The sister group relation of parmeliaceae (Lecanorales, Ascomycota)

The family Parmeliaceae (Lecanorales, Ascomycota) is possibly the largest, best known and most thoroughly studied lichen family within its order. Despite this fact the relationship between Parmeliaceae and other groups in Lecanorales is still poorly known. The aim of the present study is to contribute to finding the sister group of Parmeliaceae as an aid in future studies on the phylogeny and character evolution of the group. We do this by sampling all potential relatives to the Parmeliaceae that we have identified, i.e. Gypsoplaca, Japewia, Mycoblastus, Protoparmelia, and Tephromela, a good representation of the major groups within the Parmeliaceae s. lat. and a good representation of other taxa in the core Lecanorales. We use molecular data from two genes, the large subunit of the nuclear ribosomal RNA gene (nrLSU) and the small subunit of the mitochondrial ribosomal RNA gene (mrSSU), and a Bayesian analysis of the combined data. The results show that the closest relatives to Parmeliaceae are the two genera Protoparmelia and Gypsoplaca, which are crustose lichens. Parmeliaceae in our sense is a well supported group, including also the family segregates Alectoriaceae, Hypogymniaceae, Usneaceae and Anziaceae.     

Cetradonia,a new genus in the new family Cetradoniaceae (Lecanorales,Ascomycota)

Abstract:A taxonomic revision of the lichen genus Gymnoderma Nyl. sensu Yoshimura & Sharp (Cladoniaceae) based on an integrative analysis of polyphasic characters supports the segregation of a new genusCetradonia J.-C.Wei & Ahti in a new family Cetradoniaceae J.-C.Wei & Ahti. The monotypic genus and family are based on Cladonia linearis Evans. In addition, two species are recognized in genus Neophyllis F. Wilson and two species are retained in the genus Gymnoderma Nyl. of the Cladoniaceae.     

Using Phylogenetic,Functional and Trait Diversity to Understand Patterns of Plant Community Productivity

Background

Two decades of research showing that increasing plant diversity results in greater community productivity has been predicated on greater functional diversity allowing access to more of the total available resources. Thus, understanding phenotypic attributes that allow species to partition resources is fundamentally important to explaining diversity-productivity relationships.

Methodology/Principal Findings

Here we use data from a long-term experiment (Cedar Creek, MN) and compare the extent to which productivity is explained by seven types of community metrics of functional variation: 1) species richness, 2) variation in 10 individual traits, 3) functional group richness, 4) a distance-based measure of functional diversity, 5) a hierarchical multivariate clustering method, 6) a nonmetric multidimensional scaling approach, and 7) a phylogenetic diversity measure, summing phylogenetic branch lengths connecting community members together and may be a surrogate for ecological differences. Although most of these diversity measures provided significant explanations of variation in productivity, the presence of a nitrogen fixer and phylogenetic diversity were the two best explanatory variables. Further, a statistical model that included the presence of a nitrogen fixer, seed weight and phylogenetic diversity was a better explanation of community productivity than other models.

Conclusions

Evolutionary relationships among species appear to explain patterns of grassland productivity. Further, these results reveal that functional differences among species involve a complex suite of traits and that perhaps phylogenetic relationships provide a better measure of the diversity among species that contributes to productivity than individual or small groups of traits.     

Phylogenetic and structural studies in the thelebolaceae (Ascomycota)

Several minute dung-inhabiting discomycetes have been classified in the family Thelebolaceae, which has traditionally been included in the order Pezizales. The non-operculate type-genusThelebolus has recently been excluded from the Pezizales. The phylogenetic distribution of other genera associated with Thelebolaceae is still obscure. We have analysed ca. 580 bp from a variable part of the nuclear SSU rRNA gene fromAscozonus, Caccobius, Lasiobolus andThecotheus, and compared these with ca. 1700 bp sequences fromThelebolus, Pleospora, Pezizales, leotiales and Leotiales-related taxa. In the resulting tree,Ascozonus andCaccobius group withThelebolus and the inoperculate discomycetes;Lasiobolus groups withAscodesmis, andThecotheus withAscobolus within Pezizales. SEM pictures of fruit-bodies and ascus apices ofAscozonus, and ascospores fromThecotheus are presented to illustrate characteristic features of these taxa. Submitting author: FAX: +47-22 85 46 64, TEL: +47-22 85 46 61.     

Homology Assessment of the Boundary Tissue in Fruiting Bodies of the Lichen Family Sphaerophoraceae (Lecanorales, Ascomycota)

Abstract: The ascoma ontogeny of the family Sphaerophoraceae is reviewed. The development of the boundary tissue in Leifidium tenerum is described and compared with similar structures in some other mazaediate representatives of the family ( Sphaerophorus globosus, Bunodophoron dodgei and B. diplotypum ), and with the non-mazaedia-producing genera Austropeltum and Neophyllis. The dominant structure in the base of mature ascomata in all genera is a boundary tissue forming the border between ascomatal ("generative") and thalline ("vegetative") tissue. In the mazaedia-forming genera, the boundary tissue is composed of two layers. The upper layer is a zone of ascogenous hyphae, homologous to similar zones in Neophyllis and Austropeltum. The lower layer is a pseudoparenchymatic and often strongly pigmented zone formed by generative tissue, homologous to a zone of generative tissue present in Neophyllis but lacking in Austropeltum.     

Genetic diversity and photobiont associations in selected taxa of the Tephromela atra group (Lecanorales, lichenised Ascomycota)

Mycobiont and photobiont genetic diversity was investigated in four taxa of the Tephromela atra complex, which differ in ecology and substratum preference (from siliceous rocks, limestone to bark), and are differently interpreted by taxonomists. Phylogenetic analyses were performed using mycobiont nuclear ITS, beta tubulin and homologous polyketide synthase gene (PKS) sequences obtained from freshly collected material sampled from the Mediterranean region to the Southern Alps. The silicicolous samples from the Alps form a basal lineage of the entire complex, and despite the morphological similarity, they do not form a monophyletic group with the Mediterranean samples. No resolution was found among the calcicolous and the silicicolous taxa from Mediterranean habitats, which are traditionally segregated at variety or species level. The epiphytic taxon, although nested with the other ecotypes, splits in two well-supported lineages. Among the four taxa, Tephromela grumosa is the only morphologically, chemically and genetically distinct taxon. However, it is also nested in the large T. atra complex. Phylogenetic analysis of photobionts ITS sequences revealed that thalli from the Mediterranean region are associated with two distinct lineages of Trebouxia, but the lineages are not correlated with substrate or mycobiont phenotype. The thalli from the Alps are exclusively associated with T. simplex, suggesting a protracted isolation from the other lineages.     

Phylogenetic placement of the anamorphic tribe Ustilaginoideae (Hypocreales, Ascomycota)

Tribe Ustilaginoideae (Hypocreales, Ascomycetes) is made up of three anamorph genera, Munkia, Neomunkia and Ustilaginoidea. Species of Munkia and Neomunkia develop on the culms of bamboo (Chusquea spp.) and have a neotropical distribution while species of Ustilaginoidea infect the florets of various grasses and are pantropical in distribution. In this study we evaluated the phylogeny of the tribe and assessed hypotheses regarding its affinity to clavicipitalean teleomorphic groups. To support phylogenetic analyses, morphology of representatives of several key species of Ustilaginoideae was examined also. Phylogenetic analyses using sequences of the large subunit of the ribosomal RNA gene suggest that members of Ustilaginoideae are distinct from teleomorphic genera of Clavicipitaceae and that Ustilaginoideae should be recognized as a monophyletic group within Hypocreales. However, phylogenetic analyses did not resolve the placement of Ustilaginoideae in Clavicipitaceae or Hypocreaceae, suggesting that it might be a distinct lineage within Hypocreales. This evaluation supported the monophyly of tribes Balansieae and Clavicipeae in the family Clavicipitaceae.     

The limitations of ancestral state reconstruction and the evolution of the ascus in the Lecanorales (lichenized Ascomycota)

Ancestral state reconstructions of morphological or ecological traits on molecular phylogenies are becoming increasingly frequent. They rely on constancy of character state change rates over trees, a correlation between neutral genetic change and phenotypic change, as well as on adequate likelihood models and (for Bayesian methods) prior distributions. This investigation explored the outcomes of a variety of methods for reconstructing discrete ancestral state in the ascus apex of the Lecanorales, a group containing the majority of lichen-forming ascomycetes. Evolution of this character complex has been highly controversial in lichen systematics for more than two decades. The phylogeny was estimated using Bayesian Markov chain Monte Carlo inference on DNA sequence alignments of three genes (small subunit of the mitochondrial rDNA, large subunit of the nuclear rDNA, and largest subunit of RNA polymerase II). We designed a novel method for assessing the suitable number of discrete gamma categories, which relies on the effect on phylogeny estimates rather than on likelihoods. Ancestral state reconstructions were performed using maximum parsimony and maximum likelihood on a posterior tree sample as well as two fully Bayesian methods. Resulting reconstructions were often strikingly different depending on the method used; different methods often assign high confidence to different states at a given node. The two fully Bayesian methods disagree about the most probable reconstruction in about half of the nodes, even when similar likelihood models and similar priors are used. We suggest that similar studies should use several methods, awaiting an improved understanding of the statistical properties of the methods. A Lecanora-type ascus may have been ancestral in the Lecanorales. State transformations counts, obtained using stochastic mapping, indicate that the number of state changes is 12 to 24, which is considerably greater than the minimum three changes needed to explain the four observed ascus apex types. Apparently, the ascus in the Lecanorales is far more apt to change than has been recognized. Phylogeny corresponds well with morphology, although it partly contradicts currently used delimitations of the Crocyniaceae, Haematommataceae, Lecanoraceae, Megalariaceae, Mycoblastaceae, Pilocarpaceae, Psoraceae, Ramalinaceae, Scoliciosporaceae, and Squamarinaceae.     

A new species of Phyllopsora (Lecanorales, lichen-forming Ascomycota) from Dominican amber, with remarks on the fossil history of lichens

Phyllopsora dominicanus sp. nov. (Bacidiaceae, Lecanorales,lichen-forming Ascomycota) is described and illustrated fromDominican amber. The diagnostic features of the lichen includea minute subfolious thallus of lacinulate, ascending squamules,a well-developed upper cortex, and a net-like pseudocortex onthe lower surface. The algal symbionts are unicellular greenalgae, forming a distinct layer immediately below the uppercortex. The fossil demonstrates that distinguishing featuresof Phyllopsora have remained unchanged for tens of millionsof years. The fossil also provides the first detailed viewsof mycobiont–photobiont contacts in Tertiary green algallichens. The mycobiont hyphae formed apical and intercalaryappressoria by pressing closely against the photobiont cells.This indicates that a conserved maintenance of structure isalso seen in the fine details of the fungal–algal interface. Key words: Amber, fossil, fungi, lichen, Phyllopsora, symbiosis, Tertiary Received 30 May 2007; Revised 30 November 2007 Accepted 21 December 2007     

On the Diversity of the Laccase Gene: A Phylogenetic Perspective from Botryosphaeria rhodina (Ascomycota: Fungi) and Other Related Taxa

The present study is the first describing the sequencing of a fragment of the copper-oxidase domain of a laccase gene in the family Botryosphaeriaceae. The aim of this work was to assess the degree of genetic and evolutionary relationships of a laccase gene from Botryosphaeria rhodina MAMB-05 with other ascomycete and basidiomycete laccase genes. The 193-amino acid sequences of the copper-oxidase domain from several different fungi, insects, a plant, and a bacterial species were retrieved from GenBank and aligned. Phylogenetic analyses were performed using neighbor-joining, maximum parsimony, and Bayesian inference methods. The organisms studied clustered into five gene clades: fungi (ascomycetes and basidiomycetes), insects, plants, and bacteria. Also, the topologies showed that fungal laccases of the ascomycetes and basidiomycetes are clearly separated into two distinct clusters. This evidence indicated that B. rhodina MAMB-05 and other closely related ascomycetes are a new biological resource given the biotechnological potential of their laccase genes.     

Chemosyndromes in the lichen genus Teloschistes (Teloschistaceae, Lecanorales)

The secondary metabolites of 150 specimens belonging to 29 species of Teloschistes were analysed with HPLC. Seven anthraquinones were detected of which parietin dominated with minor proportions of emodin, teloschistin, fallacinal and parietinic acid. The depsidones vicanicin, caloploicin, and isofulgidin occurred together with some compounds of unknown identity in varying proportions in T. flavicans, T. peruensis, T. stellatus, and one unnamed taxon. Nine chemosyndromes were found in the genus. Most species had only one chemosyndrome, but T. flavicans s. lat. had six syndromes. The geographical distribution patterns of these chemosyndromes in T. flavicans are discussed as well as the applicability of chemical characters for species delimitation in Teloschistes.     

地衣型真菌石果衣(疣孢菌科，子囊菌门)次级代谢产物的多样性

地衣能够产生大量的新型次级代谢产物,但以往对石果衣Endocarpon pusillum的研究中未能检测出任何次级代谢产物。然而,对其共生菌进行基因组测序发现其中含有14个沉默的PKS基因和2个沉默的NRPS基因。在此研究中,为激活其途径,使用了优化马铃薯培养基和大米培养基对石果衣共生真菌进行了培养。从优化马铃薯培养物中分离得到9个次级代谢产物,包括2个新的异吲哚-1-酮类化合物(1, 2)。而从大米培养物中分离到3个已知化合物和1个新的萘醌类化合物(9)。通过核磁共振和质谱数据确定了新化合物的结构。研究结果表明,大量地衣中未能检测出任何次级代谢产物,或仅能检测出少量次级代谢产物,可能与其基因组中的沉默基因有关。因此,通过对沉默基因的激活方法为地衣次级代谢产物资源的研究与开发开辟了有效途径。     

Chemistry,Anatomy and Morphology of Foliicolous Species of Fellhanera and Badimia (Lichenized Ascomycotina: Lecanorales)

A comparison of secondary chemistry and a variety of anatomical and morphological characters of Fellhanera and Badimia (Pilocarpaceae) has been conducted in an effort to clarify the systematic position of both genera. Based on our results we conclude that Fellhanera and Badimia are closely related and separated mainly by the slightly different paraphyses, amyloid reactions of their asci, apothecial size, and the presence or absence of campylidia. Fellhanera badimioides sp.n. is described, and the following systematic changes are proposed: Badimia cateilea (Vain.) comb.n. B. lecanorina (Zahlbr.) comb.n., B. tuckermanii (R.Sant.) comb.n. and Fellhanera stanhopeae (Müll. Arg.) comb.n.     

Phylogenetic significance of morphological characters in the tropical Hypotrachyna clade of parmelioid lichens (Parmeliaceae, Ascomycota)

Lichen-forming ascomycetes exhibit often complex morphologies of the vegetative thallus that are usually not found in non-lichenized fungi. This includes the thallus organization and appendical structures associated with the main thallus, such as cilia and rhizines. Such morphological characters are widely employed in the taxonomy of parmelioid lichens, especially at generic level. Within parmelioid lichens, several monophyletic groups can be distinguished, the Hypotrachyna clade being one of them, which includes mostly tropical taxa. In this first molecular study focused specifically on the Hypotrachyna clade, we used maximum parsimony and Bayesian analyses of a combined data set of nuclear ITS and mitochondrial SSU rDNA sequences to (1) test the monophyly of genera presently accepted within the clade and (2) evaluate the phylogenetic value of the morphological characters used to circumscribe genera in parmelioid lichens. Out of the 89 mtSSU and 88 nuITS sequences included in the present study, 121 sequences were newly obtained. Our results show that the taxa within the clade fall into two major groups and that the genus Hypotrachyna is polyphyletic. Everniastrum and Parmelinopsis are nested within Hypotrachyna sensu stricto, the latter being also polyphyletic. Bulbothrix is paraphyletic with Parmelinella nested within and is basal to the second major Hypotrachyna clade. Monophylies of Bulbothrix and Hypotrachyna are significantly rejected. The phylogenetic analysis demonstrates that morphological characters currently used to circumscribe genera in parmelioid lichens, such as cortical anatomy, lobe configuration, cilia, and rhizines have been overestimated and have only minor value in identifying monophyletic groups.     

On the ascus types in thePhysciaceae (Lecanorales)

Comparative studies in thePhysciaceae revealed that characters of the apical apparatus of asci differ between the various genera. Two major ascus types are observable in this family. They are found to correspond with certain ascospore types.     

Species delimitation and evolution of metal bioaccumulation in the lichenized Acarospora smaragdula (Ascomycota, Fungi) complex

The crustose lichenized fungi in the Acarosporaceae are splendid examples of organisms managing to survive in extremely harsh environments, such as highly mineralized rocks and low-pH habitats. Some representatives of the Acarospora smaragdula complex are known to accumulate substantial amounts of potentially toxic metals including iron and copper, resulting in populations with highly divergent coloration and morphology. These populations have often been treated as distinct species by lichen taxonomists. Parsimony and parsimony jackknifing analyses of β-tubulin, nuclear ITS rDNA, and mtSSU rDNA sequence data sets was used to investigate the evolution of iron and copper accumulation and the production of the secondary compound norstictic acid in populations within the A. smaragdula species complex in Sweden, with additional samples mainly from Norway and the UK. Phylogenetic species recognition (concordance of single-gene phylogenies) was used to investigate species delimitations. Seven species are recognized in the complex. Atypically green, copper-accumulating samples, often given species rank, do not form a distinct group but are nested within A. smaragdula s. str., indicating that this ability is widespread in this species. Rust-coloured, iron-accumulating samples form two well supported separate groups, indicating that two morphologically distinct, obligate, iron-accumulating species are present, but facultatively iron-accumulating populations occur in at least one additional species. Norstictic acid, sometimes claimed to characterize the whole A. smaragdula complex, is only present in A. smaragdula s. str. The evolutionary significance of metal accumulation in Acarospora is discussed, as is the significance of our results for the application of phylogenetic species recognition/gene tree concordance-based species recognition, and DNA barcoding.
© The Willi Hennig Society 2009.