MycoKeys 3: 37–47, doi: 10.3897/mycokeys.3.3201
Two new species of Lecanora sensu stricto (Lecanoraceae, Ascomycota) from east Africa
Paul Kirika 1, Sittiporn Parnmen 2, Thorsten Lumbsch 2
1 Botany Department, National Museums of Kenya, P.O. Box 40658–00100, Nairobi, Kenya
2 Department of Botany, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA

Corresponding author: H. Thorsten Lumbsch (

Academic editor: Imke Schmitt

received 5 April 2012 | accepted 2 May 2012 | Published 10 May 2012

(C) 2012 Paul Kirika. 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 new sorediate species Lecanora kenyana from Mount Kenya and Lecanora orientoafricana from the Rift Valley in Kenya are described. Lecanora kenyana has red-brown apothecia with a constricted base, a melacarpella–type amphithecium, pulicaris–type epihymenium, a hyaline hypothecium, and contains usnic acid as major constituent. Lecanora orientoafricana is characterized by having a dark hypothecium, pulicaris-type amphithecium, chlarotera-epihymenium, and contains atranorin and gangaleoidin. A phylogenetic analysis using maximum likelihood and a Bayesian approach based on DNA sequence data of mtSSU and ITS rDNA support that both new species belong to Lecanora sensu stricto and cluster with species containing usnic acid or having a dark hypothecium, respectively.


Kenya, Lecanorales, new species, taxonomy, tropical lichens


Lecanora is the major genus of Lecanoraceae (Lumbsch and Huhndorf 2010) and includes crustose (incl. placodioid) lichens with hyaline, usually non-septate ascospores, Lecanora-type asci and mostly lecanorine apothecia. The morphological and chemical diversity is large in this heterogeneous genus and molecular data have supported that the genus as currently circumscribed is not monophyletic (Arup and Grube 1998; 2000; Grube et al. 2004; Lumbsch 2002). The core group of Lecanora sensu stricto is characterized by the presence of calcium oxalate crystals in the amphithecium, filiform conidia, and the presence of atranorin and/or usnic acid. This agrees with an extended circumscription of the Lecanora subfusca group to include taxa containing usnic acid and a dark hypothecium (Guderley 1999; Lumbsch 1995; Lumbsch et al. 1995; Lumbsch et al. 1996; Lumbsch et al. 2003; Papong et al. in press). African species of Lecanora sensu stricto are poorly known but our recent studies resulted in the description of a new species and new records of Lecanora species for Kenya (Kirika et al. in press; Lumbsch et al. 2011). Among the collections from the Mount Kenya area and the Rift Valley we found two corticolous species, one sorediate taxon with usnic acid and a morphologically somewhat similar species with a dark hypothecium. The two taxa do not agree with known species (Lumbsch 1995; Lumbsch et al. 1995; Lumbsch et al. 1996; Papong et al. 2011; Papong and Lumbsch 2011) and consequently are described as new. To confirm the placement of the new species in Lecanora sensu stricto, we also generated DNA sequence data of the internal transcribed spacer region (ITS) and partial sequences of the small subunit of the mitochondrial ribosomal DNA (mtSSU) and performed a phylogenetic analysis with sequences available in Genbank.

Materials and methods Taxon sampling and molecular methods

The study is based on material deposited in EA and F and DNA sequences downloaded from Genbank. Sequences of five Ramboldia spp. were included as outgroup since the genus has been shown previously to be related to Lecanora (Kalb et al. 2008). Sequence data of the two new species were assembled with sequences of the mitochondrial small subunit (mtSSU) and nuclear ITS rDNA downloaded from Genbank (Table 1). Sample preparation, DNA isolation, PCR and direct sequencing were performed as described previously (Mangold et al. 2008; Wirtz et al. 2012). Primers for amplification were: mr SSU1 (Zoller et al. 1999) and MSU7 (Zhou and Stanosz 2001) for mtSSU and ITS1F and ITS4 (Gardes and Bruns 1993) for ITS rDNA. Sequence fragments obtained were assembled with SeqMan 4.03 (DNASTAR) and manually adjusted.


Species and specimens used in the present study. Newly obtained sequenced in bold.

Species Collection data mtSSU acc. no. ITS acc. no
Lecanora achroa JQ782663 JN943714
Lecanora aff. achroa JQ782662 JQ782708
Lecanora allophana AY567710 AF070031
Lecanora argentata JQ782664 JQ782704
Lecanora argopholis DQ787358 JQ782705
Lecanora austrotropica JQ782665 JQ782706
Lecanora californica JQ782668 JQ782707
Lecanora campestris DQ787362 AF159930
Lecanora elatinoides JQ782669 JQ782709
Lecanora flavopallida1 JQ782673 JN943723
Lecanora flavopallida2 JQ782674 JN943724
Lecanora flavoviridis JQ782675 JQ782711
Lecanora gangaleoides JQ782676 JQ782712
Lecanora helva1 JQ782679 JQ782716
Lecanora helva2 JQ782680 JQ782715
Lecanora aff. helva JQ782677 JQ782713
Lecanora aff. helva JQ782678 JQ782714
Lecanora hybocarpa DQ912273 DQ782849
Lecanora kenyana Kenya, Kirika 1179 (F) JQ900616 JQ900618
Lecanora leproplaca1 JQ782683 JQ782718
Lecanora leproplaca2 JQ782684 JQ782719
Lecanora leprosa1 JQ782682 JQ782721
Lecanora leprosa2 JQ782685 JQ782720
Lecanora orientoafricana Kenya, Kirika 2205 (F) JQ900617 JQ900619
Lecanora pacifica JQ782686 JQ782722
Lecanora paramerae EF105418 EF105413
Lecanora phaeocardia1 JQ782687 JQ782724
Lecanora phaeocardia2 JQ782688 JQ782723
Lecanora plumosa1 JQ782689 JQ782725
Lecanora plumosa2 JQ782690 JQ782726
Lecanora pseudogangaleoides ssp. verdonii JQ782691 JQ782727
Lecanora queenslandica JQ782692 JQ782728
Lecanora sp.C JQ782693 JQ782729
Lecanora sp.E (sorediate) JQ782694 JQ782730
Lecanora subimmergens1 JQ782696 JQ782732
Lecanora subimmergens2 JQ782695 JQ782731
Lecanora subimmersa JQ782697 JQ782733
Lecanora toroyensis JQ782698 JQ782734
Lecanora tropica JQ782699 JN943720
Lecanora ulrikii JQ782700 -
Lecanora vainioi1 JQ782702 JN943716
Lecanora vainioi2 JQ782701 JN943717
Lecanora wilsonii JQ782703 -
Ramboldia arandensis EU075527 EU075541
Ramboldia brunneocarpa EU075528 EU075542
Ramboldia laeta EU075530 EU075544
Ramboldia petraeoides EU075531 EU075545
Ramboldia stuartii EU075535 EU075549
Sequence alignments and phylogenetic analysis

Alignments were done using Clustal W (Thompson et al. 1994). Ambiguously aligned regions were removed manually. The single locus and concatenated alignments were analyzed by maximum likelihood (ML) and a Bayesian approach (B/MCMC). To test for potential conflict, ML bootstrap analyses were performed on the individual data sets, and 75% bootstrap consensus trees were examined for conflict (Lutzoni et al. 2004). Maximum likelihood analyses were performed using the program GARLI (Zwickl 2006), employing the general time reversible model of nucleotide substitution (Rodriguez et al. 1990), including estimation of invariant sites, and assuming a discrete gamma distribution with six rate categories. Bootstrapping (Felsenstein 1985) was performed based on 2000 replicates. The B/MCMC analysis was conducted on the concatenated data set using MrBayes 3.1.2 (Huelsenbeck and Ronquist 2001), with the same substitution model as in the ML analysis. The dataset was portioned into the two parts (mtSSU, ITS) and each partition was allowed to have own parameters (Nylander et al. 2004). A run with 20, 000, 000 generations, starting with a random tree and employing 4 simultaneous chains, was executed. Every 100th tree was saved into a file. The first 500, 000 generations (i.e. the first 5000 trees) were deleted as the “burn in” of the chain. We used AWTY (Nylander et al. 2007) to compare splits frequencies in the different runs and to plot cumulative split frequencies to ensure that equilibrium was reached. Of the remaining trees a majority rule consensus tree with average branch lengths was calculated using the sumt option of MrBayes. Posterior probabilities were obtained for each clade. Only clades that received bootstrap support equal or above 70% under ML and posterior probabilities ≥ 0.95 were considered as strongly supported. Phylogenetic trees were visualized using the program Treeview (Page 1996).

Anatomical and chemical studies

Anatomical studies were conducted using standard light microscopy on hand-cut sections mounted in water. Secondary lichen substances were identified by high performance thin-layer chromatography (HPTLC) according to the standard methods (Arup et al. 1993).

Data resources

The data underpinning the analyses reported in this paper are deposited in the Dryad Data Repository at doi: 10.10.5061/dryad.b1068.

Results and discussion The Species
Lecanora kenyana Kirika & Lumbsch, sp. nov.

Mycobank no. MB800051

Figure 1

Kenya, Eastern Prov., Mount Kenya National Park, Chogoria Track, close to Chogoria Gate, open Juniperus-Podocarpus woodland, 0°09'S, 37°26'E, 2960m alt., 27.01.2010, on Juniperus, P. Kirika 1179, G. Mugambi & H.T. Lumbsch (holotype EA, isotype F).


Thallus crustose, verrucose to verruculose, thin to thick, glossy, whitish to greenish; margin indistinct; prothallus not visible; sorediate. Soralia roundish, concave, 0.5–1.2 mm diam., remaining distinct or coalescing, with granular soredia, yellowish green to yellowish gray. Apothecia sessile, strictly constricted at base, 0.6–2.0 mm diam., lecanorine; disc red-brown, shiny, plane, epruinose; margin concolourous with thallus, prominent, thick, smooth, entire to verruculose, flexuose. Amphithecial cortex uniform, gelatinous, inspersed with crystals, hyaline, 25–45 µm thick, with hyphae growing out basally. Amphithecium with small and large crystals (=melacarpella-type). Hypothecium hyaline, 25–30 µm high, parathecium hyaline, with yellowish crystals, 5–7 µm thick. Hymenium hyaline, 55–70 µm high, clear. Epihymenium red–brown, 10–12 µm thick, with numerous, small crystals; pigmentation and crystals dissolving in K (=pulicaris–type). Paraphyses sparingly branched, apically slightly swollen, hyaline. Asci clavate, 50–60 × 10–14 µm, 8–spored. Ascospores ellipsoid to narrowly ellipsoid, 12–17 × 4.5–6.5 µm. Pycnidia not seen.

Figure 1, 2.

Morphology of the new Lecanora species. 1 Lecanora kenyana, isotype (F). 2 Lecanora orientoafricana, isotype (F). Scale bars = 1mm


Thallus and apothecial margin K+ yellow, C-, KC–, containing atranorin (minor), and usnic acid (major).


The new species is named after the country Kenya where the new species has been found.


Lecanora kenyana is characterized by relatively large, red-brown apothecia with a constricted base, a melacarpella-type amphithecium, pulicaris-type epihymenium, the presence of usnic acid as major constituent, and the presence of soralia. There are only few sorediate Lecanora sensu stricto species with usnic acid, including Lecanora brodoana, Lecanora elatinoides, Lecanora floridula, Lecanora jamesii, Lecanora mobergiana, and Lecanora transvaalensis (Brodo and Elix 1993; Lumbsch and Elix 1998; Lumbsch et al. 1995; Lumbsch and Nash 1995). The saxicolous Lecanora brodoana and Lecanora mobergiana differ in having an egranulose epihymenium among other characters, whereas Lecanora elatinoides (containing pannarin) and Lecanora jamesii (containing 2-O-methylsulphurellin) are readily distinguished by their alternative chemistry and smaller ascospores. Similar species include Lecanora floridula described from Florida (USA) and Lecanora transvaalensis from South Africa. The former species can be distinguished by having smaller apothecia (up to 1 mm), thinner and poorly developed amphithecial cortex, a chlarotera-type epihymenium, smaller ascospores, and the presence of unidentified triterpenes (Lumbsch et al. 1995). Lecanora transvaalensis differs from Lecanora kenyana in having smaller apothecia (up to 0.9 mm), a thinner and poorly developed amphithecial cortex, and smaller, broadly ellipsoid ascospores (9.5–11.5 × 7.0–8.5 µm). Further, it contains unidentified terpenoids (Lumbsch et al. 1995).

Ecology and distribution.

At present this species is known from bark of juniper trees in open habitats at altitudes above 2800m in forests dominated by Hagenia and Podocarpus. Associated lichens included Heterodermia leucomelos, Lecanora caesiorubella, Leptogium laceroides, Lobaria pulmonaria, Pannaria fulvescens, Physcia albata, Pseudocyphellaria aurata, Physcia crocata, Varicellaria velata, and several Usnea spp.

Additional specimen examined.

Kenya: Eastern Prov., Mt. Kenya National Park, Sirimon route, ca. 3km for KWS gate towards Old Moses Camp, 00°00'N, 37°15'E, mature montane forest with Podocarpus, Olea, Hagenia and Arundinaria alpina, 2870m, on bark, 7.10.2010, P. Kirika 2051, G. Mugambi, G. Gatere and M. Mutembei (EA).

Lecanora orientoafricana Kirika & Lumbsch, sp. nov.

Mycobank no. MB800052

Figure 2

Kenya, Rift Valley Prov., Cherangani Hills, Kerer forest, degraded montane forest, 3240m, on bark, 25.07.2011, P. Kirika 2205 (EA, holotype, F-isotype).


Thallus crustose, verrucose to verruculose, thin to thick, glossy, whitish to greenish grey; margin indistinct; prothallus not visible; sorediate. Soralia roundish, 0.3–1.0 mm diam., with granulose soredia, light pale greenish white to grayish green. Apothecia sessile, constricted at base, 0.4–1.4 mm diam., lecanorine; disc light red-brown to brown, matt, plane or concave, sparsely grayish pruinose; margin concolourous with thallus, prominent, thick, smooth, verruculose. Amphithecial cortex uniform, gelatinous, inspersed with crystals, hyaline, 20–30 µm thick. Amphithecium with large crystals (=pulicaris–type). Hypothecium red-brown to yellowish brown, 30–40 µm high, parathecium hyaline, lacking crystals, 5–7 µm thick. Hymenium hyaline, 70–85 µm high, clear. Epihymenium red–brown, 10–12 µm thick, with coarse crystals; pigmentation and crystals dissolving in K (=chlarotera–type). Paraphyses sparingly branched, apically slightly swollen, hyaline. Asci clavate, 50–60 × 10–12 µm, 8–spored. Ascospores ellipsoid to broadly ellipsoid, 12.5–15.5 × 6.0–8.5 µm. Pycnidia not seen.


Thallus and apothecial margin K+ yellow, C-, KC–, containing atranorin and gangaleoidin.


The new species is named after the area East Africa where it has been collected.


Lecanora orientoafricana is characterized by the presence of granular soredia, sparsely pruinose, brown apothecia, a pulicaris-type amphithecium, chlarotera-type epihymenium, dark hypothecium, broadly ellipsoid ascospores, and the presence of atranorin and gangaleoidin. Soredia are rare among Lecanora sensu stricto species with a dark hypothecium. Some specimens of Lecanora coronulans are sorediate, but this species is readily distinguished by epruinose apothecial discs, an egranulose epihymenium, and the presence of protoconstipatic acid and zeorin and major constituents in addition to atranorin (Lumbsch et al. 1996). Similar esorediate species include Lecanora egranulosa and Lecanora phaeocardia. The latter differs from Lecanora orientoafricana in having epruinose apothecial discs, a thinner amphithecial cortex, and alternative chemistry. Lecanora egranulosa is readily distinguished by darker, epruinose apothecial discs, an indistinct, thin amphithecial cortex, small crystals in the epihymenium, shorter ascospores, and the presence of zeorin (Lumbsch et al. 1996).

Ecology and distribution.

This new species is currently only known from the type locality in the Rift Valley province of Kenya, where it was found growing on bark in a degraded montane forest dominated by Podocarpus falcatus, Rapanea melanophloes and Faurea saligna at an altitude of 3240m. Associated species included Sphaerophorus melanocarpus, Pannaria cf. rubiginosa, and Ramalina spp.

Phylogenetic study

Four new sequences were generated for this study and aligned with sequences downloaded from Genbank (Table 1). The single gene locus did not show any conflicts and hence the concatenated data set was analyzed. Our combined data set included 820 unambiguously aligned positions, 174 of which were constant. The ML tree had a likelihood value of –3718.083 and in the B/MCMC analysis of the combined data set, the likelihood parameters in the sample had the following mean (Variance): LnL = -3794.172 (0.21). The ML tree and the tree from the B/MCMC tree sampling were almost identical with no differences in well-supported clades. Thus, only the ML tree is shown here (Fig. 3). In our analysis, species of the genus Lecanora form a strongly supported monophyletic group as in a previously published study (Papong et al. in press). Since Papong et al. (in press) discussed the relationships of the different Lecanora groups in detail, these discussions are not reiterated here, but we focus only on the relationships of the two newly described species here. Lecanora kenyana clusters strongly supported with Lecanora ulrikii and Lecanora wilsonii, two species which also contain usnic acid (Lumbsch et al. 1995; Papong et al. 2011; Papong et al. in press; Papong and Lumbsch 2011). Lecanora orientoafricana is sister to Lecanora flavoviridis, which also has a dark hypothecium (Lumbsch et al. 1996; Papong et al. in press). The molecular data support the placement of the new species in Lecanora sensu stricto. However, given the few sequences available from tropical Lecanora in Genbank, the molecular data cannot be used to confirm that the species have indeed not been described previously. We conclude that they are new based on our database of known Lecanora species and our examinations of type material of Lecanora spp. over more than 24 years.

Figure 3.

Phylogenetic placement of the two new Lecanora species as inferred from a concatenated alignment of mtSSU and ITS DNA sequences. This is the optimal tree under maximum likelihood. Branches in bold received likelihood bootstrap support values above 70%, and posterior probabilities equal or above 0.95


We wish to thank the Kenya Wildlife Service (KWS) and the Kenya Forest Service (KFS) for providing collecting permits and Nature Kenya for partially supporting fieldwork in the Rift valley. We also thank George Mugambi (Nairobi) for his help and support on field trips. This study was financially supported by The Field Museum/IDP Foundation, Inc. African Training Fund. The laboratory work was done at the Pritzker Laboratory for Molecular Systematics and Evolution at the Field Museum.

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