Evolution of ketosynthase domains of polyketide synthase genes in the Cladonia chlorophaea species complex (Cladoniaceae)

Lichen-forming fungi synthesize a diversity of polyketides, but only a few non-reducing polyketide synthase (PKS) genes from a lichen-forming fungus have been linked with a specific polyketide. While it is a challenge to link the large number of PKS paralogs in fungi with specific products, it might be expected that the PKS paralogs from closely related species would be similar because of recent evolutionary divergence. The objectives of this study were to reconstruct a PKS gene phylogeny of the Cladonia chlorophaea species complex based on the ketosynthase domain, a species phylogeny of the complex, and to explore the presence of PKS gene paralogs among members of the species complex. DNA was isolated from 51 individuals of C. chlorophaea and allies to screen for the presence of 13 PKS paralogs. A 128 sequence PKS gene phylogeny using deduced amino acid sequences estimated from the 13 PKS paralogs and sequences subjected to BLASTx comparisons showed losses of each of two PKS domains (reducing and methylation). This research provided insight into the evolution of PKS genes in the C. chlorophaea group, species evolution in the group, and it identified potential directions for further investigation of polyketide synthesis in the C. chlorophaea species complex.     

Phenotypic plasticity in alpine Erigeron species (Asteraceae)

Utelli, A.-B., Huber, W. & Zopfi, H.-J. 1995. Phenotypic plasticity in alpine Erigeron species (Asteraceae). — Nord. J. Bot. 15: 483–492. Copenhagen. ISSN 0107–055X.
Twelve morphological characters were analysed in 67 E. alpinus, E. neglectus and E. uniflorus plants which had been transplanted from their natural habitat to the greenhouse. Mean values and standard deviations were compared for each species. The phenotypic plasticity of the characters resp. their genetic basis was estimated from the correlation of morphological data recorded on single individuals, each grown under both ecological conditions.
A considerable phenotypic plasticity was found in all species and for most characters. E. unijlorus was the most constant species regarding taxonomically relevant characters such as pubescence of the basal leaves, number of flowering heads and number of filiform flowers. In all three species the same highly significant directional variation in plant height and involucre length was found which suggests that these characters have some genetic basis in Erigeron .     

Cladonia subturgida and C. iberica (Cladoniaceae) form a single, morphologically and chemically polymorphic species

Cladonia subturgida and C. iberica constitute the whole of a Mediterranean problematic species, which shows great morphological polymorphism. A study was carried out in order to delimit the extant taxa within this group. The variability of the group was studied morphologically, chemically and phylogenetically. The phylogeny was based on three loci (ITS rDNA, rpb2 and mtLSU), using Maximum Parsimony and Bayesian analyses. Six chemotypes were identified, the most common one containing atranorin and protolichesterinic acid. Our results prove that C. subturgida and C. iberica constitute a single, morphologically and chemically polymorphic species. The taxonomic rank of C. turgida var. corsicana was also studied based on analyses of morphological, chemical and ITS rDNA data. The new nomenclatural combination, C. corsicana, is proposed.     

New species and new records of Xanthoparmelia (lichenized Ascomycota,Parmeliaceae) from Western Australia

The following new species of Xanthoparmelia (Parmeliaceae) are described from Western Australia: X. cranfieldii Elix, X. elevata Elix, X. kimberleyensis Elix, X. monadnockensis Elix,X. nanoides Elix, X. nortegeta Elix, X. sleei Elix and X. toolbrunupensis Elix. In addition, X. luminosa (Elix) Hale and X. victoriana Elix & J. Johnst. are reported from Western Australia for the first time.     

地衣型真菌新种小囊网盘衣(微孢衣科,子囊菌门)（英文）

本文根据表型与基因型分析结果描述了网盘衣属一新种小囊网盘衣。文中提供了新种的特征提要及其描述。     

Canoparmelia scrobicularis belongs to the genus Crespoa (Parmeliaceae,lichenized Ascomycota)

Canoparmelia scrobicularis is shown to be a member of the genus Crespoa and the new combination Crespoa scrobicularis is proposed. The species is described in detail with a discussion of its relationships to other species of Crespoa, especially Crespoa carneopruinata and Crespoa crozalsiana.     

Diversity of non-reducing polyketide synthase genes in the Pertusariales (lichenized Ascomycota): a phylogenetic perspective

Lichenized fungi synthesize a great variety of secondary metabolites. These are typically crystalline compounds, which are deposited extracellularly on the fungal hyphae. While we know a lot about the chemical properties and structures of these substances, we have very little information on the molecular background of their biosynthesis. In the current study we analyze the diversity of non-reducing polyketide synthase (PKS) genes in members of the lichenized Pertusariales. This order primarily contains fully oxidized secondary metabolites from different substance classes, and is chemically and phylogenetically well studied. Using a degenerate primer approach with subsequent cloning we detected up to five non-reducing PKS sequences in a single PCR product. Eighty-five new KS sequence fragments were obtained for this study. Analysis of the 157 currently available fungal KS sequence fragments in a Bayesian phylogenetic framework revealed 18 highly supported clades that included only lichenized taxa, only non-lichenized taxa, or both. Some Pertusarialean groupings of PKS sequences corresponded partly to phylogenetic groupings based on ribosomal DNA. This is reasonable, because a correlation between well-supported phylogenetic lineages and the occurrence of secondary metabolites in the Pertusariales has been observed before. However, no clear linkage was found between the PKS genes analyzed and the ability to produce a particular secondary substance. Several PKS clades did not reveal obvious patterns of secondary compound distribution or phylogenetic association. Compared with earlier phylogenetic analyses of KS sequences the increased sampling in the current study allowed us to detect many new groupings within the fungal non-reducing PKSs.     

Phenotypic plasticity inPotamogeton (Potamogetonaceae)

Sources of the extensive morphological variation of the species and hybrids ofPotamogeton were studied, especially from the viewpoint of the stability of the morphological characters used inPotamogeton taxonomy. Transplant experiments, the cultivation of clones under different values of environmental factors, and the cultivation of different clones under uniform conditions were performed to assess the proportion of phenotypic plasticity in the total morphological variation. Samples from 184 populations of 41Potamogeton taxa were grown. The immense range of phenotypic plasticity, which is possible for a single clone, is documented in detail in 14 well-described examples. The differences among distinct populations of a single species observed in the field were mostly not maintained when grown together under the same environmental conditions. Clonal material cultivated under different values of environmental factors produced distinct phenotypes, and in a few cases a single genotype was able to demonstrate almost the entire range of morphological variation in an observed trait known for that species. Several characters by recent literature claimed to be suitable for distinguishing varieties or even species were proven to be dependent on environmental conditions and to be highly unreliable markers for the delimiation of taxa. The unsatisfactory taxonomy that results when such classification of phenotypes is adopted is illustrated by three examples from recent literature. Phenotypic plasticity was found to be the main source of morphological variation within the species ofPotamogeton, having much more influence than morphological differences caused by different genotypes.     

Geographic variation in algal partners of Cladonia subtenuis (Cladoniaceae) highlights the dynamic nature of a lichen symbiosis

Multiple interacting factors may explain variation present in symbiotic associations, including fungal specificity, algal availability, mode of transmission and fungal selectivity. To separate these factors, we sampled the lichenized Cladonia subtenuis and associated Asterochloris algae across a broad geographic range. We sampled 87 thalli across 11 sites using sequence data to test for fungal specificity (phylogenetic range of association) and selectivity (frequency of association), fungal reproductive mode, and geographic structure among populations. Permutation tests were used to examine symbiont transmission. Four associated algal clades were found. Analysis of molecular variation (amova) and partial Mantel tests suggested that the frequency of associated algal genotypes was significantly different among sites and habitats, but at random with respect to fungal genotype and clade. The apparent specificity for Clade II algae in the fungal species as a whole did not scale down to further within-species lineage-dependent specificity for particular algae. Fungal genotypes were not structured according to site and appeared to be recombining. We suggest that ecological specialization exists for a specific lichen partnership and a site, and that this selectivity is dynamic and environment-dependent. We present a working model combining algal availability, fungal specificity and selectivity, which maintains variation in symbiotic composition across landscapes.     

Phenotypic plasticity in Philonotis fontana (Bryopsida: Bartramiaceae)

Abstract

Gametophytes from six populations of the moss Philonotis fontana (Hedw.) Brid. were grown under two light and two water regimes in order to assess the effects of these environmental factors on gametophytic architecture and leaf and leaf-cell dimensions. Both light and water affectedgrowth, but the light treatments had a greater effect, and on more characters, than did the water treatments. Significant population effects under common garden conditions point to genetic variation for several traits, and population × environmental treatment interactions demonstratedgenetic variation for patterns of phenotypic plasticity, i.e. plants differed in their 'norms of reaction'. Variation among populations in leaf dimensions tended to have a strong genetic component (20–30% of the total variation), whereas cell dimensions showed relatively little geneticvariation (<10% of the total).     

Phenotypic plasticity inLemna minor (Lemnaceae)

Eight genotypes ofLemna minor, originating from four continents, were grown for 15 days in eight different environmental treatments. Fronds under each treatment were then transferred into each of the eight environmental conditions for 15 days. The rate of frond production (relative growth rate) and mean frond biomass were recorded for each pre- and post-transfer treatment and root length was measured for each pre-transfer treatment. For all the traits, the levels of response varied significantly between genotypes (G) and between environmental conditions (E). G × E interaction effect was significant for all traits under pre-transfer treatments and some post-transfer treatments. Both pattern and amount of plasticity were genotypically variable but the amount of variation depended on the trait. The trait representing the best estimate of fitness, growth rate, exhibited the least amount of plasticity and on average, showed the most conservative pattern of plasticity. In contrast, the trait least related to fitness, root length, was the most plastic and showed the most divergent pattern of plasticity. Under some post-transfer treatments, growth rate and mean frond biomass were affected by origin (initial treatment) effect. Pattern and amount of plasticity were also influenced by initial treatments. Since some genotypes may be more affected than others by environmental conditions, origin effect may accentuate G × E interaction and therefore, modify the pattern and amount of plasticity. Comparison between dendrograms based on genetic and phenotypic similarities suggested that there is no relationship between genetic and phenotypic divergence. This lack of relationship may be due to the fact that plasticity is not necessarily adaptive.     

Phenotypic plasticity inCrepis tectorum (Asteraceae)

Two experiments were carried out using two different approaches to compare populations ofCrepis tectorum (Asteraceae). One was based on a comparison of means of various vegetative and reproductive characters and another was based on a comparison of response patterns of the same characters in a series of environments. Population divergence within two earlier recognized form series, one from weed habitats and one from alvar habitats on Baltic islands, resulted in a partially overlapping pattern in cluster analyses based on character means. However, the pattern revealed by a comparison of the direction and amount of plastic response suggested that populations within the two form series had more similar response patterns than other combinations of populations. It was concluded that patterns of plasticity may provide useful additional information on the overall similarity among taxa. An hypothesis that plants in weed populations should exhibit a greater phenotypic response to the environments than plants in alvar populations was rejected.     

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.     

The conservation of polyol transporter proteins and their involvement in lichenized Ascomycota

In lichen symbiosis, polyol transfer from green algae is important for acquiring the fungal carbon source. However, the existence of polyol transporter genes and their correlation with lichenization remain unclear. Here, we report candidate polyol transporter genes selected from the genome of the lichen-forming fungus (LFF) Ramalina conduplicans. A phylogenetic analysis using characterized polyol and monosaccharide transporter proteins and hypothetical polyol transporter proteins of R. conduplicans and various ascomycetous fungi suggested that the characterized yeast’ polyol transporters form multiple clades with the polyol transporter-like proteins selected from the diverse ascomycetous taxa. Thus, polyol transporter genes are widely conserved among Ascomycota, regardless of lichen-forming status. In addition, the phylogenetic clusters suggested that LFFs belonging to Lecanoromycetes have duplicated proteins in each cluster. Consequently, the number of sequences similar to characterized yeast’ polyol transporters were evaluated using the genomes of 472 species or strains of Ascomycota. Among these, LFFs belonging to Lecanoromycetes had greater numbers of deduced polyol transporter proteins. Thus, various polyol transporters are conserved in Ascomycota and polyol transporter genes appear to have expanded during the evolution of Lecanoromycetes.     

Cladonia (sect. Cocciferae) norvegica, a new lichen species

Cladonia (sect. Cocciferae , subsect. Ochroleucae) norvegica T0nsb. & Holien sp. nov., is closely related to C. bacilliformis (Nyl.) DT. & Sarnth. but is morphologically, chemically, and ecologically distinct. Superficially it may resemble C. (sect. Cladonia) coniocraea auct., which is often growing with it. C. norvegica is known from Norway only.     

Parallel evolution and phenotypic divergence in lichenized fungi: a case study in the lichen-forming fungal family Graphidaceae (Ascomycota: Lecanoromycetes: Ostropales)

A molecular phylogeny of combined mtSSU, nuLSU, and RPB2 data revealed previously unrecognized levels of parallel evolution and phenotypic divergence in the lichen family Graphidaceae. Five clades were supported within the family: the Fissurina, Ocellularia, Graphis, Topeliopsis, and Thelotrema clades, containing 33 of the 42 currently accepted genera within the family. The results for the first time provide a fully resolved phylogeny of this family and confirm the synonymy of Graphidaceae and Thelotremataceae. Ancestral character state reconstruction using likelihood, Bayesian, and parsimony approaches indicate that lirellate ascomata evolved independently in each of the five clades. Carbonized ascomata evolved independently in at least four of the five clades. An unexpected result was the independent evolution of columella structures in the Fissurina and Ocellularia clades. Besides these more general findings, we document several cases in which evolution of several traits in parallel resulted in striking look-alikes within unrelated lineages, such as Topeliopsismuscigena and Chapsameridensis in the Topeliopsis and Thelotrema clades, Leptotremawightii, Myriotremalaeviusculum, and Leucodectonphaeosporum in the Ocellularia and Thelotrema clades, Ocellulariastylothecia and Melanotremameiosporum in the Fissurina and Ocellularia clades, and Myriotremapycnoporellum, Myriotremaclandestinum and Wirthiotremaglaucopallens in the Fissurina, Ocellularia, and Topeliopsis clades. Pagel's test of independent character evolution suggested that at least for some of the traits involved in these cases, ecological constraints may have caused their evolution in parallel. The most intriguing find is the correlation between gall-forming thalli and vertical columns of calcium oxalate crystals, suggesting that these crystals do not function as light distributors, as previously assumed, but instead stabilize the thalli which are usually hollow beneath, similar to a dome-shaped structure. Ancestral character state reconstruction together with an approach to visualize the phenotype of putative ancestral lineages suggested the alpha-Graphidaceae to resemble some of the extant species currently classified in Myriotrema s.lat., with pore-like ascomata, and non-amyloid ascospores with lens-shaped lumina.     

A new isidiate species of Arthonia (Ascomycota: Arthoniaceae) from Costa Rica

The new corticolous species Arthonia isidiata is described from the Pacific lowlands of Costa Rica. A. isidiata is characterized by minute, cylindrical to coralloid isidia produced on the thallus surface. The species currently is known only from the type locality in Corcovado National Park, where it occurs abundantly in the coastal rainforest around Sirena Biological Station.