Matthew P. Nelsen

A class-wide phylogenetic assessment of Dothideomycetes

We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.

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.

Revisiting photobiont diversity in the lichen family Verrucariaceae (Ascomycota)

The Verrucariaceae (Ascomycota) is a family of mostly lichenized fungi with a unique diversity of algal symbionts, including some algae that are rarely or never associated with other lichens. The phylogenetic position of most of these algae has not yet been studied and, because morphology-based identifications can often be misleading, molecular data is necessary to revisit their identity and to explore patterns of association between fungal and algal partners. For this reason, the diversity of photobionts in this lichen family was investigated using molecular markers (rbcL and nuSSU) amplified from DNA extracts of lichen thalli and cultured isolates. Although a single algal genus, Diplosphaera (Trebouxiophyceae), was associated with 12 out of the 17 sampled genera of Verrucariaceae, representatives of eight other genera in five orders of the Chlorophyta and one genus in the Xanthophyceae also form lichen associations with members of the family. Fungal genera with simple crustose thalli (e.g. Hydropunctaria, Wahlenbergiella, Bagliettoa) use a high diversity and unusual selection of photobionts. In contrast, fungal genera with more complex thalli (e.g. Placidium, Dermatocarpon) tend to have lower photobiont diversity. Habitat requirements and phylogenetic histories are both partly reflected in the observed patterns of associations between lichenized fungi from the family Verrucariaceae and their photobionts.

Unravelling the phylogenetic relationships of lichenised fungi in Dothideomyceta

We present a revised phylogeny of lichenised Dothideomyceta (Arthoniomycetes and Dothideomycetes) based on a combined data set of nuclear large subunit (nuLSU) and mitochondrial small subunit (mtSSU) rDNA data. Dothideomyceta is supported as monophyletic with monophyletic classes Arthoniomycetes and Dothideomycetes; the latter, however, lacking support in this study. The phylogeny of lichenised Arthoniomycetes supports the current division into three families: Chrysothrichaceae (Chrysothrix), Arthoniaceae (Arthonia s. l., Cryptothecia, Herpothallon), and Roccellaceae (Chiodecton, Combea, Dendrographa, Dichosporidium, Enterographa, Erythrodecton, Lecanactis, Opegrapha, Roccella, Roccellographa, Schismatomma, Simonyella). The widespread and common Arthonia caesia is strongly supported as a (non-pigmented) member of Chrysothrix. Monoblastiaceae, Strigulaceae, and Trypetheliaceae are recovered as unrelated, monophyletic clades within Dothideomycetes. Also, the genera Arthopyrenia (Arthopyreniaceae) and Cystocoleus and Racodium (Capnodiales) are confirmed as Dothideomycetes but unrelated to each other. Mycomicrothelia is shown to be unrelated to Arthopyrenia s.str., but is supported as a monophyletic clade sister to Trypetheliaceae, which is supported by hamathecium characters. The generic concept in several groups is in need of revision, as indicated by non-monophyly of genera, such as Arthonia, Astrothelium, Cryptothecia, Cryptothelium, Enterographa, Opegrapha, and Trypethelium in our analyses.

Molecular phylogeny and symbiotic selectivity of the green algal genus Dictyochloropsis s.l. (Trebouxiophyceae): a polyphyletic and widespread group forming photobiont‐mediated guilds in the lichen family Lobariaceae

Dictyochloropsis s.l. is an ecologically important, common but little-studied genus of green algae. Here, we examined the diversity and host selectivity of algae attributed to this genus at both species-to-species and species-to-community levels. We conducted a molecular investigation of 15 cultured strains and several lichen photobionts, using 18S rRNA, rbcL and ITS sequence data. We further used seven alga-specific microsatellite markers to study algal sharing among fungi of the family Lobariaceae in two populations in Madeira and Taiwan (454 lichens). We found that the genus Dictyochloropsis s.l. is polyphyletic. Dictyochloropsis clade 1 comprises only free-living algae whereas Dictyochloropsis clade 2 includes lichenized algae as well as free-living algae. Fungal selectivity towards algae belonging to Dictyochloropsis clade 2 is high. Selectivity varies geographically, with photobionts being restricted to a single region. Finally, we showed that Dictyochloropsis clade 2 individuals are shared among different fungal hosts in communities of lichens of the Lobariaceae. As for other green algal lineages, there is a high amount of cryptic diversity in Dictyochloropsis. Furthermore, co-evolution between Dictyochloropsis clade 2 algae and representatives of the Lobariaceae is manifested at the community level, with several unrelated fungal species being horizontally connected by shared photobiont clones.

Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi.

We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes.

Symbiont flexibility in Thamnolia vermicularis (Pertusariales: Icmadophilaceae)

Abstract Algal and fungal symbionts of the lichenized genus Thamnolia typically co-disperse through thallus fragmentation, which may be expected to lead to fungal associations with a restricted range of algal symbionts. Here we examine the range of algae that associate with the fungus Thamnolia vermicularis. Phylogenetic analyses of internal transcribed spacer rDNA (ITS) sequences suggest that Trebouxia algae associated with T. vermicularis are not monophyletic. Algal and fungal phylogenies were compared, and although some congruence was found, a Mantel test found no significant correlation between fungal and algal genetic distances. An AMOVA suggested that ecogeographic factors play a stronger role than fungal genotype in structuring photobiont diversity. Additionally, as a species, T. vermicularis associates with a range of algae equal to or greater than that of many other fungal taxa.

New insights into relationships of lichen-forming Dothideomycetes

Here we continue to investigate the phylogenetic relationships of taxa ascribed to the primarily lichen-forming families Trypetheliaceae, Monoblastiaceae and Arthopyreniaceae. We demonstrate that the genera Julella and Arthopyrenia do not form monophyletic groups with taxa from these genera instead being placed both in Pleosporales and Trypetheliales. Within Dothideomycetes, lichen-forming species with brown ascospores are generally placed in the genera Mycomicrothelia, Architrypethelium, and Aptrootia in the family Trypetheliaceae. We tested the taxonomic placement of Anisomeridium phaeospermum, in Monoblastiaceae. This species produces brown-spores with wall ornamentation and therefore appears morphologically similar to Mycomicrothelia. Despite these morphological similarities, molecular data confirmed its placement in Anisomeridium. Consequently, the distinction between these two genera is in need of clarification and ascus characters are identified as the principal discriminating feature. Finally, we identify the non-lichenized taxa Heleiosa barbatula and Funbolia dimorpha as being part of the otherwise lichen-forming family Monoblastiaceae. This is confirmed by the perithecial anatomy of the sexually reproducing Heleiosa barbatula.

PHYLOGENETIC DIVERSITY OF TRENTEPOHLIALEAN ALGAE ASSOCIATED WITH LICHEN-FORMING FUNGI(1).

Nearly one‐fourth of the lichen‐forming fungi associate with trentepohlialean algae, yet their genetic diversity remains unknown. Recent work focusing on free‐living trentepohlialean algae has provided a phylogenetic context within which questions regarding the lichenization of these algae can be asked. Here, we concentrated our sampling on trentepohlialean algae from lichens producing a diversity of growth forms (fruticose and crustose) over a broad geographic substratum, ecological, and phylogenetic range. We have demonstrated that there is no evidence for a single clade of strictly lichenized algae; rather, a wide range demonstrated the ability to associate with lichenized fungi. Variation was also observed among trentepohlialean algae in lichens from a single geographic area and tree, suggesting that fungi in close proximity can associate with different trentepohlialean algae, consistent with the findings of trebouxiophycean algae and cyanobacteria.