T. Sprib., X. erratica T. Sprib., X. lagoi T. Sprib. & Pérez-Ortega, X. schofieldii T. Sprib., X. septentrionalis T. Sprib., X. stenospora T. Sprib. & Resl and X. vermicularis T. Sprib. The combinations Lambiella insularis (Nyl.) T. Sprib. and Xylographa carneopallida (Räsänen) T. Sprib. are newly proposed. Xylographa constricta from southern South America represents the first known case of secondary de-lichenization in the Baeomycetales. Xylographa parallela s.str. is confirmed as bipolar on the basis of sequenced collections from both southern Chile and the northern Hemisphere.

Multilocus approach to species recognition in the Cladonia humilis complex (Cladoniaceae, Ascomycota)

PREMISE OF THE STUDY

The members of the Cladonia humilis complex are characterized by a well-developed primary thallus and broadly scyphose podetia. In the present study, this complex was phylogenetically analyzed to test the boundaries between the species and to determine the usefulness of the phenotypic characters to distinguish them. The species C. conista, C. cyathomorpha, C. hammeri, C. humilis, C. kurokawae, C. nashii, C. pulvinella, and C. subconistea were examined.

METHODS

Four DNA loci were sequenced and analyzed to test the monophyly of the species. For the phylogenetic reconstructions, maximum parsimony, maximum likelihood, and Bayesian methods were employed. The genealogical sorting index was used to quantify the exclusive ancestry of the nonmonophyletic species on the tree.

KEY RESULTS

The performed phylogenetic analyses showed that the C. humilis complex is not monophyletic. Cladonia nashii is not closely related to the remaining taxa within the complex. Seven monophyletic lineages were identified, most of which comprise specimens belonging to more than one chemotype. Cladonia hammeri and C. pulvinella are conspecific, and this taxon is not present in Europe.

CONCLUSIONS

This study suggests that morphological characters and secondary metabolites have less taxonomical value than thought in the Cladonia humilis complex. Use of multilocus phylogeny is recommended to delimit species.

Basal cell carcinomas without histological confirmation and their treatment: an audit in four European regions

BACKGROUND

Limited data are available on how often basal cell carcinomas (BCCs) are clinically diagnosed without histological confirmation and how they are treated.

OBJECTIVES

Within the framework of the EPIDERM project, an audit was conducted in four European countries to study the occurrence of clinically diagnosed BCCs without histological confirmation and to investigate how these are treated.

METHODS

In the Netherlands, Scotland, Finland and Malta studies were performed within different timeframes. Patients with one or more BCC(s) were selected and the number of clinically diagnosed BCCs without histological confirmation and their treatment was investigated by (manually) reviewing the (electronic) patient records and checking the (hospital) pathology databases to find evidence of histological confirmation.

RESULTS

In the Netherlands, 1089 patients with a first histologically confirmed BCC developed 1974 BCCs of which 1833 (92·9%) were histologically confirmed and 141 (7·1%) were not. A 4-month retrospective study conducted in Scotland selected 294 patients with 344 BCCs; 306 (89·0%) were histologically confirmed and 38 (11·0%) were not. A 3-month prospective study performed at the same centre in Scotland identified 44 patients who developed 58 BCCs; 44 (75·9%) of these were histologically confirmed and 14 (24·1%) were not. In Finland, there were 701 patients who developed 977 BCCs, of which 807 (82·6%) were histologically and 170 (17·4%) nonhistologically confirmed. In Malta, there were 420 patients with 477 BCCs. Only three (0·7%) of them were clinically diagnosed without histological confirmation. In the Netherlands and Finland, clinically diagnosed BCCs without histological confirmation were most often treated with cryotherapy, whereas in Scotland 5% imiquimod cream was the preferred treatment modality.

CONCLUSIONS

Although the frequency of clinically diagnosed BCCs without histological confirmation differed between the four European regions (range 0·7-24·1%), this confirms that the burden of BCC in Europe is underestimated when based on data from pathology and/or cancer registries.

Phylogeny of bipolar Cladonia arbuscula and Cladonia mitis (Lecanorales, Euascomycetes)

Phylogenetic relationships and levels of geographic differentiation of two closely related bipolar taxa, Cladonia arbuscula and Cladonia mitis, were cladistically examined with ITS regions, SSU rDNA introns, partial beta-tubulin, and partial glyceraldehyde 3-phosphate dehydrogenase (GAPDH) genes. In the combined analysis of the four genes, C. arbuscula was paraphyletic, while C. mitis, nested within C. arbuscula, formed a strongly supported monophyletic group. C. arbuscula samples were divided into three separate clades: "arbuscula I," appearing as basal to the other ingroup taxa, "arbuscula II," and "arbuscula III" (the latter represented by only one specimen), which were not correlated with any morphological trait. Only C. mitis specimens formed a morphologically and chemically distinct group. None of the main clades was correlated with geographic origin. The separate analyses were poorly resolved, and in most cases samples from "arbuscula I," "arbuscula II," and "arbuscula III" clades were intermixed. An incongruence test revealed conflict among the four gene regions in almost all cases. Only ITS regions and introns were not significantly incongruent, suggesting lack of recombination within the ribosomal DNA locus. Incomplete lineage sorting and recombination were considered to be the main reasons accounting for the incongruencies. The high proportion of shared polymorphisms between the "arbuscula I" and "arbuscula II" clades, especially found from the beta-tubulin gene and from the ITS regions, and the lack of corroborating morphological characters both indicate a short history of reproductive isolation among the groups. The lack of genetic differentiation among the northern and southern samples within the main clades indicates a relatively recent gene flow, which may have resulted from migrations during the Pleistocene glaciations or from more recent long-distance dispersal.

The lichen family Cladoniaceae in Paraiba, Pernambuco and Sergipe, Northeast Brazil

Field and herbarium studies of the lichen family Cladoniaceae in the states of Paraíba, Pernambuco and Sergipe, Northeast Brazil, yielded 22 species, many of them being new reports for the region. The phenolic compounds identified in each species are reported. Cladonia clathrata Ahti & Xavier Filho, Cladonia polita Ahti, Cladonia polyscypha Ahti & Xavier Filho, and Cladonia rugicaulis Ahti are described as new. C. clathrata, C. rhodoleuca Vainio, C. rugicaulis, C. salzmannii Nyl., and C. subminiata Stenroos appear to represent an element confined to northeastern Brazil.

Contribución al conocimiento del género Cladonia (Cladoniaceae-Liquenes) de Argentina y regiones limítrofes

<span style="font-family: arial, sans-serif; font-size: 16px;"><span><em>Cladonia subradiata</em> (Vain.) Sandst. </span><span>se reporta como nueva para la Argentina y Paraguay, <em>C.turgidior</em> (Nyl.) Ahti para la Argentina, y <em>C.peziziform</em>, es (With.) Laundon para Paraguay. </span><span><em>Cladonia ramulosa</em> (With.) Laundon y <em>C.humilis</em> (With.) Laundon se reportan por primera vez para el norte de Argentina. </span><span>Cinco especies de <em>Cladonia</em> son reconocidas ahora en la provincia de Corrientes. Se presenta una clave e ilustraciones.</span></span>