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The genus Micarea was studied for the first time in the Taita Hills, Kenya. Based on new collections and existing data, we reconstructed a phylogeny using ITS, mtSSU and Mcm7 regions, and generated a total of 27 new sequences. Data were analyzed using maximum likelihood and maximum parsimony methods. Based mainly on new collections, we discovered four undescribed well-supported lineages, characterized by molecular and phenotypic features. These lineages are described here as Micarea pumila, M. stellaris, M. taitensis and M. versicolor. Micarea pumila is characterized by a minutely granular thallus, small cream-white or pale brownish apothecia, small ascospores and the production of prasinic acid. Micarea stellaris has a warted-areolate thallus, cream-white apothecia usually darker at the centre, a hymenium of light grey or brownish pigment that dissolves in K, and intense crystalline granules that appear as a belt-like continuum across the lower hymenium when studied in polarized light. Micarea taitensis is characterized by a warted-areolate thallus and cream-white or yellowish apothecia that sometimes produce the Sedifolia-grey pigment. Micarea versicolor is characterized by a warted-areolate, sometimes partly granular thallus and apothecia varying from cream-white to light grey to blackish in colour. This considerable variation in the coloration of its apothecia is caused by an occasional mixture of the Sedifolia-grey pigment in the epihymenium and another purplish brown pigment in the hymenium. Micarea stellaris, M. taitensis and M. versicolor produce methoxymicareic acid. The main distinguishing characters are presented in a species synopsis. Three of the new species are nested in the M. prasina group, and the fourth one (M. taitensis) resolves as a basal taxon to the M. prasina group. The new species inhabit montane cloud forests, which have fragmented dramatically throughout the Eastern Arc Mountains in recent decades. The genus Micarea was studied for the first time in the Taita Hills, Kenya. Based on new collections and existing data, we reconstructed a phylogeny using ITS, mtSSU and Mcm7 regions, and generated a total of 27 new sequences. Data were analyzed using maximum likelihood and maximum parsimony methods. Based mainly on new collections, we discovered four undescribed well-supported lineages, characterized by molecular and phenotypic features. These lineages are described here as Micarea pumila, M. stellaris, M. taitensis and M. versicolor. Micarea pumila is characterized by a minutely granular thallus, small cream-white or pale brownish apothecia, small ascospores and the production of prasinic acid. Micarea stellaris has a warted-areolate thallus, cream-white apothecia usually darker at the centre, a hymenium of light grey or brownish pigment that dissolves in K, and intense crystalline granules that appear as a belt-like continuum across the lower hymenium when studied in polarized light. Micarea taitensis is characterized by a warted-areolate thallus and cream-white or yellowish apothecia that sometimes produce the Sedifolia-grey pigment. Micarea versicolor is characterized by a warted-areolate, sometimes partly granular thallus and apothecia varying from cream-white to light grey to blackish in colour. This considerable variation in the coloration of its apothecia is caused by an occasional mixture of the Sedifolia-grey pigment in the epihymenium and another purplish brown pigment in the hymenium. Micarea stellaris, M. taitensis and M. versicolor produce methoxymicareic acid. The main distinguishing characters are presented in a species synopsis. Three of the new species are nested in the M. prasina group, and the fourth one (M. taitensis) resolves as a basal taxon to the M. prasina group. The new species inhabit montane cloud forests, which have fragmented dramatically throughout the Eastern Arc Mountains in recent decades.

Tropical mountains and especially their forests are hot spots of biodiversity threatened by human population pressure and climate change. The diversity of lichens in tropical Africa is especially poorly known. Here we use the mtSSU and nuITS molecular markers together with morphology and ecology to assess Leptogium (Peltigerales, Ascomycota) diversity in the tropical mountains of Taita Hills and Mt. Kasigau in Kenya and Mt. Kilimanjaro in Tanzania. The sampled habitats cover a wide range of ecosystems from savanna to alpine heath vegetation and from relatively natural forests to agricultural environments and plantation forests. We demonstrate that Leptogium diversity in Africa is much higher than previously known and provide preliminary data on over 70 putative species, including nine established species previously known from the area and over 60 phylogenetically, morphologically, and/or ecologically defined Operational Taxonomic Units (OTUs). Many traditional species concepts are shown to represent morphotypes comprised of several taxa. Many of the species were only found from specific ecosystems and/or restricted habitats and are thus threatened by ongoing habitat fragmentation and degradation of the natural environment. Our results emphasize the importance of molecular markers in species inventories of highly diverse organism groups and geographical areas.

During lichenological explorations of tropical montane forests in Kenya, a remarkable new lichenicolous fungus was repeatedly found growing on thalli of the epiphytic tripartite cyanolichen Crocodia cf. clathrata. Molecular phylogenetic analyses placed the fungus within Gomphillaceae (Ostropales, Lecanoromycetes), a family mainly of lichen-symbiotic species in the tropics. The anatomical features (unitunicate, non-amyloid asci and simple, septate paraphyses) as well as the hemiangiocarpic ascoma development confirm its taxonomic affinity. DNA sequence data showed the closest relationship was with Gyalidea fritzei, followed by Corticifraga peltigerae. A monotypic genus, Taitaia, is introduced to incorporate a single species, T. aurea. The new fungus is characterized by aggregated ascomata with yellow margins and salmon red discs developing from a single base.

Lichens that reproduce by means of vegetative propagules (soredia or isidia) are generally thought to have broad geographic distributions. However, recent studies have shown that some asexually reproducing lichens with broad distribution may be comprised of multiple, independent species-level lineages. Our understanding of species diversity in asexually reproducing lichenized fungal species may be further confounded by the fact that otherwise morphologically similar taxa separated based on the presence or absence of vegetative reproductive structures may in fact be conspecific. In this study, we investigate genetic diversity of the pantropical sorediate species Hypotrachyna sorocheila using molecular sequence data. Specifically, we generated a three-marker dataset for Hypotrachyna subgen. Everniastrum specimens, and reconstructed a multilocus, molecular phylogeny. Our results show that sorediate samples phenotypically identifiable as H. sorocheila do not form a monophyletic group, but form two di...

WOS: 000365393000021, PubMed ID: 26299211, 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., Spanish Ministerio de Ciencia e Innovacion [CGL2010-21646/BOS, CGL2011-25003, CGL2013-42498-P]; Universidad Complutense-Banco Santander [GR3/14]; Comunidad Autonoma de Madrid [REMEDINAL S-2009/AMB-1783]; National Science Foundation [DEB-0949147]; Swedish Research Council [VR621-2009-5372, VR 621-2012-3990]; Academy of Finland [1133858]; Estonian Science Foundation [9109]; European Regional Development Fund (Center of Excellence FIBIR); German Academic Exchange Service (DAAD); Tromso University Museum, We are indebted to Adriano A. Spielmann, Joel Mercado, Robert Egan, Udeni Jayalal and Daniel Sanchez Mata for providing a few samples, and to Rosario G. Gavilan for assisting in collecting expeditions. We also thank editors and anonymous reviewers for valuable comments and suggestions. This work was supported by the Spanish Ministerio de Ciencia e Innovacion (projects CGL2010-21646/BOS, CGL2011-25003 and CGL2013-42498-P), the Universidad Complutense-Banco Santander (GR3/14), Comunidad Autonoma de Madrid (REMEDINAL S-2009/AMB-1783), the National Science Foundation ('Hidden diversity in parmelioid lichens'; DEB-0949147), the Swedish Research Council (VR621-2009-5372 and VR 621-2012-3990), the Academy of Finland (grant 1133858), the Estonian Science Foundation (grant 9109), and the European Regional Development Fund (Center of Excellence FIBIR). G.S. was supported by a fellowship from the German Academic Exchange Service (DAAD). I.K.K.T. was supported by a grant from Tromso University Museum.

Lichens constitute an important component of tropical forest biodiversity. This study inventoried corticolous lichens and examined their variation in various forest types with varying climatic conditions in Mt. Kenya, East Africa. Specifically we evaluated variation of lichen assemblages in relation to forest types and tree diversity along an altitudinal gradient (1800-3100m). Ten study sites were established on two contrasting sides of Mt. Kenya in the indigenous forest: six of them at Chogoria which is on the humid southeastern windward side of the mountain and four sites on the Sirimon side located on the drier northwestern leeward side. Overall 242 lichen taxa were documented; with Chogoria and Sirimon forests having 148 and 94 species that translated to an adequate sampling effort of 74 % and 68 %, respectively. The two contrasting forest types (Chogoria and Sirimon) supported slightly different lichens assemblages. Meanwhile lichen assemblages were found to significantly vary with elevation (or forest types) and with tree host. Posterior analyses showed that the differences were significant among sampling sites (or forest types) on the Chogoria side and insignificant on the Sirimon side. Similarly the number of lichens differed significantly among the host tree species. This study stresses the urgent need to upscale the sustainable management of the presently threatened tropical forests in order to preserve their structural heterogeneity.

Pertusarialean lichens include more than 300 species belonging to several independent phylogenetic lineages. Only some of these phylogenetic clades have been comprehensively sampled for molecular data, and formally described as genera. Here we present a taxonomic treatment of a group of pertusarialean lichens formerly known as "Pertusaria amara-group", "Monomurata-group", or "Variolaria-group", which includes widespread and well-known taxa such as P. amara, P. albescens, or P. ophthalmiza. We generated a 6-locus data set with 79 OTUs representing 75 species. The distinction of the Variolaria clade is supported and consequently, the resurrection of the genus Lepra is followed. Thirty-five new combinations into Lepra are proposed and the new species Lepra austropacifica is described from mangroves in the South Pacific. Lepra is circumscribed to include species with disciform ascomata, a weakly to non-amyloid hymenial gel, strongly amyloid asci without clear apical amyloid structures, containing 1 or 2, single-layered, thin-walled ascospores. Chlorinated xanthones are not present, but thamnolic and picrolichenic acids occur frequently, as well as orcinol depsides. Seventy-one species are accepted in the genus. Although the distinction of the genus from Pertusaria is strongly supported, the relationships of Lepra remain unresolved and the genus is tentatively placed in Pertusariales incertae sedis.

The delimitation of species boundaries of tropical lichen-forming fungi remains relatively poorly known. Recent studies demonstrated higher species diversity in tropical areas than previously assumed. Here we focus on the genus Hypotrachyna, which is a speciose group of parmelioid lichens with a center of distribution in tropical areas and on collections made over the last decade in Kenya. We gathered DNA sequences of nuclear ribosomal internal transcribed spacer region (ITS), large subunit (nuLSU) and mitochondrial small subunit (mtSSU) from 136 samples and analyzed them in phylogenetic frameworks. Morphological, chemical and ecological features were re-evaluated. We show that several species that were supposed to have wide, intercontinental distributions consist of separate lineages. Consequently, three new species are described from Kenya: H. kenyana, H. meridionalis, and H. nyandaruaensis. Furthermore, the separation of H. meyeri from H. sinuosa is supported by molecular data and we propose to use the name H. imbricatula for Neotropical samples and H. orientalis for Paleotropical specimens of H. imbricatula s.l. Our study supports the hypothesis that distributional ranges in parmelioid lichens are more restricted than previously assumed.

Diversity of tropical lichen-forming fungi, especially crustose lichens is currently poorly known. Since lichens are important bioindicators of air pollution, forest health, and climate change, we addressed the lichen diversity in Kenya. Our study focused on the diversity of lichen-forming fungi in the Mount Kenya montane forests, where we sampled corticolous lichens at ten localities in the Mount Kenya forest. The lichen diversity in the study area was very rich with fifty-nine species recorded for the first time from Kenya; 18 of them are new records for the African continent. Diagnostic features and distribution areas are given for each species reported. The crustose genera Auriculora, Candelariella, Clandestinotrema, Diorygma, Hemithecium, Lecanactis, Lepraria, Letrouitia, Megalospora, Mycoporum, Ocellularia, Placynthiella, Piccolia, Ramboldia, Tephromela and Thelotrema are reported here from Kenya for the first time. The majority of new records belong to pan- or palaeotropical species, in ad...

A number of lichen-forming fungal species are widely distributed. Here, we investigate biogeographic patterns in a widely distributed isidiate taxon – Parmelinella wallichiana – using molecular sequence data. Our results revealed that Parmelinella wallichina, as currently circumscribed, is not monophyletic but falls into four clades, two of them represented by a sample only. A third clade, occurring in Africa and southern India is described as a new species, Parmelinella schimperiana Kirika & Divakar, sp. nov. Our study adds a further example of previously overlooked, geographically distinct, lineages that were discovered using molecular data.

The phylogenetic position of the monotypic genus Bulborrhizina is studied using molecular data from three loci (mtSSU, nuLSU and ITS) aligned with sequences from 95 other samples of parmelioid lichens. Bulborrhizina africana clusters within the predominantly paleotropical Bulbothrix ‘clade II’ with strong support. However, its relationships within this clade remain uncertain. The morphological characters used to circumscribe Bulborrhizina are interpreted as adaptations to the habitat of this species in semi-arid regions of eastern Africa. A formal synonymy of the genus Bulborrhizina with either Bulbothrix or Parmelinella is postponed until sequences of the type species of Bulbothrix become available that will allow us to identify which of the two clades of species currently placed in Bulbothrix represents Bulbothrix s.str.