MycoKeys 4: 23–36, doi: 10.3897/mycokeys.4.3545
A new circumscription of the genus Varicellaria (Pertusariales, Ascomycota)
Imke Schmitt 1,2, Jürgen Otte 1, Sittiporn Parnmen 3, Anna D. Sadowska-Deś 1,2, Robert Lücking 3, H. Thorsten Lumbsch 3
1 Biodiversity and Climate Research Centre (BiK-F), Forschungsinstitut Senckenberg, Senckenberganlage 25, D-60325 Frankfurt, Germany
2 Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany
3 Department of Botany, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA

Corresponding author: Imke Schmitt (

Academic editor: Cecile Gueidan

received 18 June 2012 | accepted 26 July 2012 | Published 8 August 2012

(C) 2012 Imke Schmitt. This is an open access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC-BY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

For reference, use of the paginated PDF or printed version of this article is recommended.


The lichen-forming genus Pertusaria under its current circumscription is polyphyletic and its phylogenetic affiliations are uncertain. Here we study the species of the genera Pertusaria and Varicellaria which containlecanoric acid as major constituent, have disciform apothecia, strongly amyloid asci, non-amyloid hymenial gel, 1-2-spored asci, and 1- or 2-celled ascospores with thick, 1-layered walls. We infer phylogenetic relationships using maximum likelihood and Bayesian analyses based on four molecular loci (mtSSU, nuLSU rDNA, and the protein-coding, nuclear RPB1 and MCM7 genes). Our results show that the lecanoric acid-containing species form a well-supported, monophyletic group, which is only distantly related to Pertusaria s.str. The phylogenetic position of this clade is unclear, but placement in Pertusaria s.str. is rejected using alternative hypothesis testing. The circumscription of the genus Varicellaria is enlarged to also include species with non-septate ascospores. Seven species are accepted in the genus: Varicellaria culbersonii (Vězda) Schmitt & Lumbsch, comb. nov., Varicellaria hemisphaerica (Flörke) Schmitt & Lumbsch, comb. nov., Varicellaria kasandjeffii (Szatala) Schmitt & Lumbsch, comb. nov., Varicellaria lactea (L.) Schmitt & Lumbsch, comb. nov., Varicellaria philippina (Vain.) Schmitt & Lumbsch, comb. nov., Varicellaria rhodocarpa (Körb.) Th. Fr., and Varicellaria velata (Turner) Schmitt & Lumbsch, comb. nov. A key to the species of Varicellaria is provided.

Key words

Agyriales, Ascomycota, lichen-forming fungi, molecular phylogeny, Ostropomycetidae, Pertusaria, Pertusariales, taxonomy


Generic classifications in lichen-forming fungi have changed dramatically since the introduction of molecular data. Numerous genera have been shown to be polyphyletic or nested within larger genera (e.g., Amo de Paz et al. 2010a, b; Blanco et al. 2004a, b, 2005, 2006; Crespo et al. 2007; 2010; Crewe et al. 2006; Divakar et al. 2006; Ertz and Tehler 2011; Gueidan et al. 2009; Högnabba 2006; Muggia et al. 2010; Printzen 2010; Rivas Plata and Lumbsch 2011; Rivas Plata et al. 2012; Tehler and Wedin 2008; Wedin et al. 2005; Westberg et al. 2010). A further example of incongruence of current classification and phylogenetic relationships as inferred from DNA sequences is the heterogeneous genus Pertusaria. It is the largest genus within Pertusariales, with possibly over 1000 species (Archer and Elix 2011, Messuti and Archer 2009). However, it has been shown to be polyphyletic with species belonging even to different families within the order (Lumbsch and Schmitt 2001, 2002; Schmitt and Lumbsch 2004; Schmitt et al. 2006; 2010).

Schmitt and Lumbsch (2004) identified a combination of phenotypical characters to distinguish between three of the clades of Pertusaria. These characters include secondary metabolites, ascoma-morphology, amyloidity of ascus walls and hymenial gel, number of ascospores per ascus, and ascospore wall thickness and layers. Later, Schmitt et al. (2010) identified a fourth clade with gyalectoid ascomata and found it to be related to Coccotremataceae. The latter clade was distinguished as the genus Gyalectaria and was placed in Coccotremataceae. However, the two remaining major clades that are not closely related to Pertusaria s.str., the Variolaria and Varicellaria groups identified in Schmitt and Lumbsch (2004), have not yet been reclassified. In continuation of our studies on pertusarialean fungi, we are here addressing the issue of monophyly and classification of the so-called Varicellaria clade of Pertusaria. Thisis a group of pertusarialean lichenized fungi characterized by disciform apothecia, non-amyloid hymenial gel, strongly amyloid asci, 1-2-spored asci, and 1- or 2-celled ascospores with more or less thick, 1-layered walls (Schmitt and Lumbsch 2004). Chemically, the clade is characterized by the presence of lecanoric acid as major metabolite. Recent collections of Pertusaria culbersonii, a neotropical species with lecanoric acid, prompted us to address the phylogeny of this group and to classify those Pertusaria species belonging to the Varicellaria group. We have compiled a data set of 29 pertusarialean fungi including all but two species (Pertusaria kasandjeffii and Pertusaria philippina – no fresh material available) that were thought to belong to the Varicellaria group based on phenotypical evidence.

Materials and methods Taxon sampling and molecular methods

We assembled a four-locus data set consisting of mtSSU rDNA, nuLSU rDNA, and the protein-coding genes RPB1 and MCM7. The alignment contained 31 species. Specimens and sequences used for molecular analyses are listed in Table 1. Two sequences of Parmeliaceae (Lecanoromycetes) were used as outgroup, since Lecanoromycetes was shown to be a sister-group of Ostropomycetidae to which Pertusariales belongs (Grube et al. 2004; Miadlikowska et al. 2006; Schmitt et al. 2009). Molecular methods were the same as in a previous study (Schmitt et al. 2010).

Table 1.

Species and sequences used in this study. New sequences are indicated in bold.

Name Phylogenetic lineage Family nuLSU mtSSU 1RPB 7MCM
Varicellaria culbersonii* Varicellaria ? JX101871 JX101873 JX101875 JX101874
Varicellaria hemisphaerica Varicellaria ? AF381556 AF381563 DQ902341 GU980998
Varicellaria lactea Varicellaria ? AF381557 AF381564 DQ870971 GU981000
Varicellaria rhodocarpa Varicellaria ? AF381559 AF381569 N/A N/A
Varicellaria velata Varicellaria ? AY300855 GU980981 DQ870982 GU981005
Pertusariaamara Variolaria ? AF274101 AY300900 DQ870965 GQ272423
Pertusariacorallina Variolaria ? AY300850 AY300901 DQ870967 GU980997
Pertusariascaberula Variolaria ? AF274099 AF431959 DQ870980 GU981003
Pertusariasubventosa Variolaria ? AY300854 AY300905 DQ870981 GU981004
Circinaria contorta Megasporaceae DQ986782 DQ986876 DQ986852 GU980989
Circinaria hispida Megasporaceae DQ780305 HM060722 DQ870933 DQ780273
Lobothallia radiosa Megasporaceae DQ780306 DQ780274 DQ870954 GQ272397
Ochrolechia parella Ochrolechiaceae AF274097 GU980977 DQ870959 GQ272421
Ochrolechia subpallescens Ochrolechiaceae GU980985 GU980978 GU981008 GU980994
Ochrolechia upsaliensis Ochrolechiaceae GU980986 GU980979 GU981009 GU980995
Coccotrema cucurbitula Coccotremataceae AF274092 AF329161 DQ870939 GU980990
Coccotrema maritimum Coccotremataceae AF329164 AF329163 N/A GU980991
Coccotrema pocillarium Coccotremataceae AF274093 AF329166 DQ870940 GU980992
Gyalectaria diluta Coccotremataceae GU980982 GU980974 N/A N/A
Gyalectaria gyalectoides Coccotremataceae GU980983 GU980975 GU981006 GU980993
Gyalectaria jamesii Coccotremataceae GU980984 GU980976 GU981007 N/A
Thamnolia vermicularis Icmadophilaceae AY961599 AY853345 DQ915599 N/A
Icmadophila ericetorum Icmadophilaceae DQ883694 DQ986897 DQ883723 N/A
Dibaeis baeomyces Icmadophilaceae AF279385 AY300883 DQ842011 N/A
Agyrium rufum Agyriaceae EF581826 EF581823 EF581822 GU980988
Miltidea ceroplasta** Miltideaceae HQ391558 HQ391557 JQ900620 N/A
Pertusaria hermaka*** Pertusaria s. str. Pertusariaceae DQ780334 DQ780299 JX101872 GU980999
Pertusaria paramerae Pertusaria s. str. Pertusariaceae DQ780328 GU980980 GU981012 GU981001
Pertusaria pustulata Pertusaria s. str. Pertusariaceae DQ780332 DQ780297 GU981013 GU981002
Parmeliopsis hyperopta outgroup Parmeliaceae AY607823 AY611167 EF092142 GQ272426
Everniopsis trulla outgroup Parmeliaceae EF108290 EF108289 EF105429 GQ272396

*source: Costa Rica, R. Lücking 15424 (F)

**source: Australia, H.T. Lumbsch 20004b, S. Parnmen & T. Widhelm (F)

***source: Australia, A. Mangold, 22 March 2005 (MIN)

Sequence alignments and phylogenetic analysis

We assembled partial sequences using Geneious Pro 5.4.3 (Drummond et al. 2011) and edited conflicts manually. We aligned the sequences using Clustal W (Thompson et al. 1994) (nuLSU, RPB1, MCM7) or PRANK (Loytynoja and Goldman 2005, 2010) (mtSSU). MtSSU sequences are highly variable and contain substantial length polymorphisms that disrupt the alignment. Thus, we eliminated unreliably aligned sites from the mtSSU alignment using the program Aliscore 2.0 (Misof and Misof 2009). Aliscore settings were: window size of six positions, and gaps treated as ambiguous characters (-N option invoked). After cutting 1084 unreliably aligned positions, 698 positions (39%) of the original mtSSU alignment were left.

We analyzed the alignments using maximum likelihood (ML) and Bayesian inference. To test for potential conflict between data sets, we performed ML analyses on the individual alignments and examined the trees for conflicts supported by 75% bootstrap support. ModelTest (Posada and Crandall 1998) selected the following models as best fits for our data: GTR+G+I for nuLSU, RPB1, MCM7, and GTR+G for mtSSU. The individual alignments were analyzed in Geneious using MrBayes 3.1 (Huelsenbeck and Ronquist 2001) with the following settings: 1, 100, 000 generations starting with a random tree and employing 12 simultaneous chains. Two runs were executed, and every 1000th tree was saved into a file. The first 100 trees were discarded as burn in. We checked the traces in Geneious to ensure that stationarity was achieved after the first 100, 000 generations. MrBayes settings for the concatenated alignment were the same as above but with 8, 000, 000 generations and the data split into 8 partitions (mtSSU, nuLSU, and each codon position of RPB1 and MCM7). We used the model GTR+I+G and the burn in was set to 1000. Of the remaining trees, a majority rule consensus tree with average branch lengths was calculated. Posterior probabilities were obtained for each clade. Only clades with posterior probabilities equal or above 0.95 in the Bayesian analysis or bootstrap support equal or above 75 % under ML were considered as strongly supported.

The ML analysis of the concatenated alignment was performed with the program RAxML (Stamatakis 2006) using the default rapid hill-climbing algorithm. The model of nucleotide substitution chosen was GTRMIX. The data set was partitioned into eight parts (mtSSU, nLSU and each codon position of RPB1 and MCM7). Rapid bootstrap estimates were carried out for 2000 pseudoreplicates. Phylogenetic trees were visualized using the program TreeView (Page 1996).

As in previous studies (e.g. Schmitt and Lumbsch 2004) the lecanoric acid-containing species of Pertusaria clustered outside Pertusaria s.str., and instead with the genus Varicellaria, hence contradicting current classification. Thus, we tested whether our data are sufficient to reject monophyly of Pertusaria s.str. + lecanoric acid containing Pertusaria spp. For hypothesis testing, we used two different methods: i) Shimodaira-Hasegawa (SH) test (Shimodaira and Hasegawa 2001) and ii) expected likelihood weight (ELW) test (Strimmer and Rambaut 2002). The SH and ELW test were performed using Tree-PUZZLE 5.2 (Schmidt et al. 2002) with the combined data set, comparing the best tree agreeing with the null hypotheses, and the unconstrained ML tree. These trees were inferred in Tree-PUZZLE using the GTR+I+G nucleotide substitution model.


We obtained six new sequences indicated in Table 1. The combined alignment of the nuLSU, mtSSU rDNA, RPB1, and MCM7 included 2790 unambiguously aligned nucleotide position characters, 1226 of which were variable. The single locus ML topologies did not show any conflicts and hence a concatenated analysis was performed. The maximum likelihood tree did not contradict the Bayesian tree topologies and thus only the majority-rule consensus tree of the Bayesian tree sampling is shown here (Fig. 1). In the phylogenetic tree, species of the Varicellaria-group form a strongly supported monophyletic group, including Pertusaria culbersonii. The Varicellaria-group is sister to the Variolaria-group, but this relationship lacks support. The genus Ochrolechia is a well-supported sister-group to Megasporaceae (Circinaria and Lobothallia), and this clade is sister to the Varicellaria- and Variolaria-groups, but again this relationship lacks support. Agyrium and Miltidea form a supported sister-group, which is strongly supported sister to the well-supported, monophyletic Pertusaria s.str. The well-supported, monophyletic genera Coccotrema and Gyalectaria have a well-supported sister-group relationship. The sister-group relationship of Coccotremataceae and the clade including Agyrium, Miltidea, and Pertusaria s.str. lacks support. A placement of the Varicellaria clade in Pertusaria s.str. is rejected significantly (p≤0.001 in both tests) using alternative hypothesis testing.

Figure 1.

Phylogeny of pertusarialean fungi based on mtSSU, nuLSU, RPB1 and MCM7 sequences. This is a 50% majority rule consensus tree based on 14, 000 trees from a Bayesian analysis. Values above the branches are posterior probabilities/ML bootstrap support (ML based on 2000 replicates).


The current study confirms previous results on the polyphyly of Pertusaria (Lumbsch and Schmitt 2001, 2002; Lumbsch et al. 2006; Schmitt and Lumbsch 2004; Schmitt et al. 2006, 2010). It also confirms that species with lecanoric acid as major constituent and disciform apothecia are closely related to Varicellaria rhodocarpa and therefore should be included in the genus Varicellaria. Our taxon sampling included all but two species putatively belonging to the Varicellaria-group and hence we feel confident to draw formal nomenclatural consequences.

We will address the issue of the phylogeny and classification of the species-rich Variolaria-group in the future using an extended and geographically balanced taxon sampling. Our study shows that additional, molecular markers will be necessary to elucidate the phylogenetic relationships of major clades within Pertusariales (incl. Agyriales) (Hodkinson and Lendemer 2011), since the backbone of the phylogeny of the order almost entirely lacks support.

Taxonomic consequences and key to the species
Varicellaria Nyl. Mém. Soc. Imp. Sci. Nat. Cherbourg 5: 119. 1858.
Type species.

Varicellaria microsticta Nyl. Mém. Soc. Imp. Sci. Nat. Cherbourg 5: 119. 1858. [=Varicellaria rhodocarpa (Körb.) Th.Fr.]

=Clausaria Nyl. Annls Sci. Nat., Bot., sér. 4 15: 45. 1861.

Type species. Clausaria fallens Nyl., Ann. Sci. Nat., Bot., sér. 4 15: 45. 1861. [=Varicellaria velata (Turner) Schmitt & Lumbsch]

The genus in its enlarged circumscription includes species with disciform ascomata, non-amyloid hymenial gel, strongly amyloid, 1-2-spored asci, and 1- or 2-celled ascospores with thick, 1-layered walls. All species contain lecanoric acid, and may also contain lichexanthone or variolaric acid. Currently, we accept seven species in this genus. The accepted names and authorities are listed below.

Varicellaria culbersonii (Vězda) Schmitt & Lumbsch, comb. nov.

Mycobank: MB800038


Pertusaria culbersonii Vězda. Lich. sel. exs. 60: 4 (no. 1487). 1977. Type. Costa Rica, San José, Cerro de la Muerte, 3330m alt., 1976, on soil, W.L. Culberson 13195J (holotype PRA-V).

Varicellaria hemisphaerica (Flörke) Schmitt & Lumbsch, comb. nov.

Mycobank: MB800039


Variolaria hemisphaerica Flörke. Deutsche Lich. 2: 6. 1815. Type. Germany, Berlin [Flörke, Deutsche Lichenen exs. 29] (isotype BM).


Pertusaria hemisphaerica (Flörke) Erichsen. Hedwigia 72: 85. 1932.

Varicellaria kasandjeffii (Szatala) Schmitt & Lumbsch, comb. nov.

Mycobank: MB800040


Pertusaria kasandjeffii Szatala. Magy. Bot. Lapok 29: 83. 1930. Type. Bulgaria, Cepelarska planina, in monte Turluka, par Pamsakli, 1500m alt., 6.1929, Szatala (isotype HBG-1233).

This species is only known from a few localities in Bulgaria and Romania (Hanko 1983). Since no fresh material was available, we could not generate molecular data. However, the species agrees morphologically and chemically with the Varicellaria-group (Fig. 2) and in fact its distinction from Pertusaria lactea is not entirely clear. Both taxa contain lecanoric and variolaric acid, but Pertusaria kasandjeffii differs in being esorediate and having a thick, bulbate thallus. Additional collections are required to test whether Pertusaria kasandjeffii is indeed different from Pertusaria lactea.

Figure 2.

The species of Varicellaria. A Varicellaria culbersonii. Costa Rica, Buck 44182 (F) B Varicellaria hemisphaerica. Germany, 15.4.2004, Schmitt (FR) C, D Varicellaria kasandjeffii. Isotype. Bulgaria, Cepalarska planina: in monte Turluka, par Pasmakali, 1500 m, 9.6.1929, Szatala (HBG-1233) E Varicellaria lactea. Spain, Schmitt 5.6.2003 (FR) F Varicellaria philippina. Holotype. Philippines, Mindanao Dist. Lanao, Camp Keithley by lake Lanao, Sept. 1907, M.S. Clemens, (TUR-V-0006709) G Varicellaria rhodocarpa. Sweden, Printzen 6908 (FR) H Varicellaria velata. Colombia, Moncada & Davila 1537 (F). Scale bar: 1mm. Images were taken with an Olympus SC30 camera under an Olympus SZX7 stereomicroscope.

Varicellaria lactea (L.) Schmitt & Lumbsch, comb. nov.

Mycobank: MB800041


Lichen lacteus L., Mant. Pl. 1: 132. 1767. Type. Sweden, Västergötland, Mularp, 6.08.1922, Vrang [=Malme, Lich. Suec. Exs. 848] (neotype UPS, designated by Jørgensen et al. (1994)).


Lepra lactea (L.) F.H.Wigg. Prim. fl. Holsat.: 97. 1780. Variolaria lactea (L.) Pers. Ann. Bot. 1: 24. 1794. Psora lactea (L.) P.Gaertn., G.Mey. & Scherb. Ökonom.-techn. Fl. Wetterau 3: 214. 1801. Zeora lactea (L.) Arnold. Flora, Jena 53: 214. 1870. Pertusaria lactea (L.) Arnold. Verh. zool.-bot. Ges. Wien 22: 283. 1872. Ochrolechia lactea (L.) Matzer & Hafellner. Bibl. Lichenol. 37: 101. 1990.

Varicellaria philippina (Vain.) Schmitt & Lumbsch, comb. nov.

Mycobank: MB 800589


Pertusaria philippina Vain. Philipp. J. Sci., C, Bot. 8: 131. 1913. Type. Philippines, Mindanao, Lanao, Castra Keithley at Lake Lanao, 1907, Clemens 1302 (holotype TUR-V 6391!).

This species is only known from the Philippines (Wainio 1913) and Papua New Guinea (Elix et al. 1997). We could not generate molecular data since no fresh material was available. Morphologically and chemically the species agrees with Pertusaria velata (Fig. 2), but differs in having 2-spored asci.

Varicellaria rhodocarpa (Körb.) Th.Fr. Lich. Scand. (Uppsala) 1: 322. 1871.

Pertusaria rhodocarpa Körb. Syst. lich. germ.: 384. 1855.


Varicellaria microsticta Nyl. Mém. Soc. Imp. Sci. Nat. Cherbourg 5: 119. 1858. Varicellaria kemensis Räsänen. Ann. Soc. zool.-bot. Fenn. Vanamo 3: 295. 1926.

Varicellaria velata (Turner) Schmitt & Lumbsch, comb. nov.

Mycobank: MB800042


Parmelia velata Turner. Trans. Linn. Soc. London 9: 143. 1808. Type. Great Britain, England, Sussex, 1805, Borrer (holotype BM-4109).


Lichen velatus (Turner) Sm. & Sowerby. Engl. Bot. 29: tab. 2062. 1809. Variolaria velata (Turner) Ach. Lich. univ.: 696. 1810. Pertusaria velata (Turner) Nyl. Lich. Scand. (Uppsala): 179. 1861.

Pertusaria conglobata (Ach.) Th.Fr. Lichenogr. Scand. 1: 321. 1871. Variolaria conglobata Ach. Syn. Lich.: 132. 1814.

Pertusaria haematommoides Zahlbr., Feddes Rep. 33: 50. 1933. Type. Taiwan, Rengechi, Asahina 263 (W – holotype!).

Pertusaria obvelata Nyl. Bih. K. svenska Vetensk. Akad. Handl. 3: 1–156. 1888.

Key to the species of Varicellaria
1a Ascospores 2-celled, thallus esorediate or rarely sorediate, containing lecanoric acid, growing on soil, detritus or mosses in arctic-alpine habitats of the northern Hemisphere Varicellaria rhodocarpa
1b Ascospores 1-celled, thallus esorediate or sorediate, chemistry and habitat various 2
2a Thallus esorediate 3
2b Thallus sorediate 6
3a Thallus thin, coarsely wrinkled to rimose-cracked, containing lecanoric acid, ± lichexanthone, and ± variolaric acid 4
3b Thallus thick, bullate, apothecia rare or unknown, when present 1-1.5 mm in diam., lacking lichexanthones, Neotropical or restricted to eastern Europe 5
4a Asci 1-spored, cosmopolitan Varicellaria velata
4b Asci 2-spored, so far only known from Philippines and Papua New Guinea Varicellaria philippina
5a Growing on siliceous rocks, known only from the Balkan region of Europe Varicellaria kasandjeffii
5b Growing on soil, detritus or mosses, known from high altitudes in Central America Varicellaria culbersonii
6a Thallus containing lecanoric acid, on bark, rarely on rocks Varicellaria hemisphaerica
6b Thallus containing lecanoric acid and variolaric acid, on rocks, rarely on bark Varicellaria lactea

We thank Armin Mangold (Berlin) and Todd Widhelm (Omaha) for collecting material used in this study, and Miklós Bálint (Frankfurt) for assisting with running phylogenetic analyses on the “FUCHS” computing cluster of the Center for Scientific Computing, Frankfurt am Main. Matthias Schultz (Hamburg), Seppo Huhtinen (Turku), and Anton Igersheim (Vienna) kindly sent type material on loan, and Klaus Kalb (Neumarkt) provided literature. This study was funded by ‘LOEWE, Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz’ of Hesse’s Ministry of Higher Education, Research, and the Arts. A.S-D. was supported by a stipend from Deutsche Bundesstiftung Umwelt (DBU).

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