Taxonomy and phylogeny of the family Fuscideaceae (Umbilicariales, Ascomycota) with special emphasis on Fuscidea
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Introduction: For several decades, the taxonomic position of the lichen family Fuscideaceae and its associated genera, including the type genus Fuscidea V. Wirth & Vĕzda, has been debated. Amongst the species of Fuscidea, there are many questions about species limitation. The identity of the photobiont in Fuscidea is poorly known and has not been studied by molecular methods. To fill these gaps, the objectives of this thesis were the following: 1) Investigate the placement of Fuscideaceae within Ascomycota and to designate the genera to be included in this family (Paper I); 2) Examine the phylogenetic relationships within the genus Fuscidea (Paper I); 3) Elucidate the taxonomy of the F. lightfootii-F. pusilla species complex (Paper II); 4) Assess the infraspecific taxonomy of F. cyathoides (Ach.) V. Wirth & Vĕzda and the status of F. fagicola (Zschacke) Hafellner & Türk and F. stiriaca (A. Massal.) Hafellner (Paper III); 5) Identify the photobiont in Fuscidea and clarify its systematic placement (Paper IV).
Methods: The concatenated data sets comprising the mitochondrial SSU and nuclear LSU, ITS rDNA regions of the fungal sequences (Papers I–III) as well as the individual 18S rDNA and partitioned ITS data sets of algal sequences (Paper IV) were analysed by Bayesian inference, maximum parsimony and maximum likelihood (ML) analysis. Principal Components Analysis (PCA) was used to assess selected morphological characters among varieties of F. cyathoides (Paper III). The ITS data set of algal sequences was run in the program Gblocks under relaxed and stringent masking to minimize the ambiguous positions in the alignment. The program SATé-II was used to analyse the non-aligned data matrix of ITS. The topologies and support values of the Bayesian and the ML trees recovered from the resulting aligned data sets were compared and their topologies with the ML tree calculated by SATé-II. The secondary structures of the ITS2 region were folded in order to identify Compensatory Base Changes (CBCs) and hemi-CBCs of the retrieved ITS groups (Paper IV).
Results: Fuscideaceae included four genera and was located in Umbilicariales. The new genus Printzeniella Palice, Tønsberg & Zahradn. ined. was found to be closely related to Fuscidea. Ropalospora A. Massal. appeared as the first diverging lineage within Fuscideaceae and Maronea A. Massal. was nested within the Fuscidea-clade. The lichenicolous Lettauia D. Hawksw. & R. Sant. and Cryptodiscus Corda were nested in Stictidaceae within Ostropales. Loxospora A. Massal. was grouped with Sarrameana Vĕzda & P. James in Sarrameanaceae, Sarrameanales, and closely related to Ostropales. Orphniospora Körb. may be related to Lecideaceae s. str. within Lecideales (Paper I). Fuscidea lightfootii (Sm.) Coppins & P. James and F. pusilla Tønsberg were not conspecific, but phylogenetically well distinct. Fertile specimens of F. pusilla were recorded for the first time (Paper II). Genetic, chemical or morphological differences were not significant among the current varieties of F. cyathoides. The variation in apothecia and the presence of tuberculate apothecia were not significant for F. fagicola and F. stiriaca (Paper III). The photobiont in Fuscidea was identified as Apatococcus F. Brand, but its taxonomic position remained unresolved within Trebouxiophyceae due to poor supports in the deep phylogeny. Apatococcus fuscideae A. Beck & Zahradn. ined. differs from A. lobatus (Chodat) J.P. Petersen by the presence of typical reticulate chloroplasts in the mature cells and by three CBCs and five hemi-CBCs on the conserved part of helix III. The photobiont of F. lightfootii differs from A. fuscideae by having four CBCs and three hemi-CBCs on the conserved part of helix III. Six ITS groups, including both lichenized and free-living species, were retrieved and supported by different CBCs and hemi-CBCs found on ITS2. (Paper IV).
Discussion: Fuscideaceae accommodates genera with a brownish hypothallus (sometimes inconspicuous in Maronea or invisible in Printzeniella), a green coccoid alga, a distinct pigmentation of the apothecium, slightly tapered or cylindrical-clavate asci of the Fuscideatype and short bacilliform conidia. The genus Fuscidea is tentatively split into three groups, possibly defined by the shape of the ascospores and the secondary chemistry. Some Fuscidea species remained unresolved. Fuscidea is paraphyletic as Maronea is nested inside Fuscidea. To make Fuscidea monophyletic there are three possibilities: to lump all Fuscidea species in Maronea, to transfer the Fuscidea species in the F. pusilla-clade (the sister to Maronea) to Maronea, or to introduce a new genus for the F. pusilla clade. As the backbone of the Fuscidea-clade is poorly resolved, at this point no nomenclatural changes at the generic level have been proposed (Paper I). Fuscidea lightfootii and F. pusilla are chemically identical, anatomically and morphologically similar but molecularly different. The two species are difficult to identify without molecular methods. The records of non-sequenced material need revision (Paper II). The diagnostic characters for F. cyathoides are the sessile apothecia with persistent margin, the bean-shaped ascospores becoming brown when mature and the presence of fumarprotocetraric acid (Paper III). The photobiont in F. lightfootii differed from A. fuscideae and may represent another new Apatococcus species. SATé-II provides a phylogeny similar to those from the aligned ITS matrices (Paper IV).
Conclusion: Fuscideaceae belongs to Umbilicariales and is comprised of Fuscidea, Maronea, Ropalospora and Printzeniella gen. nov. Hueidea is treated as a tentative member of the family. The four genera Lettauia, Loxospora, Orphniospora and Sarrameana are not closely related to Fuscideaceae (Paper I). Although some morphotypes of F. lightfootii and F. pusilla appear to be distinguishable based on morphology, DNA sequencing is recommended for their definitive identification (Paper II). The varieties of F. cyathoides are synonymized with the typical saxicolous form and F. fagicola and F. stiriaca synonymous with F. cyathoides (Paper III). Apatococcus fuscideae is the photobiont in most of the studied Fuscidea species and Apatococcus is treated as a genus with uncertain position within Trebouxiophyceae (Paper IV).