Marcela Eugenia da Silva Cáceres

Coalescent-Based Species Delimitation Approach Uncovers High Cryptic Diversity in the Cosmopolitan Lichen-Forming Fungal Genus Protoparmelia (Lecanorales, Ascomycota)

Species recognition in lichen-forming fungi has been a challenge because of unsettled species concepts, few taxonomically relevant traits, and limitations of traditionally used morphological and chemical characters for identifying closely related species. Here we analyze species diversity in the cosmopolitan genus Protoparmelia s.l. The ~25 described species in this group occur across diverse habitats from the boreal -arctic/alpine to the tropics, but their relationship to each other remains unexplored. In this study, we inferred the phylogeny of 18 species currently assigned to this genus based on 160 specimens and six markers: mtSSU, nuLSU, ITS, RPB1, MCM7, and TSR1. We assessed the circumscription of species-level lineages in Protoparmelia s. str. using two coalescent-based species delimitation methods – BP&P and spedeSTEM. Our results suggest the presence of a tropical and an extra-tropical lineage, and eleven previously unrecognized distinct species-level lineages in Protoparmelia s. str. Several cryptic lineages were discovered as compared to phenotype-based species delimitation. Many of the putative species are supported by geographic evidence.

Notes for genera: Ascomycota

Knowledge of the relationships and thus the classification of fungi, has developed rapidly with increasingly widespread use of molecular techniques, over the past 10–15xa0years, and continues to accelerate. Several genera have been found to be polyphyletic, and their generic concepts have subsequently been emended. New names have thus been introduced for species which are phylogenetically distinct from the type species of particular genera. The ending of the separate naming of morphs of the same species in 2011, has also caused changes in fungal generic names. In order to facilitate access to all important changes, it was desirable to compile these in a single document. The present article provides a list of generic names of Ascomycota (approximately 6500 accepted names published to the end of 2016), including those which are lichen-forming. Notes and summaries of the changes since the last edition of ‘Ainsworth & Bisby’s Dictionary of the Fungi’ in 2008 are provided. The notes include the number of accepted species, classification, type species (with location of the type material), culture availability, life-styles, distribution, and selected publications that have appeared since 2008. This work is intended to provide the foundation for updating the ascomycete component of the “Without prejudice list of generic names of Fungi” published in 2013, which will be developed into a list of protected generic names. This will be subjected to the XIXth International Botanical Congress in Shenzhen in July 2017 agreeing to a modification in the rules relating to protected lists, and scrutiny by procedures determined by the Nomenclature Committee for Fungi (NCF). The previously invalidly published generic names Barriopsis, Collophora (as Collophorina), Cryomyces, Dematiopleospora, Heterospora (as Heterosporicola), Lithophila, Palmomyces (as Palmaria) and Saxomyces are validated, as are two previously invalid family names, Bartaliniaceae and Wiesneriomycetaceae. Four species of Lalaria, which were invalidly published are transferred to Taphrina and validated as new combinations. Catenomycopsis Tibell & Constant. is reduced under Chaenothecopsis Vain., while Dichomera Cooke is reduced under Botryosphaeria Ces. & De Not. (Art. 59).

A reappraisal of orders and families within the subclass Chaetothyriomycetidae (Eurotiomycetes, Ascomycota)

The subclass Chaetothyriomycetidae (Eurotiomycetes, Ascomycota) is an assemblage of ecologically diverse species, ranging from mutualistic lichenised fungi to human opportunistic pathogens. Recent contributions from molecular studies have changed our understanding of the composition of this subclass. Among others, ant-associated fungi, deep-sea fungi and bryophilous fungi were also shown to belong to this group of ascomycetes. The delimitation of orders and families within this subclass has not previously been re-assessed using a broad phylogenetic study and the phylogenetic position of some taxa such as the lichenised family Celotheliaceae or the Chaetothyrialean bryophilous fungi is still unclear. In our study, we assemble new and published sequences from 132 taxa and reconstruct phylogenetic relationships using four markers (nuLSU, nuSSU, mtSSU and RPB1). Results highlight several shortfalls in the current classification of this subclass, mainly due to un-assigned paraphyletic taxa. The family Epibryaceae is therefore described to circumscribe a previously un-assigned lineage. Celotheliales ad int. is suggested for the lineage including the lichen genus Celothelium and various plant pathogens. The delimitation of the family Trichomeriaceae is also broadened to include the genus Knufia and some anamorphic taxa. As defined here, Chaetothyriomycetidae includes four orders (Celotheliales ad int., Chaetothyriales, Pyrenulales, and Verrucariales) and ten families (Adelococcaceae, Celotheliaceae, Chaetothyriaceae, Cyphellophoraceae, Epibryaceae fam. nov., Herpotrichiellaceae, Pyrenulaceae, Requienellaceae, Trichomeriaceae, and Verrucariaceae).

Twenty-one new species of Pyrenula from South America, with a note on over-mature ascospores

Abstract: Twenty-three species of Pyrenula from Latin America are treated here. Several speciesshow characters that were not previously reported in the genus and are rare or new to lichenizedfungi, viz. yellow, orange or red (KOH+ green) oil inspersion in the hymenium, yellow oil in youngascospores or longitudinal ridges on the ascospore wall. Two taxonomically significant types of over-mature spores are illustrated. The following new species are described: Pyrenula aggregataspisteaAptroot & M. Ca´ceres, P. aurantioinspersa Aptroot & Sipman, P. cornutispora Aptroot & M. Ca´ceres,P. flavoinspersa Aptroot & Sipman, P. guyanensis Sipman & Aptroot, P. infraleucotrypa Aptroot & M.Ca´ceres, P. inframamillana Aptroot & M. Ca´ceres, P. infrastroidea Aptroot & Sipman, P. maritimaSipman & Aptroot, P. mattickiana Sipman & Aptroot, P. minoides Aptroot & Sipman, P. monosporaAptroot & Sipman, P. paraminarum Aptroot & M. Ca´ceres, P. perfecta Aptroot & Sipman, P. plicataSipman & Aptroot, P. rubroinspersa Aptroot & Sipman, P. rubronitidula Aptroot & M. Ca´ceres, P.rubrostigma Aptroot & M. Ca´ceres, P. tetraspora Aptroot & Sipman, P. triangularis Aptroot & Sipman,P. viridipyrgilla Aptroot & M. Ca´ceres. Pyrenula seminuda (Mu¨ll. Arg.) Sipman & Aptroot is a newcombination.Key words: lichen, lichenized fungi, Neotropics, Pyrenulaceae, Rondoˆnia, taxonomyAccepted for publication 26 September 2012

Diversity of Brazilian Fungi

Ate 2010, o conhecimento sobre a diversidade de fungos do Brasil estava registrado em publicacoes esparsas de taxonomia e ecologia e em algumas poucas listas de especies. Com a publicacao do Catalogo de Plantas e Fungos do Brasil, e a disponibilizacao da lista online, tem sido possivel agregar o conhecimento disperso. A versao ora apresentada acrescenta 2.111 nomes de especies aos 3.608 listados em 2010. Sao citadas 5.719 especies de fungos distribuidas em 1.246 generos, 102 ordens e 13 divisoes, consistindo em consideravel aumento em relacao a 2010, quando estavam registrados 924 generos e 78 ordens. Predominam os Basidiomycota (2.741 especies, em 22 ordens) e Ascomycota (1.881 especies, em 41 ordens). A Mata Atlântica possui a maior quantidade de registros, com 3.017 especies, seguido pela Amazonia (1.050), Caatinga (999), Cerrado (638) e Pampa e Pantanal com 84 e 35 especies, respectivamente. A regiao Nordeste tem a maior riqueza (2.617 especies), seguida pelo Sudeste (2.252), Sul (1.995), Norte (1.301) e Centro Oeste (488 especies). Em relacao aos Estados da Federacao, Sao Paulo (1.846 especies), Pernambuco (1.611) e Rio Grande do Sul (1.377) sao os mais diversos.

New and interesting lichens from the Caxiuanã National Forest in the Brazilian Amazon

As part of an ongoing inventory of the lichenized mycota of the Caxiuana 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 (Mull. Arg.) M. Caceres & Lucking comb. nov., Graphis brachylirellata M. Caceres & Lucking sp. nov., Malmidea leucogranifera M. Caceres & Lucking sp. nov., Ocellularia conformalis (Kremp.) M. Caceres & Lucking comb. nov., Redingeria microspora (Zahlbr.) M. Caceres & Lucking comb. nov., and Sarcographa megistocarpa (Leight.) M. Caceres & Lucking comb. nov.

Malmographina , a new genus for Graphina malmei (Ascomycota: Ostropales : Graphidaceae )

The new genus Malmographina Caceres, Rivas Plata & Lucking is introduced for Opegrapha plicosa Meissn. (syn. Graphis malmei Redinger), with the new combination Malmographina plicosa (Meiss.) Caceres, Rivas Plata & Lucking. The taxon is characterized by prominent, striate, orange-pigmented, non-carbonized lirellae, a more or less clear hymenium, and large, muriform, hyaline ascospores. Malmographina is most similar to Hemithecium in lirellae morphology and anatomy, but in a molecular phylogenetic analysis falls within a clade containing Phaeographis and other genera with usually inspersed hymenium and brown ascospores. Within that clade, it is thus far the only taxon that has persistently hyaline ascospores. It is otherwise similar to Pallidogramme but does not cluster within that genus. A preliminary phylogenetic analysis of the Phaeographis clade confirms monophyly of the genera Halegrapha , Pallidogramme , and Platygramme , and suggests that Phaeographis should be divided into several generic lineages and that Leiorreuma and Sarcographa perhaps be merged.

A key to the corticolous microfoliose, foliose and related crustose lichens from Rondonia, Brazil, with the description of four new species

A key is given to the foliose and squamulose lichens known so far from Rondonia, including also corticolous crustose lichens with a chlorococcoid alga. The foliicolous Lecanorales found are also listed. The following four new corticolous Lecanorales are described from Rondonia: Calopadia gran- ulosa with a granular, corticate thallus and ascospores 1 per ascus, 33-38 � 10� 5-13� 0 mm; Crustospa- thula amazonica with irregularly capitate to nearly globose, c. 0� 2-0� 4 mm diam. soralia on cartilagi- nous stalks; Flavoparmelia plicata with a thallus containing usnic and protocetraric acids, with laminal, irregular, globose to cylindrical isidia which are often easily abraded and showing the whitish medulla, but not sorediate or postulate; Physcidia striata with ascending squamules, without hypo- thallus, often with laminal isidia in defined areas towards lobe tips of some, usually sterile lobes, and often with biatorine apothecia with ascospores simple to 1-septate, (6� 2-)7� 5-10� 0 � (2� 5-)3� 0-3� 5 mm. In the whole lichen flora of the lowland rainforest region of Rondonia, the following traits can be discerned: foliose lichens amount to only 17 species (2� 7% of nearly 600), 33 (5� 5%) are squamulose, while the vast majority (91� 8%) are crustose. Cyanobacteria are present in only 6 (1%) species. A chlorococcoid alga present in c. 100 (16%), 12 of which (2%) have a myrmecioid alga. The re- mainder of the species, a staggering 83%, have trentepohlioid alga, including 6 (1%) with Phycopeltis. In neotropical lowland rainforest, the vast majority of the lichens are crustose and contain a trente- pohlioid alga, and the Arthoniales, Graphidaceae and pyrenocarpous lichens are the main groups, each accounting for roughly a quarter of the lichen biodiversity.

Molecular phylogeny resolves a taxonomic misunderstanding and places Geisleria close to Absconditella s. str. ( Ostropales : Stictidaceae )

The phylogenetic position of the genus Geisleria and its type species G. sychnogonioides was reconstructed using sequence data of the mitochondrial small subunit (mtSSU), the nuclear large subunit rDNA (nuLSU) and the first subunit of the RNA polymerase ( RPB1 ). The species, previously classified in Verrucariaceae (Eurotiomycetes) and Strigulaceae (Dothideomycetes), is sister to the type of the genus Absconditella , A. sphagnorum , and nested within the genera Absconditella and Cryptodiscus combined (which also includes the lichenized Bryophagus ). At first glance it appears to be a further example of parallel evolution of perithecioid ascomata within Stictidaceae (Lecanoromycetes: Ostropales ), besides Ostropa and Robergea , adding to the growing list of perithecioid forms nested within apothecioid lineages in Ostropomycetidae, and specifically Ostropales , with other examples known from Graphidaceae (several genera), Gyalectaceae ( Belonia ), and Porinaceae . However, revision of type material collected by Nitschke revealed that the species actually develops typical apothecia with a narrowly exposed disc. We conclude that Geisleria sychnogonoides was erroneously considered a pyrenocarpous taxon, because in dry conditions the apothecia are closed and not recognizable as such. The species usually grows on unstable soil and therefore often only develops young, more or less closed ascomata (yet with mature ascospores), and has also been confused with the superficially similar Belonia incarnata , in which the ascomata remain closed even when mature. Geisleria sychnogonioides has so far only been known as a rarely reported pioneer species from loamy soils in Europe and North America. Here it is reported to occur abundantly on lateritic soils in subtropical Brazil, suggesting that it is cosmopolitan and possibly common, but much overlooked.

New species and interesting records of Arthoniales from the Amazon, Rondônia, Brazil

The following new species of Arthoniales are described from Rondonia: Alyxoria fuscospora with 3-septate clavate ascospores of 20-23 � 4� 5-5� 5 mm having a gelatinous layer soon appearing evenly brown (also known from other tropical countries). Chiodecton complexum with discrete soralia, immersed apothecia in branched lines and 3-septate ascospores (26-)33-40 � 2� 5-3� 5 mm. Coniartho- nia rosea, similar to C. pulcherrima but with the apothecia pink and more irregular in outline and the ascospores 13-16 � 5� 5-6� 5 mm. Cresponea flavosorediata with yellow-olive soralia, apothecia with yellow pruina and 7-9-septate ascospores, 26-38(-50) � 5� 0-6� 5 mm. Cresponea lichenicola, lichenico- lous on a Pyrenula ,w ith 0� 1-0� 3 mm wide apothecia with yellow pruina. Eremothecella helicella with helicoid curved c. 17-29-septate conidia c. 70-95 � 2 mm long if uncoiled, with septa 3-6 m ma part. The Arthoniales are a speciose component of the lowland rainforest of Rondonia. A key is provided to the corticolous species of most groups of Arthoniales found in Rondonia. The foliicolous species found so far are listed. Most are new records for Rondonia. Chrysothrix occidentalis is new to the Neotropics.