André Aptroot

The ascomycota tree of life: A phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits

We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.

Fossil ascomycetes in Quaternary deposits

Abstract: Remains of various ascomycetes, mainly ascospores, have been detected during palynological studies of lake sediments, peat deposits and samples from archaeological sites. Many taxa can be identified to genus or species level of extant taxa. Ascospore remains may sometimes give indications about the palaeohabitat: for instance, Amphisphaerella dispersella suggests the presence of Populus in the vicinity. Among the identified fungi are several species of the Sordariales, which are valuable dung indicators in archaeological sites. Coprophilous fungi also characterise samples from the Pleistocene mammoth steppe.

Families of Dothideomycetes

Dothideomycetes comprise a highly diverse range of fungi characterized mainly by asci with two wall layers (bitunicate asci) and often with fissitunicate dehiscence. Many species are saprobes, with many asexual states comprising important plant pathogens. They are also endophytes, epiphytes, fungicolous, lichenized, or lichenicolous fungi. They occur in terrestrial, freshwater and marine habitats in almost every part of the world. We accept 105 families in Dothideomycetes with the new families Anteagloniaceae, Bambusicolaceae, Biatriosporaceae, Lichenoconiaceae, Muyocopronaceae, Paranectriellaceae, Roussoellaceae, Salsugineaceae, Seynesiopeltidaceae and Thyridariaceae introduced in this paper. Each family is provided with a description and notes, including asexual and asexual states, and if more than one genus is included, the type genus is also characterized. Each family is provided with at least one figure-plate, usually illustrating the type genus, a list of accepted genera, including asexual genera, and a key to these genera. A phylogenetic tree based on four gene combined analysis add support for 64 of the families and 22 orders, including the novel orders, Dyfrolomycetales, Lichenoconiales, Lichenotheliales, Monoblastiales, Natipusillales, Phaeotrichales and Strigulales. The paper is expected to provide a working document on Dothideomycetes which can be modified as new data comes to light. It is hoped that by illustrating types we provide stimulation and interest so that more work is carried out in this remarkable group of fungi.

Naming and outline of Dothideomycetes-2014 including proposals for the protection or suppression of generic names

Article 59.1, of the International Code of Nomenclature for Algae, Fungi, and Plants (ICN; Melbourne Code), which addresses the nomenclature of pleomorphic fungi, became effective from 30 July 2011. Since that date, each fungal species can have one nomenclaturally correct name in a particular classification. All other previously used names for this species will be considered as synonyms. The older generic epithet takes priority over the younger name. Any widely used younger names proposed for use, must comply with Art. 57.2 and their usage should be approved by the Nomenclature Committee for Fungi (NCF). In this paper, we list all genera currently accepted by us in Dothideomycetes (belonging to 23 orders and 110 families), including pleomorphic and non-pleomorphic genera. In the case of pleomorphic genera, we follow the rulings of the current ICN and propose single generic names for future usage. The taxonomic placements of 1261 genera are listed as an outline. Protected names and suppressed names for 34 pleomorphic genera are listed separately. Notes and justifications are provided for possible proposed names after the list of genera. Notes are also provided on recent advances in our understanding of asexual and sexual morph linkages in Dothideomycetes. A phylogenetic tree based on four gene analyses supported 23 orders and 75 families, while 35 families still lack molecular data.

A world-wide key to the genus Graphis ( Ostropales : Graphidaceae )

A world-wide key to the genus Graphis is presented, based on extensive type studies and revision of several thousand historical and recent collections. A total of 330 species are accepted and included in the key, and a further 205 epithets are listed as synonyms. The structured key includes taxonomic information on type specimens of epithets considered to be synonyms of the accepted species. In addition, 28 species of other genera ( Carbacanthographis, Diorygma, Dyplolabia, Glyphis ) with carbonized excipulum and hyaline ascospores likely to be confused with Graphis are mentioned under the corresponding key couplets. Although the key is preliminary and some taxonomic and nomenclatural problems remain unresolved at this time, it should allow reliable identification of most specimens especially from tropical regions. The following 14 species are described as new: Graphis brahmanensis Aptroot sp. nov., G. cupei Vain. ex Lucking sp. nov., G. funilina Aptroot sp. nov., G. inspersolongula Aptroot sp. nov., G. leucaenae Aptroot sp. nov., G. lourdesina Aptroot sp. nov., G. myolensis Aptroot sp. nov., G. nadurina Aptroot sp. nov., G. norstictica Archer & Lucking sp. nov., G. sarawakensis Hale ex Lucking sp. nov., G. slendrae Hale ex Lucking sp. nov., G. subintermedians Hale ex Lucking sp. nov., G. subserpens Staiger sp. nov., and G. syzygii Aptroot sp. nov. In addition, 22 new combinations are proposed: Carbacanthographis cleitops (Fee) Lucking comb. nov., C. coccospora (Aptroot) Aptroot & Lucking comb. nov., C. induta (Mull. Arg.) Lucking comb. nov., C. triphoroides (M. Wirth & Hale) Lucking comb. nov., Graphis apoda (Zahlbr.) Lucking comb. et stat. nov., G. cremicolor (H. Magn.) Lucking & Archer comb. nov., G. enteroleuca (Ach.) Lucking comb. nov., G. evirescens (Redinger) Lucking comb. nov., G. galactoderma (Zahlbr.) Lucking comb. nov., G. ingarum (Vain.) Lucking comb. et stat. nov., G. isidiata (Hale) Lucking comb. nov., G. japonica (Mull. Arg.) A. W. Archer & Lucking comb. nov., G. kousyuensis (Horik. & M. Nakan.) Lucking comb. nov., G. negrosina (Vain.) Lucking comb. et stat. nov., G. oxyspora (Zahlbr.) Lucking comb. nov., G. plumbea (Zahlbr.) Lucking comb. nov., G. riopiedrensis (Fink) Lucking comb. nov., G. semirigida (Mull. Arg.) Lucking comb. nov., G. subradiata (Nyl.) Lucking comb. et stat. nov., G. subtecta (Nyl.) Lucking comb. et stat. nov., and G. sulphurella (Zahlbr.) Lucking comb. nov. Replacement names are established for six taxa: Graphis jeanmuelleri Lucking nom. nov. [≡ Graphina elegantula Mull. Arg., non Graphis elegantula Zahlbr.], Graphis neoelongata Lucking nom. nov. [≡ G. elongata Vain., non G. elongata Zenker], Graphis novopalmicola A. W. Archer & Lucking nom. nov. [≡ Graphina palmicola Mull. Arg., non Graphis palmicola Makhija & Adaw.], Graphis paralleloides Caceres & Lucking nom. nov. [≡ G. rimulosa var. parallela Mull. Arg., non G. parallela Mull. Arg.], Graphis subalbostriata Lucking nom. nov. [≡ G. angustata var. albostriata Vain., non G. albostriata Vain.], and Graphis subvernicosa Lucking nom. nov. [≡ Opegrapha vernicosa Fee, non G. vernicosa Nyl.]. Three new synonyms are established for Glyphis substriatula (Nyl.) Staiger: Graphina sulcatula Mull. Arg., G. sulcatula var. conglomerata Mull. Arg., and G. bakeri Zahlbr.

A First Assessment of the Ticolichen Biodiversity Inventory in Costa Rica: The Genus Graphis, with Notes on the Genus Hemithecium (Ascomycota: Ostropales: Graphidaceae)

Abstract The genus Graphis sensu Staiger is treated as a further contribution to the TICOLICHEN biodiversity inventory in Costa Rica. Graphis s.str. is the largest tropical lichen genus, with more than 300 accepted species worldwide, and also the largest in Costa Rica, with a total of 115 species recognized in this work. The following 25 species are described as new: Graphis altamirensis Sipman & Lücking sp. nov., G. argentata Lücking & Umaña sp. nov., G. bettinae Lücking, Umaña, Chaves & Sipman sp. nov., G. duplicatoinspersa Lücking sp. nov., G. firferi Lücking sp. nov., G. flavoaltamirensis Sipman & Lücking sp. nov., G. flavominiata Moncada & Lücking sp. nov., G. fournierii Lizano & Lücking sp. nov., G. gomezii Lücking, Will-Wolf & Umaña, G. gregmuelleri Sipman & Lücking, sp. nov., G. hypocrellina Lücking & Chaves sp. nov., G. inspersostictica Sipman & Lücking sp. nov., G. litoralis Lücking, Sipman & Chaves sp. nov., G. mirabilis Lücking, Sipman, Umaña & Chaves sp. nov., G. nudaeformis Lücking sp. nov., G. oryzaecarpa Lücking sp. nov., G. paradisserpens Sipman & Lücking sp. nov., G. paraserpens Lizano & Lücking sp. nov., G. pittieri Lücking, Umaña, Sipman & Chaves sp. nov., G. pseudocinerea Lücking & Umaña sp. nov., G. pseudoserpens Chaves & Lücking sp. nov., G. subflexibilis Lücking & Chaves sp. nov., G. subruiziana Sipman, Chaves & Lücking sp. nov., G. subturgidula Lücking & Sipman sp. nov., and G. tenoriensis Chaves & Lücking sp. nov. Graphis immersoides Lücking, nom. nov. [Bas. Graphina immersa Müll. Arg.; non Graphis immersa Fink], Graphis subchrysocarpa Lücking, nom. nov. [Bas.: Phaeographina ochracea C. W. Dodge; non Graphis ochracea Hepp], and Graphis submarginata Lücking, nom. nov. [Bas. Graphis marginata G. Mey. & Flot.; non Graphis marginata Raddi] are introduced as replacement names. Furthermore, 17 new combinations are proposed: G. bipartita (Müll. Arg.) Lücking, comb. nov., G. chondroplaca (Redinger) Lücking comb. et stat. nov., G. consanguinea (Müll. Arg.) Lücking, comb. nov., G. dichotoma (Müll. Arg.) Lücking, comb. nov., G. granulosa (Müll. Arg.) Lücking comb. nov., G. insulana (Fée) Lücking & Sipman, comb. nov., G. lutea (Chevall.) Aptroot, comb. nov., G. multisulcata (Müll. Arg.) Lücking & Chaves comb. nov., G. myrtacea (Müll. Arg.) Lücking, comb. nov., G. nuda (H. Magn.) Staiger & Lücking, comb. nov., G. plurispora (Redinger) Lücking & Chaves, comb. nov., G. puiggarii (Müll. Arg.) Lücking, comb. nov., G. rhizocola (Fée) Lücking & Chaves, comb. nov. [syn. G. anguilliformis Taylor; G. serpens Fée], G. subcontorta (Müll. Arg.) Lücking & Chaves, comb. nov., G. subhiascens (Müll. Arg.) Lücking comb. nov., G. xylophaga (R. C. Harris) Lücking, comb. nov., and Hemithecium plicosum (Meissn.) Lücking & Aptroot, comb. nov. [syn. Graphina malmei Redinger]. The new name Pallidogramme Staiger, Kalb & Lücking, nom. nov. is introduced for Leucogramma A. Massal. [nom. illeg.;  =  Hemithecium subgen. Leucogramma Staiger], comprising a group of three species formerly included in Hemithecium: Pallidogramme chapadana (Redinger) Staiger, Kalb & Lücking, comb. nov., P. chlorocarpoides (Nyl.) Staiger, Kalb & Lücking, comb. nov., and P. chrysenteron (Mont.) Staiger, Kalb & Lücking, comb. nov. More than 600 types of Graphidaceae suspected to represent species of Graphis s.str. were examined for this study, and notes on type material are given when appropriate. Also, the names previously reported for Costa Rica by the Swiss lichenologist Müller Argoviensis in 1891 and 1893 were checked when possible, and 175 unpublished collections from Costa Rica housed at the Farlow Herbarium (fh) of Harvard University and collected and identified by Carroll William Dodge and colleagues and students were revised. A key is presented to all species, including an image-based identification guide, and diagnostic characters in the genus Graphis are briefly discussed and illustrated. Diagnoses and remarks are given for all species treated here, as are more detailed descriptions for the taxa new to science. Data from 803 collections were analyzed using the ordination technique of principal component analysis to display habitat and microhabitat preferences for species groups.

Mycosphaerella punctiformis revisited: morphology, phylogeny, and epitypification of the type species of the genus Mycosphaerella ( Dothideales , Ascomycota )

Mycosphaerella punctiformis, the type species of the genus Mycosphaerella, is epitypified by material collected on Quercus robur in The Netherlands. The teleomorph is described in planta, and the Ramularia anamorph, for which the new name R. endophylla is proposed, and the Asteromella spermatial state are characterized in vitro. Sequence data of the nuclear ribosomal DNA are presented and analyzed together with other Mycosphaerella spp. with Ramularia and several other anamorphs. Several strains originating from Quercus, Acer and Tilia showed diverging ITS sequences, indicating that the M. punctiformis complex may comprise more than a single phylogenetic species, but this could not be confirmed by the analysis of our dataset. An endophytic phase is established for the first time in the life-cycle of M. punctiformis, as the species was repeatedly isolated from surface sterilized green healthy leaves of Quercus robur in summer at the epitype locality.

Where are the missing lichens

The taxonomy of lichenized fungi (lichens) is relatively well-known compared to that of other fungi because lichens are long-lived and possess a thallus that requires exposure to light. Therefore they are easily observed on their natural substratum and sampling can be carried out much more thoroughly than in other fungal groups. Comprehensive catalogues of lichen taxa known worldwide are available and currently about 13500 species are accepted. An analysis of selected, recently revised groups suggests that there has been a mean increase in species number of about 25% since 1931. One third of the species recognized before 1931 were withdrawn, and almost half of the currently recognized species have been described after 1931. Some 3000 names seem to be ‘orphaned’, not included in currently accepted genera and not appearing in recent species counts. New species are being described at an increasing rate, so that large numbers of ‘missing lichens’ seem to be present. However, there is no clear indication how numerous they are, only an estimation that they amount to some 25% of all species. A geographical analysis of checklists suggests that most missing species will be found in the tropics and the southern hemisphere. A taxonomic analysis of recently published species suggests that there is no particular group yielding more novelties than others. Our own fieldwork impressions suggest that tropical primary forests are the most productive in revealing undescribed species. These are found in particular on leaves and on bark high up on the tree trunks. In well-studied areas like western Europe the new discoveries tend to be cryptic species or species rarely producing ascocarps. In conclusion, the ‘missing’ lichens are estimated at about 4000, and are to be found everywhere and in all taxonomic groups, but predominantly in primary tropical forests. This would result in a total of about 18000 lichen species.

An evaluation of the monophyly of Massarina based on ribosomal DNA sequences

The monophyletic status of the genus Massarina was evaluated on the basis of phylogenetic analysis of the partial small subunit gene (SSU), internal transcribed spacers (ITS 1 & 2), and 5.8S gene sequences of the ribosomal DNA. Species of Massarina used in the study clustered into two distinct clades with high bootstrap support in trees generated from maximum parsimony, weighted parsimony, maximum likelihood, and neighbor-joining analyses. The hypothesis that Massarina species belong to a phylogenetically monophyletic group is rejected. Species with narrowly fusiform ascospores form a monophyletic clade with Lophiostoma, a genus highly similar in morphology. The five species currently accepted in Massarina with such spore morphology are here transferred into the genus Lophiostoma. Massarina species with broadly fusiform to ellipsoidal ascospores are retained as Massarina s. str., lectotypified by M. eburnea. Massarina walkeri is presently excluded from both Massarina and Lophiostoma. The transfer of M. papulosa to a new genus Oletheriostrigula is verified.

A world key to the species of Anthracothecium and Pyrenula

An identification key is presented for the accepted species of the lichen genera Anthracothecium (comprising 5 species) and Pyrenula (with 169 species, including 7 still undescribed). The key also contains some similar taxa and is complete for Blastodesmia (1 species), Sulcopyrenula (4 species), and Eopyrenula (6 species), but not for others such as Aptrootia, Architrypethelium , and Lithothelium , of which only the corticolous brown-spored taxa are treated. The following new combinations were found to be necessary: Anthracothecium interlatens (Nyl.) Aptroot , Pyrenula breutelii (Mull. Arg.) Aptroot, Pyrenula ceylonensis (Ajay Singh & Upreti) Aptroot, Pyrenula fusispora (Malme) Aptroot, Pyrenula gibberulosa (Vain.) Aptroot, Pyrenula lyoni (Zahlbr.) Aptroot , Pyrenula papillifera (Nyl.) Aptroot, Pyrenula platystoma (Mull. Arg.) Aptroot , Pyrenula schiffneri (Zahlbr.) Aptroot, Pyrenula welwitschii (Upreti & Ajay Singh) Aptroot, and Sulcopyrenula subglobosa (Riddle) Aptroot. Pyrenula sexluminata Aptroot is a new name for Pyrenula quinqueseptata Aptroot, and Pyrenula neosandwicensis Aptroot is a new name for Anthracothecium sandwicense Zahlbr. In addition, all known and many novel synonyms are cited, and the disposition of all other taxa in the two genera Anthracothecium (with 155 names) and Pyrenula (with 745 names) and their generic synonyms. Bogoriella was found to be an older name for Mycomicrothelia .