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The article is a review of the book "Flechten der Schweiz" which provides a comprehensive overview of Swiss lichens, focusing on their diversity, biology, and conservation. It includes numerous color photographs and is suitable for both experts and general readers. The review praises the authors for their expertise and the book's emphasis on outreach and conservation. It also compares the book to other similar publications and highlights its strengths in providing information on lichen biology and ecosystem services. However, it mentions some minor issues with organization and presentation. Overall, the review recommends the book as a valuable resource for anyone interested in Swiss lichens. [Extracted from the article]

Four species of the genus Sticta are described as new from Bolivia, based on morphological examination and phylogenetic analysis of the fungal ITS barcoding marker. Additionally, two species are reported as new to Bolivia (their identification confirmed by molecular data) and one previously reported species is confirmed by molecular data for the first time. Detailed morphological and anatomical descriptions are provided for all new species. Two of the new species, S. isidiolobulata Ossowska, B. Moncada, Lücking & Kukwa and S. madidiensis Ossowska, B. Moncada, Lücking & Kukwa belong to clade I, as defined in previous studies. In contrast, S. montepunkuensis Ossowska, B. Moncada, Lücking & Kukwa and S. macrolobata Ossowska, B. Moncada, Lücking & Kukwa, also described here as new to science, belong to clade III. Sticta isidiolobulata has an irregular to suborbicular thallus of medium size, with isidia developing into spathulate lobules, cyanobacterial photobiont and apothecia with entire to weakly-crenate margins. The large irregular thallus of the cyanobacteria-associated S. macrolobata has broad lobes, apothecia with verrucous to tomentose margins and cyphellae with raised margins, whereas S. madidiensis has a medium-sized, palmate to irregular thallus with a stipe, but without vegetative propagules and apothecia. Sticta montepunkuensis has large and irregular thalli with green algae as photobiont, apothecia with crenate to verrucous margins and urceolate cyphellae with a wide pore and a scabrid basal membrane. Two species, S. beauvoisii Delise and S. riparia Merc.-Díaz are reported as new to Bolivia (the latter also as new to South America) and belong to clade III. Sticta tomentosa (Sw.) Ach., species confirmed from Bolivia by molecular data, belongs to clade II. Sticta beauvoisii is characterised by a smooth yellowish-brown upper surface with darker apices and abundant, marginal isidia and a brown lower surface with golden-chocolate brown primary tomentum and sparse, golden-brown rhizines. Sticta riparia has a strongly branched thallus, with undulate lobes and abundant, marginal, palmate, grey to dark brown phyllidia and greyish-brown lower surface with the primary tomentum absent towards the margins. Sticta tomentosa has palmate, bluish thalli with white cilia and abundant, submarginal apothecia and creamy-white lower surface with a sparse, white primary tomentum. [ABSTRACT FROM AUTHOR]

The foliicolous lichen Gallaicolichen pacificus exhibits unique goniocystangia-like structures named peltidiangia and peltidia. Its taxonomic classification within the Ascomycota has been unclear due to the absence of ascomata and lack of molecular data. Here we clarify the phylogenetic affinities of Gallaicolichen pacificus by analyzing mitochondrial small subunit ribosomal RNA (mtSSU) sequences obtained from specimens collected in New Caledonia. Ascomata and ascospores of G. pacificus , previously unknown, are described and illustrated for the first time. The results from the molecular and morphological analyses clearly indicate that Gallaicolichen pacificus belongs to the Porinaceae and is closely related to Porina guianensis. This is a remarkable extension of the already known, wide morphological diversity of thalli and diaspores produced within this family. [ABSTRACT FROM AUTHOR]

The genus Wetmoreana was studied using quantitative integrative taxonomy methods to resolve the genus delimitation and explore its taxonomy diversity at the species level. As a result, the genus Fulgogasparrea is synonymized with Wetmoreana, and the latter includes 15 formally described species, one subspecies, and three further, thus far undescribed species: W. appressa, W. awasthii comb. nov., W. bahiensis sp. nov., W. brachyloba comb. nov., W. brouardii, W. chapadensis comb. nov., W. circumlobata sp. nov., W. decipioides, W. intensa comb. nov., W. ochraceofulva comb. nov., W. rubra sp. nov., W. sliwae sp. nov., W. sliwae ssp. subparviloba subsp. nov., W. subnitida comb. nov., W. texana, and W. variegata sp. nov. Eleven of 19 examined taxa are newly placed within this genus or confirmed to belong to it. Two species, W. awasthii and W. intensa, are transferred to Wetmoreana without additional analysis but based on previous studies. The W. brouardii and W. ochraceofulva species complexes are discussed in detail. Additionally, Caloplaca muelleri and C. rubina var. evolutior are transferred to Squamulea, and the latter is elevated to the species rank. [ABSTRACT FROM AUTHOR]

We describe 43 new lichen species in the family Graphidaceae, mainly from the Amazon basin: Fissurina bispora, F. diamantica, F. endothallina, F. lirelloreagens, F. reticulolirellina, Graphis inspersonorstictica, G. polystriatosubmuriformis, G. viridithallina, Heiomasia hypostictica, Leucodecton aurantiacum, Mangoldia thallolomoides, Myriochapsa negativa, M. triseptata, Myriotrema inspersosticticum, M. reticulatum, M. roseum, M. xanthonicum, Ocellularia coronatoverrucosa, O. griseosorediata, O. inspersomuriformis, O. inspersulascens, O. microschizidiata, O. norsorediata, O. pallidocolumellata, O. pedicellata, O. pertusella, O. pseudocyphellata, O. psorinspersa, O. psorsorediata, O. roseoisidiata, O. sorediopseudochapsa, O. verruciinspersa, O. vulcanica, O. wirthiotremoides, Phaeographis aureopruinosa, P. coccinea, P. fuscobilabiata, P. macrocephalica, P. norscalpturata, P. pallidoxanthonica, Rhabdodiscus lineatus, Stegobolus negativus, and Thalloloma xanthohypoleptum (the last species also from Puerto Rico). Relatively many are fertile but also form vegetative propagules. A few of the species contain no mature ascospores, but are so deviating from any other described species that we decided to describe them nonetheless. Also, we propose the following 22 new combinations for species of Graphidaceae that were previously described from Brazil and currently are accepted species but were so far assigned to the other genera: Allographa basaltica (≡ Graphis basaltica Kremp.), A. brevissima (≡ Graphis brevissima Fée), A. byrsonimae (≡ Graphina byrsonimae Redinger), A. heteroplaca (≡ Graphina heteroplaca Müll.Arg.), A. platypoda (≡ Phaeographina platypoda Zahlbr.), A. pseudoserpens (≡ Graphis pseudoserpens Chaves & Lücking), A. subargentata (≡ Graphis subargentata S.C.Feuerst., Dal Forno & Eliasaro), A. tricolorata (≡ Graphina tricolorata Redinger), Diorygma album (≡ Graphina alba Müll.Arg.), Fissurina adscripturiens (≡ Graphis adscripturiens Nyl.), F. egenella (≡ Graphina egenella Müll.Arg.), Graphis fasciata (≡ Ustalia fasciata Eschw.), Mangoldia lecideicarpa (≡ Graphina lecideicarpa Zahlbr.), O. endocrocea (≡ O. cinchonarum var. endocrocea Müll.Arg.), O. minarum (≡ Thelotrema minarum Vain.), Phaeographis atrolabiata (≡ Phaeographina atrolabiata Redinger), Phaeographis cheilomegas (≡ Graphis cheilomegas Fée), P. coriaria (≡ Phaeographina coriaria M.Wirth & Hale), P. crassa (≡ Platygramme crassa Fée), P. oxalifera (≡ Phaeographina oxalifera Redinger), P. scriptitata (≡ Phaeographina scriptitata C.W.Dodge), and Stegobolus trachodes (≡ Thelotrema trachodes Nyl.). Finally, we report several species new to Brazil or to one of the states: Allographa pitmanii new to Amapá, Cryptoschizotrema minus new to Alagoas, Glaucotrema glaucophaenum new to Amapá, Graphis pyrrhocheiloides new to Amapá, Graphis subserpentina new to Pará, Melanotrema astrolucens new to Brazil in Amazonas and Pará, Myriotrema hartii new to Amazonas, O. bullata new to Brazil in Pará, O. inspersipallens new to Brazil in Rondônia, O. jutaratiae new to Amapá, O. parvidisca new to Brazil in Amapá, O. rondoniana new to Alagoas, and Thelotrema wilsoniorum new to Brazil in Amapá. [ABSTRACT FROM AUTHOR]

Previous molecular phylogenetic analysis in comparison with phenotype characters of Gomphillaceae resolved a total of 38 genus-level clades among the studied species, 17 of which in need to be recognized and formally established as new or reinstated genera. The four reinstated genus names, including one validation, are Microxyphiomyces Bat., Valle & Peres, Psathyromyces Bat. & Peres, Spinomyces Bat. & Peres ex Xavier-Leite, M. Cáceres & Lücking, gen. nov., and Sporocybomyces H. Maia. The remaining 13 are newly described: Adelphomyces Xavier-Leite, M. Cáceres & Lücking, gen. nov., Aptrootidea Xavier-Leite, M. Cáceres & Lücking, gen. nov., Aulaxinella Xavier-Leite, M. Cáceres & Lücking, gen. nov., Batistomyces Xavier-Leite, M. Cáceres & Lücking, gen. nov., Bezerroplaca Xavier-Leite, M. Cáceres & Lücking, gen. nov., Caleniella Xavier-Leite, M. Cáceres & Lücking, gen. nov., Monocalenia Xavier-Leite, M. Cáceres & Lücking, gen. nov., Pseudocalenia Xavier-Leite, M. Cáceres & Lücking, gen. nov., Roselviria Xavier-Leite, M. Cáceres & Lücking, gen. nov., Santricharia Xavier-Leite, M. Cáceres & Lücking, gen. nov., Sipmanidea Xavier-Leite, M. Cáceres & Lücking, gen. nov., Verruciplaca Xavier-Leite, M. Cáceres & Lücking, gen. nov., and Vezdamyces Xavier-Leite, M. Cáceres & Lücking, gen. nov. The following 53 new combinations are introduced for the species included in the new and reinstated genera: Adelphomyces cochlearifer (Lücking & Sérus.) Xavier-Leite, M. Cáceres & Lücking, comb. nov., A. epithallina (Lücking) Xavier-Leite, M. Cáceres & Lücking, comb. nov., A. parvula (Hafellner & Vězda) Xavier-Leite, M. Cáceres & Lücking, comb. nov., Aptrootidea amapensis (Bat. & Poroca) Xavier-Leite, M. Cáceres & Lücking, comb. nov., A. atrofusca (R. Sant.) Xavier-Leite, M. Cáceres & Lücking, comb. nov., A. atromuralis (Lücking) Xavier-Leite, M. Cáceres & Lücking, comb. nov., A. marginata (Lücking) Xavier-Leite, M. Cáceres & Lücking, comb. nov., A. triseptata (Lücking) Xavier-Leite, M. Cáceres & Lücking, comb. nov., A. wilsoniorum (Lücking) Xavier-Leite, M. Cáceres & Lücking, comb. nov., Aulaxinella corticola (Kalb & Vězda) Xavier-Leite, M. Cáceres & Lücking, comb. nov., A. minuta (R. Sant.) Xavier-Leite, M. Cáceres & Lücking, comb. nov., A. multiseptata (R. Sant.) Xavier-Leite, M. Cáceres & Lücking, comb. nov., Batistomyces pallidus (Vězda) Xavier-Leite, M. Cáceres & Lücking, comb. nov., B. hyalinus (Kalb & Vězda) Xavier-Leite, M. Cáceres & Lücking, comb. nov., Bezerroplaca fusconitida (Lücking) Xavier-Leite, M. Cáceres & Lücking, comb. nov., B. incrustatociliata (Sérus.) Xavier-Leite, M. Cáceres & Lücking, comb. nov., B. lucernifera (Kalb & Vězda) Xavier-Leite, M. Cáceres & Lücking, comb. nov., B. pachyparaphysata (R. Sant.) Xavier-Leite, M. Cáceres & Lücking, comb. nov., B. streimannii (Sérus.) Xavier-Leite, M. Cáceres & Lücking, comb. nov., Caleniella maculans (Vain.) Xavier-Leite, M. Cáceres & Lücking, comb. nov., C. triseptata (Zahlbr.) Xavier-Leite, M. Cáceres & Lücking, comb. nov., Microxyphiomyces cuneatus (L.I. Ferraro & Vězda) Xavier-Leite, M. Cáceres & Lücking, comb. nov., M. demoulinii (Sérus.) Xavier-Leite, M. Cáceres & Lücking, comb. nov., M. elegans (Sérus.) Xavier-Leite, M. Cáceres & Lücking, comb. nov., M. kashiwadanii (G. Thor, Lücking & Tat. Matsumoto) Xavier-Leite, M. Cáceres & Lücking, comb. nov., M. lancicarpus (Kalb & Vězda) Xavier-Leite, M. Cáceres & Lücking, comb. nov., M. vainioi (R. Sant.) Xavier-Leite, M. Cáceres & Lücking, comb. nov. (syn.: M. manaosensis Bat., Valle & Peres.), M. santessonianus (Kalb & Vězda) Xavier-Leite, M. Cáceres & Lücking, comb. nov., M. santessonii (D. Hawks.) Xavier-Leite, M. Cáceres & Lücking, comb. nov., M. similis (Vězda) Xavier-Leite, M. Cáceres & Lücking, comb. nov., M. variratae (Lücking & Sipman) Xavier-Leite, M. Cáceres & Lücking, comb. nov., Monocalenia monospora (Vězda) Xavier-Leite, M. Cáceres & Lücking, comb. nov., Psathyromyces planus (Vězda) Xavier-Leite, M. Cáceres & Lücking, comb. nov., P. heterellus (Stirt.) Xavier-Leite, M. Cáceres & Lücking, comb. nov., Pseudocalenia solorinoides (Lücking) Xavier-Leite, M. Cáceres & Lücking, comb. nov., Roselviria lobulimarginata (Sipman & Lücking) Xavier-Leite, M. Cáceres & Lücking, comb. nov., R. purulhensis (Lücking, Sérus. & Vězda) Xavier-Leite, M. Cáceres & Lücking, comb. nov., Santricharia farinosa (R. Sant.) Xavier-Leite, M. Cáceres & Lücking, comb. nov., Sipmanidea neotropica (Lücking) Xavier-Leite, M. Cáceres & Lücking, comb. et stat nov., S. furcata (Sérus.) Xavier-Leite, M. Cáceres & Lücking, comb. nov., Spinomyces aggregatus (Lücking) Xavier-Leite, M. Cáceres & Lücking, comb. et stat. nov., S. albostrigosus (Lücking, Sérus. & Vězda) Xavier-Leite, M. Cáceres & Lücking, comb. nov., S. deslooveri (Sérus.) Xavier-Leite, M. Cáceres & Lücking, comb. nov., S. guatemalensis (Lücking & Barillas) Xavier-Leite, M. Cáceres & Lücking, comb. nov., S. microcarpus (Etayo & Lücking) Xavier-Leite, M. Cáceres & Lücking, comb. nov., S. verrucosus (Sérus.) Xavier-Leite, M. Cáceres & Lücking, comb. nov., Sporocybomyces leucomuralis (Lücking) Xavier-Leite, M. Cáceres & Lücking, comb. nov., S. leucotrichoides (Vain.) Xavier-Leite, M. Cáceres & Lücking, comb. nov., S. macgregorii (Vain.) Xavier-Leite, M. Cáceres & Lücking, comb. nov., Verruciplaca calcarea (Lücking) Xavier-Leite, M. Cáceres & Lücking, comb. et stat. nov., V. verrucifera (Lücking) Xavier-Leite, M. Cáceres & Lücking, comb. nov., Vezdamyces albopruinosus (Lücking) Xavier-Leite, M. Cáceres & Lücking, comb. et stat. nov., and V. vulgaris (Müll. Arg.) Xavier-Leite, M. Cáceres & Lücking, comb. nov. [ABSTRACT FROM AUTHOR]

The genus Coenogonium, the only genus in the family Coenogoniaceae, is mostly found in tropical and subtropical regions. Approximately 100 species of Coenogonium are known worldwide, and about 52 species have been previously recorded from Brazil. Here, we describe four species as new to science from the Atlantic Forest in the states of Bahia, Minas Gerais, and Sergipe, and present a few new state records. The new species are C. carassense, C. itabaianense, C. pilosum, and C. subtomentosum. An annotated checklist of the species of Coenogonium from Brazil is also included. [ABSTRACT FROM AUTHOR]

We describe 14 new lichen species in the family Graphidaceae, mainly from the Amazon basin: Acanthothecis aggregata, Allographa ancelina, A. apicalinspersa, Chapsa constrictospora, C. diorygmoides, C. lichexanthonica, Clandestinotrema caloplacosporum, Diorygma defectoisidiatum, D. gyrosum, D. lichexanthonicum, D. norsubmuriforme, D. salxanthonicum, D. toensbergianum, and Ocellularia flavoradiata. For each species, it is indicated where and how it would key out in a recent identification key. Two of the Diorygma species are sterile and were assigned to this genus by sequencing the mtSSU gene. Five additional species are new to Brazil and 27 others, including some Gomphillaceae, are new state records. [ABSTRACT FROM AUTHOR]

Fungi comprise approximately 20% of all eukaryotic species and are connected to virtually all life forms on Earth. Yet, their diversity remains contentious, their distribution elusive, and their conservation neglected. We aim to flip this situation by synthesizing current knowledge. We present a revised estimate of 2–3 million fungal species with a "best estimate" at 2.5 million. To name the unknown >90% of these by the end of this century, we propose recognition of species known only from DNA data and call for large-scale sampling campaigns. We present an updated global map of fungal richness, highlighting tropical and temperate ecoregions of high diversity. We call for further Red List assessments and enhanced management guidelines to aid fungal conservation. Given that fungi play an inseparable role in our lives and in all ecosystems, and considering the fascinating questions remaining to be answered, we argue that fungi constitute the next frontier of biodiversity research. [ABSTRACT FROM AUTHOR]

A first integrative survey of the genus Usnea in the southern Philippines, taking into account morphological, anatomical, chemical and molecular characters, resulted in the recognition of 20 taxa, including three species new to science: Usnea angulata Ach., U. baileyi (Stirt.) Zahlbr., U. bismolliuscula Zahlbr., U. brasiliensis (Zahlbr.) Motyka, U. confusa Asah., U. croceorubescens Stirt., U. dasaea Stirt., U. himalayana C. Bab., U. krogiana P. Clerc, U. longissima Ach., U. nidifica Taylor, U. norsticornuta A. Gerlach & P. Clerc sp. nov. (characterized by a moderately thick cortex and by the presence of norstictic acid), U. paleograndisora A. Gerlach & P. Clerc sp. nov. (characterized by an orange subcortical pigmentation in the medulla, with enlarging soralia and a moderately thick and shiny cortex), U. pectinata Taylor, U. pygmoidea (Asahina) Y. Ohmura, U. rubicunda Stirt., U. rubrotincta (Stirt.) Zahlbr., U. spinulifera (Vain.) Motyka, U. subscabrosa Motyka and U. yoshihitoi P. Clerc & A. Gerlach sp. nov. (characterized by a lax medulla with non-conglutinated hyphae). Usnea krogiana is a new record for Asia; Usnea brasiliensis , Usnea confusa and U. croceorubescens are new records for the Philippines. This is the first phylogenetic study to include DNA sequences of Usnea from the Philippines. Molecular data from the ITS rDNA (76 newly generated sequences) are presented for most taxa except for U. himalayana , U. longissima and U. subscabrosa. At least six further taxa remain unidentified, awaiting the collection of additional specimens. [ABSTRACT FROM AUTHOR]

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]

A survey of the lichen family Graphidaceae in Macaronesia (Madeira, the Canary Islands, and the Azores) is presented, with detailed treatments for the genera Allographa, Fissurina, and Graphis. All other species are listed and new records provided. A key to all Graphicacy known from Macaronesia, except the thelotremoid species, is presented. The following species are newly described: Fissurina azorica, Fissurina elaiocarpoides, Fissurina nigrolabiata, and Topeliopsis juniperina. Many species are newly recorded for one or more islands of the three archipelagos. [ABSTRACT FROM AUTHOR]

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In this study, we revised the lichen collection at the Herbario Amazonico Colombiano (coah) in Bogotá, Colombia. The collection has a total of nearly 2,400 specimens, with some duplicates in the Herbario Nacional (col) and in the herbarium of the Botanic Garden in Berlin (b). The revision of 1,861 specimens revealed 574 species in 142 genera and 44 families, among which there are 28 species new to science and seven new combinations. Previously, 324 species had been reported from the Colombian Amazon, and our revision resulted in a new total of 666 species, more than doubling the previous number. All 666 species are enumerated here in the first comprehensive checklist of lichens from the Colombian Amazon. A total of 157 new country records (53 already reported in the new Catalogue of Fungi of Colombia) increase the number of lichens known from Colombia to 2,827. The following species are described as new: Allographa exuens, differing from A. argentata by the lirellae with the corticiform layer soon flaking off and exposing the black labia, the only finely inspersed hymenium, and the narrower ascospores; A. guainiae, differing from Graphis syzygii in the prominent ascomata with lateral thalline margin and whitish thallus remnants between the striae; A. labiata, differing from A. immersa in the prominent lirellae with conspicuous, entire, exposed labia, an inspersed hymenium, longer ascospores, and stictic acid as secondary compound; A. lichexanthonica, differing from A. sitiana in producing lichexanthone; A. sessilis, differing from A. contortuplicata in the muriform ascospores; A. suprainspersata, differing from A. angustata in the very thin thalline cover of the ascomata and the apically inspersed hymenium; Astrothelium bireagens, differing from A. cinnamomeum by the broader, apically flattened perithecia covered by a thin, ferruginous-red, K+ deep purple pruina and internally with an ochraceous-yellow, K+ deep yellow pigment; A. stromatolucidum, differing from A. neovariolosum in the distinctly pseudostromatic ascomata; Carbacanthographis submultiseptata, differing from C. multiseptata in the narrower ascospores and the indistinct periphysoids; Chapsa inconspicua, differing from C. angustispora in the smooth to uneven versus farinose thallus and in the much shorter ascospores; Coenogonium velutinellum, differing from C. pineti in the finely velvety, rather thick thallus composed of irregular to erect, densely packed algal threads covered by a thin pseudocortex; Fellhanera naevioides, differing from F. naevia in the finely dispersed, minutely crenulate thallus and the blackish apothecia; Fissurina sipmanii, differing from F. amazonica in the shorter and broader, slightly gaping, somewhat chroodiscoid ascomata, and the amyloid ascospores; Glyphis lirellizans, differing from Glyphis substriatula in the erumpent vs. prominent lirellae with lateral thalline margin and the exposed disc; Graphis papillifera, differing from G. stellata in the lirellae lacking a thalline margin, very elongate and irregularly to radiately branched and not in stellate clusters, and in the 5-septate ascospores; G. pseudoglyphis, differing from Graphis stellata in the non-verrucose thallus, the branched lirellae which do not, however, form stellate clusters, and the shorter ascospores; Malmidea flavimarginata, differing from M. bacidinoides in the pale yellow, K+ deep yellow medulla and yellow, K+ deep yellow excipular crystals, as well as the smaller ascospores; M. isidiopiperina, differing from M. taytayensis in the smaller ascospores; M. papillitrailiana, differing from M. trailiana in the papillose apothecial margins; Myriotrema araracuarense, differing from Myriotrema muluense in the non-annulate pores of the apothecia and in the longer ascospores; Ocellularia areolata, differing from Ocellularia rhicnoporoides in the pigmented medulla and the larger, more prominent apothecia with completely carbonized excipulum; O. caquetensis, differing from Ocellularia rotundifumosa in the absence of a columella; O. inspersipallens, differing from O. viridipallens in the inspersed hymenium and the 5–7-septate ascospores; O. rufocinctoides, differing from O. rufocincta in the thallus lacking large and irregular crystal clusters, in the more prominent apothecia and in the smaller ascospores; O. sipmanii, differing from Ocellularia abbayesiana in the smaller, 3-septate ascospores; Pseudopyrenula daironii, differing from all other species of the genus in the aggregate perithecia with shared ostiole and the internal orange-red pigment granules lining the perithecial wall; Pyrenula asymmetrica, differing from Pyrenula papilligera in the longer, almost rectangular ascospores; and Redingeria pseudostromatica, differing from other species in the genus in the pseudostromatic ascomata with small, rounded apothecia, in combination with 1-septate ascospores. In addition, the following seven new combinations are proposed: Bacidina cyanophila (≡ Bacidina simplex var. cyanophila), Malmidea sorediifera (≡ Lecanora sorediifera), Ocellularia fuscescens (≡ Thelotrema fuscescens), Phaeographis cymbegrapha (≡ Graphis cymbegrapha; = Phaeographis amazonica Staiger], Polyblastidium flavosquamosum (≡ Heterodermia flavosquamosa), Polyblastidium lamelligerum (≡ Parmelia lamelligera), and Polyblastidium rottboellii (≡ Anaptychia hypoleuca var. rottboellii). [ABSTRACT FROM AUTHOR]

We sequenced over 200 recent specimens of Lecanora s.lat. from Brazil, delimiting 28 species in our material. Many seem to represent undescribed species, some of which being morphologically and chemically similar to each other or to already described species. Here, we present a phylogenetic analysis based on ITS, including our specimens and GenBank data. We describe nine new species. The purpose of the paper is to illustrate the diversity of the genus in Brazil, not to focus on segregate genera. However, we found that all Vainionora species cluster together and these will be treated separately. Other Lecanora species with dark hypothecium clustered in several different clades. Species with the morphology of Lecanora caesiorubella, in which currently several subspecies with different chemistry and distribution are recognized, fall apart in different, distantly related clades, so they cannot be regarded as subspecies but should be recognized at species level. A key is given for the Lecanora species from Brazil. [ABSTRACT FROM AUTHOR]

The access to molecular collections worldwide greatly improves the quality of scientific research by making a growing number of data available for investigation. The efforts on digitisation also aim at facilitating the exchange of material between institutions and researchers that must follow regulations in place and respect best practice. The handbook presented here proposes a workflow to follow to safely exchange materials, in accordance with international laws and legislation. We make numerous recommendations here to help the institutions and researchers to navigate the legal and administrative procedures, in order to manage molecular collections in the best way possible. [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]

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]

In this study we present an analysis of the Pyrenula ochraceoflava group (Pyrenulaceae), focusing on the Neotropics and based on morphological, chemical, and molecular data of the mtSSU, nuLSU and ITS markers. We described three new species from tropical dry forests of Mexico, confirm the monophyly of the P. ochraceoflava group and provide evidence for the inclusion of species currently placed in the genus Mazaediothecium within Pyrenula. Pyrenula aurantiacoretis sp. nov. is characterized by an orange pigment covering the thallus in net-like fashion, muriform ascospores with 4 rows of 1–4 cells each, 12–15.5 × 8–10.5 µm, and 7-chloroemodin and emodin as major compounds. Pyrenula connexa sp. nov. is closely related to Mazaediothecium album, being characterized by mazaedioid pyrenocarps, basal and lateral excipular carbonization, highly variable mature ascospores, 1-septate to submuriform, thallus with abundant white verrucae, and lichexanthone as major compound. Pyrenula moldenkeorum sp. nov. is characterized by an orange thallus, submuriform ascospores that frequently show pigmented septa forming a cross septation pattern, 7.5–11 × 5.5–8.5 µm in size, and 7-chloroemodin and emodin as major compounds. The taxonomy of the most common and widespread species of the group, P. ochraceoflava and P. ochraceoflavens, is briefly discussed, presenting evidence to support the consideration of P. ochraceoflava as a species complex. The two species Mazaedothecium album and M. mohamedii are transferred to Pyrenula as P. aptrootiana nom. nov. [non Pyrenula alba (Schrad.) A.Massal.] and P. mohamedii comb. nov. [ABSTRACT FROM AUTHOR]

Mycocaliciales comprise non-lichenized either saprotrophic or lichenicolous fungi which occur in temperate and tropical regions. The mazaediate, saprotrophic and monospecific genus, Pyrgidium, is currently assigned to this order, yet the phylogenetic placement of the genus has remained uncertain due to the absence of molecular data. In order to investigate the systematic position of Pyrgidium, two specimens collected in Brazil and Thailand, respectively, were used to generate mtSSU, SSU, LSU and ITS sequences. However, given that most other representatives of this order only have LSU and ITS sequences available, the phylogenetic reconstruction was limited to these two markers. The phylogenetic analyses confirmed placement of the genus within Mycocaliciales, the genus possessing a sister group relationship with the lichenicolous genus Sphinctrina. Detailed morphological descriptions and illustrations are provided, including those for type specimens of the various synonyms subsumed under the hitherto only accepted species, Pyrgidium montellicum (Beltr.) Tibell. The ascospore morphology was investigated using compound and scanning electronic microscopy (SEM). Principal component analysis (PCA) was performed for the ascospore size using PC-ORD 7. The molecular data and re-examination of the type specimens support the monospecific nature of this genus. [ABSTRACT FROM AUTHOR]

Tropical regions harbor a substantial diversity of lichenized fungi, but face numerous threats to their persistence, often even before previously unknown species have been described and their evolutionary relationships have been elucidated. Megalaria (Ramalinaceae) is a lichen-forming genus of fungi that produces crustose thalli, and includes a number of lineages occupying tropical rain forests; however, taxonomic and phylogenetic work on this clade is limited. Here we leverage both morphological and sequence data to describe a new species from the tropics, M. pachaylenophila. This taxon forms a crustose thallus, lacks secondary metabolites, and occurs in mangrove forests of Thailand. We supplemented molecular data from this species with data from other species, including two genera related to and occasionally included in Megalaria, namely Catillochroma and Lopezaria. Our analyses revealed Catillochroma species form a monophyletic group embedded within Megalaria, and we therefore recognize this clade at the subgeneric level. Since we only included the type species of Lopezaria in this study, we refrain from proposing a taxonomic conclusion for that clade at the moment. Several taxonomic combinations are made to reflect phylogenetic evidence supporting the inclusion of these species in Megalaria. [ABSTRACT FROM AUTHOR]

Six species of Sticta are described as new to science on the basis of material from Bolivia and supported by phylogenetic analysis of the fungal ITS barcoding marker. The species were resolved in all three of the clades (I, II, III) widespread and common in the Neotropics, as defined in an earlier study on the genus. Comparison with material from neighbouring countries (i.e. Colombia, Ecuador, Peru) suggests that these new species may be potentially endemic to the Bolivian Yungas ecoregion. For each species, a detailed morphological and anatomical description is given. Sticta amboroensis Ossowska, Kukwa, B. Moncada & Lücking is a medium-sized green-algal species with laminal to submarginal apothecia with hirsute margins and with light to dark brown lower tomentum. Sticta aymara Ossowska, Kukwa, B. Moncada, Flakus, Rodriguez-Flakus & Lücking is a comparatively small cyanobacterial taxon with Nostoc as photo-biont, laminal, richly branched, aggregate isidia and a golden to chocolate-brown lower tomentum. The medium-sized, cyanobacterial S. bicellulata Ossowska, Kukwa, B. Moncada & Lücking has cyanobacterial photobiont, bicellular ascospores, apothecia with white to golden-brown hairs on the margins, K+ violet apothecial margin (ring around disc) and epihymenium and a white to dark brown lower tomentum. In contrast, the green-algal species, S. carrascoensis Ossowska, Kukwa, B. Moncada & Lücking is characterised by its large size, apothecia with dark brown hairs on the margins and a yellow medulla. The cyanobacterial S. catharinae Ossowska, B. Moncada, Kukwa, Flakus, Rodriguez-Flakus & Lücking forms stipitate thalli with Nostoc as photobiont, abundant, laminal to submarginal apothecia and a golden-brown lower tomentum. Finally, the cyanobacterial S. pseudoimpressula Ossowska, Kukwa, B. Moncada & Lücking produces laminal apothecia with an orange-yellow line of pruina along the margins which reacts K+ carmine-red. In addition to the six new Bolivian taxa, the cyanobacterial S. narinioana B. Moncada, Ossowska & Lücking is described as new from Colombia and it represents the closely-related sister species of the Bolivian S. aymara; it differs from the latter largely in the marginal instead of laminal isidia. [ABSTRACT FROM AUTHOR]

We assessed the status of two New Zealand endemic morphodemes in the genus Sticta , currently treated as two separate taxa, Sticta filix and Sticta lacera. Both are green-algal lichens with a distinct stipe that grow in forested habitats and are suitable indicators of the indigenous vegetation health in forest ecosystems in New Zealand. They exhibit different morphologies and substrate ecologies: S. filix forms rather robust thalli, often on exposed trunks of phorophytes, with erect stems distinctly emerging from the substrate, whereas S. lacera is a more delicate lichen growing near the base of trees, usually among bryophyte mats or sheltered in the exposed portions of the phorophyte root-plate, with a prostrate, branched, stolon-like stem barely emerging from the substrate. Throughout their range, both taxa grow sympatrically and often in close proximity (syntopically). Despite the differences, ITS barcoding does not support the two morphodemes as separate species. In this study we assessed two possible explanations: (1) S. filix and S. lacera are discrete phenotypes of a single species, caused by developmental switching triggered by a discrete environmental variable, the propagules developing either on bare substrate or between bryophytes; and (2) the two morphodemes represent separate lineages, but ITS does not provide sufficient resolution to reflect this. We performed a quantitative analysis of morphological and ecological parameters, based on vouchered herbarium collections and field observations on iNaturalist NZ (https://inaturalist.nz), to assess the level of discreteness of the growth forms and to test for a correlation with the presence of a bryophyte mat. We further took advantage of an existing molecular data set from a target capture approach, comprised of 205 protein markers. This data set was used to establish a framework of percentage identities between pairs of the same and of different species among lobarioid Peltigeraceae and then to test whether the S. filix / lacera pairing fell closer to a within-species or a between-species pairing. The morphometric analysis of herbarium material resolved S. filix and S. lacera as two discrete morphs with little overlap, supported by numerous observations on iNaturalist NZ. However, whereas herbarium material suggested a significant association of the lacera morph with bryophyte mats, no such pattern was evident from field images on iNaturalist NZ, in which both morphs frequently associated with bryophyte mats. This highlights the limitations of herbarium material to correctly assess substrate ecology, whereas iNaturalist NZ postings had issues with correct identifications, given that especially S. lacera is easily confused with Pseudocyphellaria multifida. Based on the target capture data, the percentage identity of the S. filix / lacera pairing (99.43%) was significantly higher than that of all 12 between-species pairings (93.20–98.01%); it was at the same time lower than that of all within-species pairings (99.63–99.99%) but significantly so only in comparison with five out of the eight within-species pairings. The target capture approach is thus inconclusive, but the combination of all data suggests that S. filix and S. lacera are not discrete morphodemes of a single species but represent two separate lineages which emerged recently and hence cannot be resolved using the ITS barcoding marker or even a deeper phylogenomic approach based on protein-coding markers. We propose transplantation experiments and the application of RADseq to further assess this situation. [ABSTRACT FROM AUTHOR]

Lichens collected worldwide for centuries have resulted in millions of specimens deposited in herbaria that offer the potential to assess species boundaries, phenotypic diversification, ecology, and distribution. The application of molecular approaches to historical collections has been limited due to DNA fragmentation, but high-throughput sequencing offers an opportunity to overcome this barrier. Here, we combined a large dataset of ITS sequences from recently collected material and historical collections, obtained through Sanger, 454, or Illumina Sequencing, to test the performance of ITS barcoding in two genera of lichenized Basidiomycota: Cora and Corella. We attempted to generate new sequence data for 62 fresh specimens (from 2016) and 274 historical collections (collected between 1888 and 1998), for a final dataset of 1325 sequences. We compared various quantitative approaches to delimit species (GMYC, bPTP, ASAP, ABGD) and tested the resolution and accuracy of the ITS fungal barcoding marker by comparison with a six-marker dataset. Finally, we quantitatively compared phylogenetic and phenotypic species delimitation for 87 selected Cora species that have been formally described. Our HTS approach successfully generated ITS sequences for 76% of the historical collections, and our results show that an integrative approach is the gold-standard for understanding diversity in this group. [ABSTRACT FROM AUTHOR]

The genus Dendriscosticta (Ascomycota: Peltigerales) encompasses several distinctive lichen‐forming fungal species restricted to the Northern Hemisphere. Most are flagship species of old‐growth forests with good air quality. A global phylogeny of the genus based on multilocus sequence data (ITS, RPB1, EF‐1α, MCM7), model‐based phylogenetic methods, and morphological and chemical assessments, reveals a high level of cryptic speciation often associated with restricted geographical distribution and/or chemical characters. Using sequence‐based species delimitation approaches, we circumscribe two main clades referred to as the D. wrightii clade, with five unequivocal species, including D. gelida sp. nov., and the D. praetextata clade, with eight putative species, including D. phyllidiata sp. nov. The absence of recently collected material of D. hookeri comb. nov. from the type locality unfortunately prevents assignment of this epithet to one of the five supported lineages sharing this morphotype. Three new combinations are proposed: D. hookeri, D. insinuans comb. nov. and D. yatabeana comb. nov. Epitypes are designated for D. wrightii and D. yatabeana. Species diversity within the genus increased from four to nine. Our morphological assessment confirmed that Sticta and Dendriscosticta can be readily distinguished by the presence of excipular algae whereas the structure of the lower surface pores is not a reliable diagnostic feature. [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]

As part of a revision of the genus Acanthothecis s. lat. (Graphidaceae) in Brazil, an updated world key to the known species of the genus is presented. From Brazil, the following ten new species are described: A. latispora, with single-spored asci, large, muriform ascospores, and norstictic and stictic acids; A. megalospora, with single-spored asci, very large, transversely septate ascospores, and norstictic and protocetraric acids; A. multiseptata, with 8-spored asci, medium-sized and narrow, transversely multiseptate ascospores, and lacking secondary substances except terpenoids; A. norstictica, with 1–2-spored asci, large, muriform ascospores, and norstictic acid; A. oryzoides, with 8-spored asci, medium-sized, transversely septate ascospores, and norstictic acid; A. rimosa, with 2-spored asci, small to medium-sized, muriform ascospores, and stictic acid; A. roseola, with 1–2-spored asci, large, muriform ascospores, and norstictic, stictic and subnorstictic acids; A. saxicola, with 8-spored asci, small, 3-septate ascospores, and norstictic acid; A. subfarinosa, with 8-spored asci, small, 6–8-septate ascospores, and norstictic acid; and A. submuriformis, with 8-spored asci, small, submuriform ascospores, and lichexanthone. In addition, three further species are formally validated, namely A. bicellulata, A. farinosa and A. subabaphoides, and the new combination A. bicellularis is proposed, based on Acanthotrema bicellularis. [ABSTRACT FROM AUTHOR]

We provide an updated, worldwide key to species of the genus Carbacanthographis, which is characterized by lirellate ascomata, a carbonized excipulum, warty periphysoids, and mostly non-amyloid ascospores. New collections and revision of herbarium material revealed 17 species new to science: Carbacanthographis acanthoamicta, with a thinly corticate thallus, a completely carbonized excipulum, apically warty paraphyses, small and (sub-)muriform ascospores, and salazinic acid; C. acanthoparaphysata, with a completely carbonized excipulum, apically warty paraphyses, small and submuriform, amyloid ascospores, and protocetraric acid; C. aggregata, with aggregated lirellae, a completely carbonized excipulum, small and submuriform ascospores, and salazinic acid; C. amazonica, with a completely carbonized excipulum, small and transversely septate ascospores, and stictic acid; C. aptrootii, with a completely carbonized excipulum, apically warty paraphyses, small to medium-sized and transversely septate, amyloid ascospores, and norstictic acid; C. brasiliensis, with a completely carbonized excipulum, apically warty paraphyses, medium-sized and transversely septate, amyloid ascospores, and no substances; C. chionophoroides, with a completely carbonized excipulum, small and transversely septate ascospores, and protocetraric acid; C. halei, with a corticate thallus, a completely carbonized excipulum, small and transversely septate ascospores, and stictic acid; C. latispora, with a completely carbonized excipulum, very large and transversely septate ascospores, and stictic acid; C. megalospora, with a corticate thallus, a completely carbonized excipulum, very large muriform ascospores, and stictic acid; C. multiseptata, with a completely carbonized excipulum, very large and transversely septate ascospores, and protocetraric acid; C. novoguineensis, with a completely carbonized excipulum, small and submuriform ascospores, and salazinic acid; C. pseudorustica, with a corticate thallus, a completely carbonized excipulum, medium-sized and transversely septate, amyloid ascospores, and stictic acid; C. salazinicoides, with a corticate thallus, a completely carbonized excipulum, medium-sized and muriform ascospores, and salazinic acid; C. sipmaniana, with a completely carbonized excipulum, apically warty paraphyses, small and transversely septate, weakly amyloid ascospores, and norstictic acid; C. spongiosa, with a completely carbonized excipulum, inspersed hymenium, small, transversely septate ascospores, and stictic acid; and C. subchionophora, with a completely carbonized excipulum, small and transversely septate ascospores, and protocetraric acid. New molecular data confirm the position of C. megalospora in the genus. In addition, we propose one new combination, Carbacanthographis nematoides. The known world distribution of four species is expanded: C. amicta is reported from Papua New Guinea; C. induta from Thailand; C. marcescens from French Guyana and Papua New Guinea; and C. stictica from Colombia, French Guyana, Venezuela and Suriname. For all species, short descriptions and distribution notes are given, and most species are illustrated. [ABSTRACT FROM AUTHOR]

VIETBIO [Innovative approaches to biodiversity discovery and characterisation in Vietnam] is a bilateral German-Vietnamese research and capacity building project focusing on the development and transfer of new methods and technology towards an integrated biodiversity discovery and monitoring system for Vietnam. Dedicated field training and testing of innovative methodologies were undertaken in Cuc Phuong National Park as part and with support of the project, which led to the new biodiversity data and records made available in this article collection. VIETBIO is a collaboration between the Museum für Naturkunde Berlin - Leibniz Institute for Evolution and Biodiversity Science (MfN), the Botanic Garden and Botanical Museum, Freie Universität Berlin (BGBM) and the Vietnam National Museum of Nature (VNMN), the Institute of Ecology and Biological Resources (IEBR), the Southern Institute of Ecology (SIE), as well as the Institute of Tropical Biology (ITB); all Vietnamese institutions belong to the Vietnam Academy of Science and Technology (VAST). The article collection "VIETBIO" (https://doi.org/10.3897/bdj.coll.63) reports original results of recent biodiversity recording and survey work undertaken in Cuc Phuong National Park, northern Vietnam, under the framework of the VIETBIO project. The collection consist of this "main" cover paper - characterising the study area, the general project approaches and activities, while also giving an extensive overview on previous studies from this area - followed by individual papers for higher taxa as studied during the project. The main purpose is to make primary biodiversity records openly available, including several new and interesting findings for this biodiversity-rich conservation area. All individual data papers with their respective primary records are expected to provide useful baselines for further taxonomic, phylogenetic, ecological and conservation-related studies on the respective taxa and, thus, will be maintained as separate datasets, including separate GUIDs also for further updating. [ABSTRACT FROM AUTHOR]

Background: Mendogia belongs to Dothideomycetes and its members are epiphytic on living bamboo culms or palms and distributed in tropical regions. Currently, the genus comprises seven species. Another collection resembling Mendogia was collected from the leaves of Fagales sp. in Thailand. Morphological characteristics and multilocus phylogenetic analyses, using ITS, LSU and SSU sequences, showed that the fungus is new to science, described herein as Mendogia diffusa. Mendogia diffusa is characterised by apothecial ascostromata, a carbonised epithecium, dark brown setae on the ascostromatal surface, hyaline paraphysoids, ovoid to clavate asci and oblong to elliptical, muriform ascospores. The fungus has a dark pigmented surface and is occasionally facultatively associated with patches of green algae, but not actually lichenised. Instead, the fungus penetrates the upper leaf surface, forming dark pigmented isodiametric cells below the epidermis. New information: Re-examination of specimens of M. chiangraiensis, M. macrostroma and M. yunnanensis revealed the absence of algal associations. The status of Mendogia philippinensis (= M. calami) and M. bambusina (= Uleopeltis bambusina) was established, based on morphological comparisons and previous studies. Comprehensive morphological descriptions with phylogenetic analyses support M. diffusa as a novel species in Myriangiaceae. An updated key to the known species of the genus is also provided. [ABSTRACT FROM AUTHOR]

Lichens are symbiotic associations resulting from interactions among fungi (primary and secondary mycobionts), algae and/or cyanobacteria (primary and secondary photobionts), and specific elements of the bacterial microbiome associated with the lichen thallus. The question of what is a species, both concerning the lichen as a whole and its main fungal component, the primary mycobiont, has faced many challenges throughout history and has reached new dimensions with the advent of molecular phylogenetics and phylogenomics. In this paper, we briefly revise the definition of lichens and the scientific and vernacular naming conventions, concluding that the scientific, Latinized name usually associated with lichens invariably refers to the primary mycobiont, whereas the vernacular name encompasses the entire lichen. Although the same lichen mycobiont may produce different phenotypes when associating with different photobionts or growing in axenic culture, this discrete variation does not warrant the application of different scientific names, but must follow the principle "one fungus = one name". Instead, broadly agreed informal designations should be used for such discrete morphologies, such as chloromorph and cyanomorph for lichens formed by the same mycobiont but with either green algae or cyanobacteria. The taxonomic recognition of species in lichen-forming fungi is not different from other fungi and conceptual and nomenclatural approaches follow the same principles. We identify a number of current challenges and provide recommendations to address these. Species delimitation in lichen-forming fungi should not be tailored to particular species concepts but instead be derived from empirical evidence, applying one or several of the following principles in what we call the LPR approach: lineage (L) coherence vs. divergence (phylogenetic component), phenotype (P) coherence vs. divergence (morphological component), and/or reproductive (R) compatibility vs. isolation (biological component). Species hypotheses can be established based on either L or P, then using either P or L (plus R) to corroborate them. The reliability of species hypotheses depends not only on the nature and number of characters but also on the context: the closer the relationship and/or similarity between species, the higher the number of characters and/or specimens that should be analyzed to provide reliable delimitations. Alpha taxonomy should follow scientific evidence and an evolutionary framework but should also offer alternative practical solutions, as long as these are scientifically defendable. Taxa that are delimited phylogenetically but not readily identifiable in the field, or are genuinely cryptic, should not be rejected due to the inaccessibility of proper tools. Instead, they can be provisionally treated as undifferentiated complexes for purposes that do not require precise determinations. The application of infraspecific (gamma) taxonomy should be restricted to cases where there is a biological rationale, i.e., lineages of a species complex that show limited phylogenetic divergence but no evidence of reproductive isolation. Gamma taxonomy should not be used to denote discrete phenotypical variation or ecotypes not warranting the distinction at species level. We revise the species pair concept in lichen-forming fungi, which recognizes sexually and asexually reproducing morphs with the same underlying phenotype as different species. We conclude that in most cases this concept does not hold, but the actual situation is complex and not necessarily correlated with reproductive strategy. In cases where no molecular data are available or where single or multi-marker approaches do not provide resolution, we recommend maintaining species pairs until molecular or phylogenomic data are available. This recommendation is based on the example of the species pair Usnea aurantiacoatra vs. U. antarctica, which can only be resolved with phylogenomic approaches, such as microsatellites or RADseq. Overall, we consider that species delimitation in lichen-forming fungi has advanced dramatically over the past three decades, resulting in a solid framework, but that empirical evidence is still missing for many taxa. Therefore, while phylogenomic approaches focusing on particular examples will be increasingly employed to resolve difficult species complexes, broad screening using single barcoding markers will aid in placing as many taxa as possible into a molecular matrix. We provide a practical protocol how to assess and formally treat taxonomic novelties. While this paper focuses on lichen fungi, many of the aspects discussed herein apply generally to fungal taxonomy. The new combination Arthonia minor (Lücking) Lücking comb. et stat. nov. (Bas.: Arthonia cyanea f. minor Lücking) is proposed. [ABSTRACT FROM AUTHOR]

It is now a decade since The International Commission on the Taxonomy of Fungi (ICTF) produced an overview of requirements and best practices for describing a new fungal species. In the meantime the International Code of Nomenclature for algae, fungi, and plants (ICNafp) has changed from its former name (the International Code of Botanical Nomenclature) and introduced new formal requirements for valid publication of species scientific names, including the separation of provisions specific to Fungi and organisms treated as fungi in a new Chapter F. Equally transformative have been changes in the data collection, data dissemination, and analytical tools available to mycologists. This paper provides an updated and expanded discussion of current publication requirements along with best practices for the description of new fungal species and publication of new names and for improving accessibility of their associated metadata that have developed over the last 10 years. Additionally, we provide: (1) model papers for different fungal groups and circumstances; (2) a checklist to simplify meeting (i) the requirements of the ICNafp to ensure the effective, valid and legitimate publication of names of new taxa, and (ii) minimally accepted standards for description; and, (3) templates for preparing standardized species descriptions. [ABSTRACT FROM AUTHOR]

Amazon, Atlantic forest, Brejos de Altitude, Caatinga, Carrasco, Cerradão and Restinga are major vegetation units in North and Northeast Brazil. Little is known about lichen metacommunity structure in these habitats. While species richness and composition generally depend on climatic factors, in azonal vegetation edaphic factors may have a filtering effect on tree bark structure and hence the composition of epiphytic lichen communities. We hypothesized that climatic stress and a tree bark filtering effect would result in reduced richness and phylogenetic clustering in Caatinga, Carrasco, Cerradão and Restinga, whereas high richness and phylogenetic overdispersion were predicted for Amazon and Atlantic Forest. To test this, we analyzed 2,090 lichenized species in the study area, with a supertree to assess phylogenetic metacommunity structure. Amazon and Atlantic forest exhibited high richness and phylogenetic diversity, with phylogenetic overdispersion only in the Amazon. The zonal Caatinga with drought stress and the extrazonal Brejos both exhibited phylogenetic clustering. Among the azonal, edaphic vegetation units, Cerradão exhibited phylogenetic overdispersion, whereas Restinga showed phylogenetic clustering. Nearest taxon phylogenetic distance indicated a close relationship between Amazon and Atlantic forest, Atlantic forest and Brejos and Atlantic forest and Caatinga. Carrasco was mostly closely related to Cerradão, and Restinga was distantly related to any other unit. These findings indicate more complex patterns in the phylogenetic structure of lichen metacommunities, partly reflecting those of plant metacommunities, as a result of concurrent macroecological evolutionary histories. Our data supported floristic evidence that Carrasco is part of the Cerrado complex and not related to Caatinga. [ABSTRACT FROM AUTHOR]

Recent studies have uncovered remarkable diversity in Dictyonema s.lat. basidiolichens, here recognized as subtribe Dictyonemateae. This group includes five genera and 148 species, but hundreds more await description. The photobionts of these lichens belong to Rhizonema, a recently resurrected cyanobacterial genus known by a single species. To further investigate photobiont diversity within Dictyonemateae, we generated 765 new cyanobacterial sequences from 635 specimens collected from 18 countries. The ITS barcoding locus supported the recognition of 200 mycobiont (fungal) species among these samples, but the photobiont diversity was comparatively low. Our analyses revealed three main divisions of Rhizonema, with two repeatedly recovered as monophyletic (proposed as new species), and the third mostly paraphyletic. The paraphyletic lineage corresponds to R. interruptum and partnered with mycobionts from all five genera in Dictyonemateae. There was no evidence of photobiont‐mycobiont co‐speciation, but one of the monophyletic lineages of Rhizonema appears to partner predominantly with one of the two major clades of Cora (mycobiont) with samples collected largely from the northern Andes. Molecular clock estimations indicate the Rhizonema species are much older than the fungal species in the Dictyonemateae, suggesting that these basidiolichens obtained their photobionts from older ascolichen lineages and the photobiont variation in extant lineages of Dictyonemateae is the result of multiple photobiont switches. These results support the hypothesis of lichens representing "fungal farmers," in which diverse mycobiont lineages associate with a substantially lower diversity of photobionts by sharing those photobionts best suited for the lichen symbiosis among multiple and often unrelated mycobiont lineages. see also the Perspective by Matthew P. Nelsen. [ABSTRACT FROM AUTHOR]

We describe the new lichenized fungus Lasioloma antillarum Lücking, Högnabba & Sipman from the Netherlands Antilles. The new species is characterized by a corticolous growth habit, apothecia with shortly tomentose margins, and rather small (35–50 × 12–16 µm), muriform ascospores in numbers of 2(–4) per ascus. The material had originally been identified as Calopadia phyllogena (Müll. Arg.) Vězda, with associated sequence data, but in phylogenetic analyses consistently fell outside the latter genus. Its revised identification as a species of Lasioloma is consistent with its phylogenetic position and underlines the necessity of posterior annotations in public sequence repositories, in order to correct previous identifications. Citation: Lücking R., Högnabba F. & Sipman H. J. M. 2021: Lasioloma antillarum (Ascomycota: Pilocarpaceae), a new lichenized fungus from the Antilles, and the importance of posterior annotations of sequence data in public repositories. – Willdenowia 51: 83–89. Version of record first published online on 23 March 2021 ahead of inclusion in April 2021 issue. [ABSTRACT FROM AUTHOR]

Sticta is a subcosmopolitan genus most diverse in the tropics. Traditionally, many taxa were considered to be widespread and morphologically variable, following broadly circumscribed morphodemes. Among these is the S. weigelii morphodeme, characterized by a cyanobacterial photobiont and rather narrow, flabellate to truncate or tapering lobes producing predominantly marginal isidia. Molecular phylogenetic analyses focusing on the ITS fungal barcoding marker revealed that this morphodeme represents several species, some of which are only distantly related to each other. Here we describe two species and one subspecies of this morphodeme as new to science, based on analysis of 400 specimens, for 344 of which we generated ITS barcoding data. The two new species, S. andina and S. scabrosa, are broadly distributed in the Neotropics and also found in Hawaii, where the latter is represented by the new subspecies, S. scabrosa subsp. hawaiiensis; in the case of S. andina, the species is also found in the Azores. Sticta andina exhibits high phenotypic variation and reticulate genetic diversification, whereas the phenotypically rather uniform S. scabrosa contains two main haplotypes, one restricted to Hawaii. Sticta andina occurs in well-preserved montane to andine forests and paramos, whereas the two subspecies of S. scabrosa are found in tropical lowland to lower montane forests, tolerating disturbance and extending into anthropogenic habitats. Citation: Moncada B., Mercado-Díaz J. A., Smith C. W., Bungartz F., Sérusiaux E., Lumbsch H. T. & Lücking R. 2021: Two new common, previously unrecognized species in the Sticta weigelii morphodeme (Ascomycota: Peltigeraceae). – Willdenowia 51: 35–45. Version of record first published online on 24 February 2021 ahead of inclusion in April 2021 issue. [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]

We analyzed the structure of foliicolous lichen communities in the northernmost lowland forest of the Neotropics, Los Tuxtlas Tropical Biology Station in Veracruz, Mexico, and its dependence on phorophyte and microclimate. Along a 420‐m long transect with 15 equidistant sampling points, within a 10 m radius of each point, we sampled a total 137 phorophytes and 411 leaves. The phorophytes represented 13 species, with diverse leaf traits regarding size, texture, presence of hairs and/or glands, and longevity, including: Astrocaryum mexicanum (Arecaceae), Chamaedorea ernesti‐augustii (Arecaceae), Costus scaber (Costaceae), Guarea glabra (Meliaceae), Heliconia latispatha (Heliconiaceae), Monstera acuminata (Araceae), Myriocarpa longipes (Urticaceae), Piper hispidum (Piperaceae), Poulsenia armata (Moraceae), Pseudolmedia oxyphyllaria (Moraceae), Salacia megistophylla (Celastraceae), Siparuna thecaphora (Siparunaceae) and Syngonium podophyllum (Araceae). NDMS ordination and cluster analysis grouped the phorophytes into hierarchically structured clusters variously correlated with microsite, phorophyte species and foliicolous lichen species richness. Indicator species analysis revealed statistically significant foliicolous lichen species characteristic for terminal clusters and for phorophyte species. We conclude that the principle of "diversity begets diversity" may apply, in that phorophyte diversity influences the diversity of foliicolous lichen communities through the manifestation of subtle phorophyte preferences, best seen in well‐developed communities on leaves with higher longevity. Thus, well‐preserved forest ecosystems, with a higher diversity of suitable phorophytes, will support a higher diversity of foliicolous lichens, a phenomenon that extents to epiphytes in general. [ABSTRACT FROM AUTHOR]

Members of the poorly investigated family Teloschistaceae in South America, mostly from Bolivia and Peru, were examined using molecular and morphological data here for the first time. In recent phylogenetic reclassifications of Teloschistaceae, South American representatives were poorly represented but shown to belong to subfamilies Teloschistoideae and Xanthorioideae. In this study, we expanded the sampling of South American taxa and investigated mainly the lobate, sublobate, and squamulose members of Caloplaca s.l., using morphological characters and a molecular phylogeny based on a combined three-locus data set (one mitochondrial and two nuclear loci). Building upon new phylogenies at the family and subfamily levels (Teloschistoideae), we propose here three new genera: Andina, Aridoplaca, and Cinnabaria, with the type species Andina citrinoides, Aridoplaca peltata, and Cinnabaria boliviana. We also propose to reduce Tarasginia to synonymy with Sirenophila and Tayloriellina to synonymy with Villophora and introduce three new combinations: Dufourea ottolangei, D. volkmarwirthii, and Villophora erythrosticta. Scutaria andina is reported as new to Bolivia. A critical revision of the subfamily Brownlielloideae confirmed recent findings that it is an artifactual taxon based on a "chimeric" data set, with the type genus being part of Teloschistoideae. [ABSTRACT FROM AUTHOR]

Aim: Phylogenetic diversification is a precursor to speciation, but the underlying patterns and processes are not well‐studied in lichens. Here we investigate what factors drive diversification in two tropical, morphologically similar macrolichens that occupy a similar range but differ in altitudinal and habitat preferences, testing for isolation by distance (IBD), environment (IBE), and fragmentation (IBF). Location: Neotropics, Hawaii, Macaronesia. Taxon: Sticta andina, S. scabrosa (Peltigeraceae). Methods: We analysed 395 specimens from 135 localities, using the fungal ITS barcoding marker to assess phylogenetic diversification, through maximum likelihood tree reconstruction, TCS haplotype networks, and Tajima's D. Mantel tests were employed to detect structure in genetic vs. geographic, environmental, and fragmentation distances. Habitat preferences were quantitatively assessed by statistical analysis of locality‐based BIOclim variables. Results: Sticta andina exhibited high phenotypic variation and reticulate phylogenetic diversity across its range, whereas the phenotypically uniform S. scabrosa contained two main haplotypes, one unique to Hawaii. Sticta andina is restricted to well‐preserved andine forests and paramos, naturally fragmented habitats due to disruptive topology, whereas S. scabrosa thrives in lowland to lower montane zones in exposed or disturbed microsites, representing a continuous habitat. Sticta scabrosa showed IBD only across its full range (separating the Hawaiian population) but not within continental Central and South America, there exhibiting a negative Tajima's D. Sticta andina did not exhibit IBD but IBE at continental level and IBF in the northern Andes. Main conclusions: Autecology, particularly preference for either low or high altitudes, indirectly drives phylogenetic diversification. Low diversification in the low altitude species, S. scabrosa, can be attributed to rapid expansion and effective gene flow across a more or less continuous niche due to disturbance tolerance. In contract, high diversification in the high altitude species, S. andina, can be explained by niche differentiation (IBE) and fragmentation (IBF) caused by the Andean uplift. [ABSTRACT FROM AUTHOR]

Ostropales sensu lato is a large group comprising both lichenized and non-lichenized fungi, with several lineages expressing optional lichenization where individuals of the same fungal species exhibit either saprotrophic or lichenized lifestyles depending on the substrate (bark or wood). Greatly variable phenotypic characteristics and large-scale phylogenies have led to frequent changes in the taxonomic circumscription of this order. Ostropales sensu lato is currently split into Graphidales, Gyalectales, Odontotrematales, Ostropales sensu stricto, and Thelenellales. Ostropales sensu stricto is now confined to the family Stictidaceae, which includes a large number of species that are poorly known, since they usually have small fruiting bodies that are rarely collected, and thus, their taxonomy remains partly unresolved. Here, we introduce a new genus Ostropomyces to accommodate a novel lineage related to Ostropa, which is composed of two new species, as well as a new species of Sphaeropezia, S. shangrilaensis. Maximum likelihood and Bayesian inference analyses of mitochondrial small subunit spacers (mtSSU), large subunit nuclear rDNA (LSU), and internal transcribed spacers (ITS) sequence data, together with phenotypic data documented by detailed morphological and anatomical analyses, support the taxonomic affinity of the new taxa in Stictidaceae. Ancestral character state analysis did not resolve the ancestral nutritional status of Stictidaceae with confidence using Bayes traits, but a saprotrophic ancestor was indicated as most likely in a Bayesian binary Markov Chain Monte Carlo sampling (MCMC) approach. Frequent switching in nutritional modes between lineages suggests that lifestyle transition played an important role in the evolution of this family. [ABSTRACT FROM AUTHOR]

Peter D. Crittenden served as senior editor of The Lichenologist, the flagship journal in the field of lichenological research, for a period of two decades, between 2000 and 2019. A review of the development of the journal and the publication output during this period is provided. The number of papers published during this period (1197) matches that of all papers published under the three previous senior editors, Peter W. James, David L. Hawksworth and Dennis H. Brown, during a much longer period of 42 years from 1958 to 1999. Peter oversaw important editorial changes to the layout and content of the journal: an increased size with a modern cover design, leaving behind the classic mint-coloured cover of more than 40 years; the addition of 'thematic issues' and encouragement of large monographs; implementation of substantial changes to the Code, such as effective electronic publication and obligate registration of new fungal names; and more recently a new policy to reject so-called 'single naked species descriptions'. Shortly before Peter took over as senior editor, The Lichenologist had received its first impact factor, and Peter managed to continuously increase this measure from around 0.9 to lately up to over 1.5, higher than most other competing journals. The 1197 papers between 2000 and 2019 were published by a total of 1138 different authors, more than half of whom appeared just once as author, whereas a small number participated in numerous (up to 93) papers. There was a continuous increase in the mean number of authors per paper per year, from below 2.5 to around 3.5, the highest numbers ranging between 11 and 30; still, c. 75% of all papers between 2000 and 2019 were single-authored or had up to three authors. Based on affiliations at the time of publication, two thirds of author contributions came from Europe (66%), 13% from North America, 9% from Asia and 7% from Latin America. Likewise, almost half of the study areas were located in Europe and around 10% each in North America, South America and Asia. The countries with the highest number of studies included, in descending order, the United States, Spain, the United Kingdom, Norway and Sweden. North America and Europe were over-represented in terms of author contributions, whereas Africa, Latin America, Australia and Oceania were over-represented in terms of study areas. The 1197 papers analyzed encompassed a broad diversity of topics, classified into 32 categories. Taxonomy of lichenized fungi was the most frequent component, representing the focal point in almost half of all studies, followed by phylogeny and evolution, ecology, and the taxonomy of lichenicolous fungi. Around two thirds of the currently accepted genera of lichenized fungi were treated, with a significant correlation between known species richness and the number of papers in which a genus was treated, underlining the taxonomic representativity of papers published in the journal during the past two decades. Examples of genera that were treated more frequently than expected included commonly studied model organisms, such as Lobaria, and those frequently featured in ecological or other non-taxonomic studies, such as Xanthoria. Species-rich tropical genera, particularly in the Graphidaceae, were generally under-represented. Mean number of authors per paper per volume and total number of country origins of authors per volume were the best predictors of impact factor, followed by diversity of study countries per volume, mean number of study countries per paper per volume, mean number of topics per paper per volume, and proportion of studies with phylogenetic components per volume. Individual papers that contributed to high impact factors included broad-scale revisionary treatments and worldwide keys to species-rich taxa, substantial phylogenetic reclassifications of known taxonomic groups, papers dealing with novel methodological approaches of broad interest, and broad-scale studies related to environmental change and lichen biomonitoring. [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]

DNA barcoding using the nuclear internal transcribed spacer (ITS) has become prevalent in surveys of fungal diversity. This approach is, however, associated with numerous caveats, including the desire for speed, rather than accuracy, through the use of automated analytical pipelines, and the shortcomings of reference sequence repositories. Here we use the case of a specimen of the bracket fungus Trametes s.lat. (which includes the common and widespread turkey tail, T. versicolor) to illustrate these problems. The material was collected in Vietnam as part of a biodiversity inventory including DNA barcoding approaches for arthropods, plants and fungi. The ITS barcoding sequence of the query taxon was compared against reference sequences in GenBank and the curated fungal ITS database UNITE, using BLASTn and MegaBLAST, and was subsequently analysed in a multiple alignment-based phylogenetic context through a maximum likelihood tree including related sequences. Our results initially indicated issues with BLAST searches, including the use of pairwise local alignments and sorting through Total score and E value, rather than Percentage identity, as major shortcomings of the DNA barcoding approach. However, after thorough analysis of the results, we concluded that the single most important problem of this approach was incorrect sequence labelling, calling for the implementation of third-party annotations or analogous approaches in primary sequence repositories. In addition, this particular example revealed problems of improper fungal nomenclature, which required reinstatement of the genus name Cubamyces (= Leiotrametes), with three new combinations: C. flavidus, C. lactineus and C. menziesii. The latter was revealed as the correct identification of the query taxon, although the name did not appear among the best BLAST hits. While the best BLAST hits did correspond to the target taxon in terms of sequence data, their label names were misleading or unresolved, including [Fungal endophyte], [Uncultured fungus], Basidiomycota, Trametes cf. cubensis, Lenzites elegans and Geotrichum candidum (an unrelated ascomycetous contaminant). Our study demonstrates that accurate identification of fungi through molecular barcoding is currently not a fast-track approach that can be achieved through automated pipelines. Citation: Lücking R., Truong B. V., Huong D. T. T., Le N. H., Nguyen Q. D., Nguyen V. D., Raab-Straube E. von, Bollendorff S., Govers K. & Di Vincenzo V. 2020: Caveats of fungal barcoding: a case study in Trametes s.lat. (Basidiomycota: Polyporales) in Vietnam reveals multiple issues with mislabelled reference sequences and calls for third-party annotations. – Willdenowia 50: 383–403. doi: https://doi.org/10.3372/wi.50.50302 Version of record first published online on 15 September 2020 ahead of inclusion in December 2020 issue. [ABSTRACT FROM AUTHOR]

The known collections of the genus Cora in continental North America north of Mexico, all restricted to Florida, are shown to belong to a single species, representing a previously unrecognized taxon formally described herein as C. timucua. Based on data of the fungal ITS barcoding marker, obtained through Sanger and Illumina sequencing from two historical collections, the new species is phylogenetically most closely related to C. casanarensis from Colombia and C. itabaiana from Brazil, although it is morphologically most similar to the only distantly related C. hymenocarpa from Costa Rica. Based on data from the Consortium of North American Lichen Herbaria (CNALH) and from the Global Biodiversity Information Facility (GBIF), most of the collections of C. timucua originate from around the turn of the 19th century, while a few were made in the second half of the 20th century, all between 1968 and 1985. Almost all collections originate from Florida sand pine scrub, apparently the preferred habitat of this taxon. Neither modern collections nor extant localities are known. Based on these findings and the substantial degree of land use change in Florida in the past decades, we assessed the conservation status of C. timucua using the IUCN Red List criteria and found that it should be classified as critically endangered (CR), in line with the status of another Florida endemic, Cladonia perforata, which was the first federally red-listed lichen in the United States. The most likely location where C. timucua may still be extant is Ocala National Forest in the north-central portion of the Florida peninsula, although recent macrolichen surveys in that area did not encounter this species. [ABSTRACT FROM AUTHOR]

The new genus Saxiloba is described with the two species S. firmula from the Caribbean and S. hawaiiensis from Hawaii. Saxiloba is characterized by a unique, placodioid thallus forming distinct lobes, growing on rock in shaded to exposed situations with a trentepohlioid photobiont and a fenestrate thallus anatomy with distinct surface lines. The material is often sterile, but Porina-like perithecia and ascospores had previously been described for the Caribbean taxon and were here confirmed for both species. Molecular sequence data also confirmed placement of this lineage in Porinaceae. Its position within that family supports the notion that Porinaceae should be subdivided into a larger number of genera than proposed in previous classification attempts. Compared to other Porinaceae, Saxiloba exhibits a unique morphology and anatomy that recalls taxa in the related family Graphidaceae and it substantially expands the known phenotypic variation within Porinaceae. The two recognized species are similar in overall morphology but, apart from their disjunct distribution and different substrate ecology, differ in lobe configuration, color and disposition of the crystal clusters and resulting surface patterns. [ABSTRACT FROM AUTHOR]

We tested the functionality of ITS-based DNA barcoding in lichen fungi using Colombian samples of the genus Usnea as an example. New ITS sequences were generated for 15 samples from five localities in two different ecoregions, representing varying morphologies and medullary chemistries. We employed five strategies to identify the samples: (1) BLASTn on the NCBI BLAST site with the original identifications of the best matching reference sequences; (2) as previous, but with revised identifications of the reference sequences based on a separately published revision of ITS sequences published for the genus; (3) local BLASTn in BioEdit using a separately published, revised and curated set of ITS reference sequences for the genus; (4) multiple alignment based phylogenetic analysis within the framework of all available ITS sequences for Usnea s.str.; and (5) integrative taxonomy, combining molecular phylogeny and comparative analysis of phenotype and chemical data. Using the latter approach as reference, we found that NCBI BLASTn with original identifications performed poorly, resulting in an identification success rate of only 7% (a single sample). NCBI BLASTn with revised identifications more than tripled identification success (23%), but was still unsatisfactory. Local BLASTn in BioEdit using the revised, curated reference data further doubled identification success (47%), but remained inadequate. Multiple alignment-based phylogenetic analysis achieved an identification success rate of 80% compared to the result from integrative taxonomy. Based on these results, we conclude that ITS-based DNA barcoding of the genus Usnea under the current circumstances performs poorly, but can be substantially improved using three strategies: (1) update identifications of reference sequences in primary repositories such as GenBank or alternatively use a curated reference data set; (2) perform local BLAST with a curated reference data set focusing on the target genus only, combined with multiple alignment-based phylogenetic analysis as a verification step; and (3) close substantial geographic and taxonomic gaps in the existing reference data. Our analyses suggest that if a near-complete reference data set with correct identifications existed for the genus, then standard BLAST approaches could achieve high levels of identification success close to 100%. As part of our DNA barcoding exercise, which generated the first 15 ITS sequences for Colombian samples of the genus Usnea, we confirm the presence of U. aranea and U. wasmuthii in Colombia and we report for the first time U. tenuicorticata for the country. [ABSTRACT FROM AUTHOR]

We present an exhaustive analysis of the ITS barcoding marker in the genus Usnea s.lat., separated into Dolichousnea, Eumitria, and Usnea including the subgenus Neuropogon, analyzing 1,751 accessions. We found only a few low-quality accessions, whereas information on voucher specimens and accuracy and precision of identifications was of subpar quality for many accessions. We provide an updated voucher table, alignment and phylogenetic tree to facilitate DNA barcoding of Usnea, either locally or through curated databases such as UNITE. Taxonomic and geographic coverage was moderate: while Dolichousnea and subgenus Neuropogon were well-represented among ITS data, sampling for Eumitria and Usnea s.str. was sparse and biased towards certain lineages and geographic regions, such as Antarctica, Europe, and South America. North America, Africa, Asia and Oceania were undersampled. A peculiar situation arose with New Zealand, represented by a large amount of ITS accessions from across both major islands, but most of them left unidentified. The species pair Usnea antarctica vs. U. aurantiacoatra was the most sampled clade, including numerous ITS accessions from taxonomic and ecological studies. However, published analyses of highly resolved microsatellite and RADseq markers showed that ITS was not able to properly resolve the two species present in this complex. While lack of resolution appears to be an issue with ITS in recently evolving species complexes, we did not find evidence for gene duplication (paralogs) or hybridization for this marker. Comparison with other markers demonstrated that particularly IGS and RPB1 are useful to complement ITS-based phylogenies. Both IGS and RPB1 provided better backbone resolution and support than ITS; while IGS also showed better resolution and support at species level, RPB1 was less resolved and delineated for larger species complexes. The nuLSU was of limited use, providing neither resolution nor backbone support. The other three commonly employed protein-coding markers, TUB2, RPB2, and MCM7, showed variable evidence of possible gene duplication and paralog formation, particularly in the MCM7, and these markers should be used with care, especially in multimarker coalescence approaches. A substantial challenge was provided by difficult morphospecies that did not form coherent clades with ITS or other markers, suggesting various levels of cryptic speciation, the most notorious example being the U. cornuta complex. In these cases, the available data suggest that multimarker approaches using ITS, IGS and RPB1 help to assess distinct lineages. Overall, ITS was found to be a good first approximation to assess species delimitation and recognition in Usnea s.lat., as long as the data are carefully analyzed, and reference sequences are critically assessed and not taken at face value. In difficult groups, we recommend IGS as a secondary barcode marker, with the option to employ more resource-intensive approaches, such as RADseq, in species complexes involving so-called species pairs or other cases of disparate morphology not reflected in the ITS or IGS. Attempts should be made to close taxonomic and geographic gaps especially for the latter two markers, in particular in Eumitria and Usnea s.str. and in the highly diverse areas of North America and Central America, Africa, Asia, and Oceania. [ABSTRACT FROM AUTHOR]

Numerous new taxa and classifications of Dothideomycetes have been published following the last monograph of families of Dothideomycetes in 2013. A recent publication by Honsanan et al. in 2020 expanded information of families in Dothideomycetidae and Pleosporomycetidae with modern classifications. In this paper, we provide a refined updated document on orders and families incertae sedis of Dothideomycetes. Each family is provided with an updated description, notes, including figures to represent the morphology, a list of accepted genera, and economic and ecological significances. We also provide phylogenetic trees for each order. In this study, 31 orders which consist 50 families are assigned as orders incertae sedis in Dothideomycetes, and 41 families are treated as families incertae sedis due to lack of molecular or morphological evidence. The new order, Catinellales, and four new families, Catinellaceae, Morenoinaceae Neobuelliellaceae and Thyrinulaceae are introduced. Seven genera (Neobuelliella, Pseudomicrothyrium, Flagellostrigula, Swinscowia, Macroconstrictolumina, Pseudobogoriella, and Schummia) are introduced. Seven new species (Acrospermum urticae, Bogoriella complexoluminata, Dothiorella ostryae, Dyfrolomyces distoseptatus, Macroconstrictolumina megalateralis, Patellaria microspora, and Pseudomicrothyrium thailandicum) are introduced base on morphology and phylogeny, together with two new records/reports and five new collections from different families. Ninety new combinations are also provided in this paper. [ABSTRACT FROM AUTHOR]

Traditional taxonomic studies provide only a limited understanding of species richness within a group. Their usefulness for assessing species diversity could also be limited as many lack sufficient sampling and/or fail to integrate different data types for assessing species boundaries. To explore the challenges and limitations of estimating species richness in lichens, we employed an integrative taxonomic approach to elucidate diversification patterns of the genus Sticta (Peltigeraceae) in Puerto Rico. Specimens were collected throughout the island, and a six‐locus dataset was generated to infer phylogenetic relationships among Puerto Rican Sticta and their continental counterparts. Phylogenetic analysis was combined with species delimitation methods and analysis of morpho‐anatomical characters to assess diversity patterns and clarify species‐level taxonomy. We found that Sticta is represented by 16 species in Puerto Rico and that at least 11 (69%) of them are potentially endemic to the island. We describe eight of these in this work: S. borinquensis sp. nov., S. corymbosa sp. nov., S. densiphyllidiata sp. nov., S. guilartensis sp. nov., S. harrisii sp. nov., S. parvilobata sp. nov., S. riparia sp. nov., and S. tainorum sp. nov. These species do not cluster in a monophyletic assemblage but are scattered over the broader Sticta phylogeny, indicating at least eight separate dispersal events. Putative endemic species were found to have close allies occurring in South America. Careful re‐examination of material revealed phenotypical characters that separate most species, suggesting low levels of cryptic diversity. We highlight that integrating molecular methods and other sources of information in species discovery along with comprehensive sampling efforts can greatly enhance our knowledge about diversity patterns in poorly studied groups and regions. Furthermore, species and ecosystems in the Caribbean are being threatened by substantial human‐driven changes (e.g., deforestation, climate change). Consequences of these impacts include reduction in already restricted habitats and potential extinction. We argue that studies analyzing species diversity within a phylogenetic framework could better inform conservation efforts aimed at addressing these challenges. [ABSTRACT FROM AUTHOR]