Phylogeny and taxonomy of the ‘manna lichens’

We present ataxonomic revision of the ‘manna lichens’ based on morphological, chemical, ecological and molecular data. A large number of herbarium specimens and fresh collections were examined. Phylogenetic analyses were performed using nuclear ribosomal (nrITS, nrLSU) and mitochondrial small subunit (mtSSU) sequences. Some notable phenotypic characters were plotted on the phylogenetic tree, and the analysis reveals that some of these characters are useful for genus and species level distinction of certain ‘manna lichens.’ Phylogeny of the Megasporaceae was revised using a combined data set of nrLSU and mtSSU and performing parsimony and Bayesian analyses. Five genera (Aspicilia, Circinaria, Lobothallia, Megaspora and Sagedia) are recognized. Further, the relationships of five presumably closely related genera of ‘manna lichens’, namely Agrestia (vagrant), Aspicilia (crustose) Circinaria (crustose), Chlorangium (vagrant) and Sphaerothallia (vagrant) with different growth forms were analysed. The analyses revealed that ‘manna lichens’ do not form a monophyletic group but occur in different clades within the genus Circinaria. The genera Agrestia, Chlorangium and Sphaerothallia are assigned as new synonyms under the genus Circinaria and no vagrant or erratic species remain in the genus Aspicilia. The analyses also show that five new erratic, vagrant and crustose species can be recognized. In this study two ‘manna lichens’, viz. Circinaria rostamii sp. nov. (Azerbaijan, Iran and Turkey), and Circinaria gyrosa sp. nov. (Armenia, Azerbaijan, Iran, Turkey, Turkmenistan and Spain) are described as new to science. Three potentially new species with crustose and erratic forms need additional study. Aspicilia fruticolosofoliacea is reduced to synonymy under C. alpicola, and a lectotype is designated for C. aspera. Thirteen new combinations in Circinaria are presented. The phenomenon of vagrancy is briefly discussed, and the biogeography of the ‘manna lichens’ is outlined. Illustrations, distribution maps, and an identification key to the species are provided.     

Spectral Properties of the Green Alga Trebouxia,a Phycobiont of Cryptoendolithic Lichens in the Antarctic Dry Valley

An algologically pure culture of the green alga Trebouxia, a phycobiont of cryptoendolithic lichens, was isolated from sandstone samples collected in the high-altitude polar regions of Antarctica. The absorption and second-derivative absorption spectra of acetone extract of the Antarctic phycobiont cells were studied in comparison with those of a Trebouxia phycobiont isolated recently from a Parmeliaceae lichen in the Mid-European climatic zone. The cells of the Antarctic phycobiont were characterized by a lower content of chlorophyll a and a higher ratio of chlorophyll b and carotenoids to chlorophyll a as compared to the Mid-European phycobiont. Furthermore, the carotenoids of the Antarctic phycobiont were more diverse. The low-temperature fluorescence spectra of the Antarctic phycobiont were characterized by an increased intensity of the short-wavelength fluorescence peak of chlorophyll aand a diminished intensity of fluorescence in the long-wavelength spectral region.     

Morphological and phylogenetic study of algal partners associated with the lichen-forming fungus <Emphasis Type="Italic">Tephromela atra</Emphasis> from the Mediterranean region

Recent DNA sequence analyses have revealed the diversity of algal partners in lichen symbioses. Although morphologically similar, different genetic lineages of photobionts are detected in wide geographic ranges of the same lichen fungal species. We studied the photobiont of the genus Trebouxia, which are known as partners of diverse lichen-forming fungal species in the Mediterranean region. We studied the phylogeny of these algae with a multilocus dataset including three loci: ITS, rbcL, and actin type I gene. The two lineages found, informally named Trebouxia sp. 1 and Trebouxia sp. 2, are related to Trebouxia arboricola/decolorans. The cultivation under axenic conditions succeeded only for one of them so far. We used light microscopy, confocal laser scanning microscopy and transmission electron microscopy for phenotypic characterisation. The ultrastructural characters currently used to describe species in the genus do not support the segregation of Trebouxia sp.1 from Trebouxia arboricola. The preferential presence in Mediterranean climates of these strains suggests eco-physiological adaptation. Despite their asexuality in long living lichen symbioses, coccoid algal lichen partners have apparently diversified genetically and physiologically.     

High photobiont diversity in the common European soil crust lichen Psora decipiens

The genetic diversity of green algal photobionts (chlorobionts) in soil crust forming lichens was studied as part of the SCIN-project (Soil Crust InterNational). A total of 64 lichen samples were collected from four different sites along latitudinal and altitudinal gradients in Europe (Tabernas/Spain; Hochtor-Großglockner/Austria; Gynge Alvar/Sweden; Ruine Homburg/Germany). The dominant lichen species at all four sites was Psora decipiens, often occurring with Buellia elegans, Fulgensia bracteata, F. fulgens and Peltigera rufescens. Genetic identification of chlorobionts was carried out using the nuclear marker (nrITS) and a chloroplast marker (psbL-J). We found P. decipiens to be associated with several different species of Trebouxia and Asterochloris, although previously described to only have Asterochloris sp. The phylogenetic analyses revealed a high chlorobiont diversity with 12 well supported clades, including Trebouxia asymmetrica, T. jamesii, T. impressa and other, as yet taxonomically unidentified clades (Trebouxia sp. URa1-4, T. sp. URa6, T. sp. URa7-13). Additionally, five clades of Asterochloris were identified (A. magna, A. sp. URa14 -17). Most of the chlorobiont species appeared to be cosmopolitan, but five clades were unevenly distributed between the sampling sites with only Trebouxia being found in the warm and dry Spanish habitats and combinations of Trebouxia and Asterochloris in the cooler and more humid habitats. The wide range of chlorobiont species might contribute to the observed domination of P. decipiens at all four research sites of the SCIN project which range from a desert in Spain to an alpine site in the Alps of Austria.     

Cryptic diversity in the pen shell Atrina pectinata (Bivalvia: Pinnidae): high divergence and hybridization revealed by molecular and morphological data

Cryptic species have been increasingly revealed in the marine realm through an analytical approach incorporating multiple lines of evidence (e.g., mtDNA, nuclear genes and morphology). Illustrations of cryptic taxa improve our understanding of species diversity and evolutionary histories within marine animals. The pen shell Atrina pectinata is known to exhibit extensive morphological variations that may harbour cryptic diversity. In this study, we investigated A. pectinata populations along the coast of China and one from Japan to explore possible cryptic diversity and hybridization using a combination of mitochondrial (cytochrome c oxidase subunit I, mtCOI) and nuclear (ribosomal internal transcribed spacer, nrITS) genes as well as morphology. Phylogenetic analyses of mtCOI ‘DNA barcoding gene’ sequences resolved six divergent lineages with intralineage divergences between 0.4% and 0.8%. Interlineage sequence differences ranged from 4.3% to 22.0%, suggesting that six candidate cryptic species are present. The nrITS gene revealed five deep lineages with Kimura 2‐parameter distances of 3.7–30.3%. The five nuclear lineages generally corresponded to mtCOI lineages 1–4 and (5 + 6), suggestive of five distinct evolutionary lineages. Multiple nrITS sequences of significant variance were found within an individual, clearly implying recent hybridization events between/among the evolutionary lineages, which contributed to cytonuclear discordance. Morphologically, five morphotypes matched the five genetic lineages, although the intermediates may well blur the boundaries of different morphotypes. This study demonstrates the importance of combining multiple lines of evidence to explore species cryptic diversity and past evolutionary histories.     

Comparative ultrastructure of pyrenoids inTrebouxia (Microthamniales,Chlorophyta)

Pyrenoid ultrastructure has been investigated from cultures of all 26 species ofTrebouxia with the aim of establishing pyrenoids as a taxonomic character. Different arrangements and forms of thylakoid lamellae within the pyrenoid matrix allow eight pyrenoid types to be distinguished. Each type is characteristic of a group of species. Thegigantea- andimpressa-type are similar, differing only in the form of the tubules: short, branched tubules mark thegigantea-type; ± long and straight invaginations theimpressa-type. Thearboricola-type is characterized by meandering pyrenoid membranes developing from lamellae parallel with each other in young autospores. Pyrenoids of thegelatinosa-type are traversed by thin parallel-arranged tubules. Few thylakoids with a curved profile are typical of theirregularis-type. Thecorticola-type is different from all others in having a distinct starch sheath closely connected with the pyrenoid matrix and no pyrenoglobuli being associated with the pyrenoid membranes. No true pyrenoids have been found inT. magna andT. erici. Within the chloroplast, they have indistinct areas with pyrenoglobuli, but without differentiated thylakoids. Pyrenoid morphology is stable in culture on different media as well as in phycobionts within lichen thalli. Comparing the pyrenoid of a lichenizedTrebouxia with that from cultured species, the identification of the phycobiont within the lichen thallus is possible, without the need of culturing the algae. This has been shown in species ofParmelia andHypogymnia. New aspects for the taxonomy and systematics ofTrebouxia are discussed.Dedicated to Prof. DrLothar Geitler on the occasion of the 90th anniversary of his birthday.     

A diverse chasmataspidid (Arthropoda: Chelicerata) fauna from the Early Devonian (Lochkovian) of Siberia

Examination of material held at the Palaeontological Institute, Moscow, enables the identification of two novel chasmataspidid species: Nahlyostaspis bergstroemi gen. et sp. nov. and Skrytyaspis andersoni gen. et sp. nov. ‘Eurypterus’ stoermeri and ‘Tylopterella’ menneri are both redescribed as chasmataspidids, having previously been assigned to Eurypterida. ‘T’. menneri is transferred to the new genus Dvulikiaspis gen. nov. An identical prosomal structure is identified in ‘Eurypterus’ stoermeri and Heteroaspis novojilovi from the Devonian of Germany and the two species are synonymized, with ‘E’ stoermeri having priority. The previous synonymy of H. novojilovi with Diploaspis casteri is rejected. The presence of ophthalmic ridges is confirmed within Diploaspididae, and new structural characteristics of their bucklers are identified.     

Fungal specificity and selectivity for algae play a major role in determining lichen partnerships across diverse ecogeographic regions in the lichen‐forming family Parmeliaceae (Ascomycota)

Microbial symbionts are instrumental to the ecological and long‐term evolutionary success of their hosts, and the central role of symbiotic interactions is increasingly recognized across the vast majority of life. Lichens provide an iconic group for investigating patterns in species interactions; however, relationships among lichen symbionts are often masked by uncertain species boundaries or an inability to reliably identify symbionts. The species‐rich lichen‐forming fungal family Parmeliaceae provides a diverse group for assessing patterns of interactions of algal symbionts, and our study addresses patterns of lichen symbiont interactions at the largest geographic and taxonomic scales attempted to date. We analysed a total of 2356 algal internal transcribed spacer (ITS) region sequences collected from lichens representing ten mycobiont genera in Parmeliaceae, two genera in Lecanoraceae and 26 cultured Trebouxia strains. Algal ITS sequences were grouped into operational taxonomic units (OTUs); we attempted to validate the evolutionary independence of a subset of the inferred OTUs using chloroplast and mitochondrial loci. We explored the patterns of symbiont interactions in these lichens based on ecogeographic distributions and mycobiont taxonomy. We found high levels of undescribed diversity in Trebouxia, broad distributions across distinct ecoregions for many photobiont OTUs and varying levels of mycobiont selectivity and specificity towards the photobiont. Based on these results, we conclude that fungal specificity and selectivity for algal partners play a major role in determining lichen partnerships, potentially superseding ecology, at least at the ecogeographic scale investigated here. To facilitate effective communication and consistency across future studies, we propose a provisional naming system for Trebouxia photobionts and provide representative sequences for each OTU circumscribed in this study.     

Community Structure of Tintinnid Ciliates of the Microzooplankton in the South West Pacific Ocean: Comparison of a High Primary Productivity with a Typical Oligotrophic Site

Transient ‘hot spots’ of phytoplankton productivity occur in the generally oligotrophic Southern Pacific Ocean and we hypothesized that the population structure of tintinnid ciliates, planktonic grazers, would differ from that of a typical oligotrophic sites. Samples were collected over a 1‐wk period at each of two sites between Fiji and Tahiti: one of elevated chlorophyll a concentrations and primary productivity with an abundance of N‐fixing cyanobacteria Trichodesmium, and a distant oligotrophic site. Tintinnid abundance differed between the sites by a factor of 2. A single species (Favella sp.), absent from the oligotrophic site, highly dominated the ‘hot spot’ site. However, total species richness was identical (71 spp.) as well as short‐term temporal variability (2–4 d). At both sites, species abundance distributions most closely fit a log‐series or log‐normal distribution and the abundance distributions of ecological types, forms of distinct lorica oral diameter, were the typical geometric. Morphological diversity was only slightly lower at the high productivity site. We found that communities of these plankton grazers in ‘hot spots’ of phytoplankton productivity in oligotrophic systems, although harboring different species, differ little from surrounding oligotrophic areas in community structure.     

Haustorienbefall und inäquale Teilungen desNostoc-Phycobionten vonLempholemma botryosum (Lichinaceae)

In fully developed parts of thalli ofLempholemma botryosum a relatively high number of algal cells is attacked by haustoria. They differ specifically in form and effect from haustoria of otherLempholemma species. Cells of theNostoc phycobiont attacked by hyphae developing into haustoria may divide to give inequal besides equal daughter cells.

     

Suitability of chloroplast LSU rDNA and its diverse group I introns for species recognition and phylogenetic analyses of lichen-forming Trebouxia algae

To date, species identification of lichen photobionts has been performed principally on the basis of microscopic examinations and molecular data from nuclear-encoded genes. In plants, the chloroplast genome has been more readily exploited than the nuclear genome for systematic investigations. At the present time, very little information is available about the chloroplast genome of lichen-forming algae. For this reason, we have sequenced a portion of the gene encoding for the chloroplast large sub-unit rRNA (LSU rDNA) as a new molecular marker. Sequencing of the chloroplast LSU rDNAs revealed the existence of an unusual diversity of group I introns (a total of 31) within 15 analyzed Trebouxia species. The number, sequence and insertion site of these introns were very different among species, contributing to their recognition. A relatively large intron-free portion of the chloroplast LSU rDNA and part of the nuclear ribosomal cistron (18S–5.8S–26S) between the nuclear internal transcribed spacers (nrITS) were subjected to phylogenetic analyses. The obtained results indicate that data combination from both nuclear and chloroplast sequences can improve phylogenetic accuracy. Herein, we propose the suitability of both intronic and exonic sequences of the chloroplast LSU rDNA for species recognition, and an exonic sequence spanning from position 879 to 1837 in the Escherichia coli 23S rDNA for phylogenetic analyses of Trebouxia phycobionts.     

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.     

ECOLOGY OF FOLIICOLOUS LICHENS AT THE ‘ BOTARRAMA ’ TRAIL (COSTA RICA), A NEOTROPICAL RAINFOREST. IV. SPECIES ASSOCIATIONS,THEIR SALIENT FEATURES AND THEIR DEPENDENCE ON ENVIRONMENTAL VARIABLES

A community ecology approach using an association of species test and a principal component analysis resulted in the recognition of two major and two minor foliicolous lichen communities in a neotropical rainforest. The major communities are governed by microclimatic factors, one characteristic of the shady understorey and the other confined to light gaps. The minor communities are due to subtle phorophyte preferences towards palm and dicot leaves. The shady understorey community is dominated by the families Arthoniaceae , Opegraphaceae , Trichotheliaceae and Pilocarpaceae , which predominantly have Phycopeltis as their phycobiont, thin thalli, abundant sexual reproduction, small ascospores produced in high numbers, and pycnidial conidiomata. The light-gap community is mainly composed of the families Gomphillaceae and Ectolechiaceae , with Trebouxia as their phycobiont, thickly crystalline or whitish, dispersed thalli, frequent asexual reproduction, large ascospores produced in low numbers, and specialized campylidia and hyphophores as conidiomata. Phycobiont, thallus structure, and the mode of reproduction are considered as adaptations to different microsites, whereas the shape and size of ascospores and conidia seem to be of less importance. The foliicolous lichen communities reflect the spatial and temporal structure of the forest, in particular the continuity of the shady understorey in comparison to the discontinuity of the light gaps. While the formation of the shady understorey community follows more deterministic patterns, the light-gap community exhibits high stochasticity.     

Sterols of the mycobiont and phycobiont isolated from the litchen Xanthoria parietina

The mycobiont, Xanthoria parietina, and the phycobiont, Trebouxia decolorans, of the lichen X. parietina have been cultured separately and their sterols analysed. X. parietina contained ergosterol and lichesterol as the major constituents together with lower levels of three other C₂₈ sterols. Culture of the mycobiont in the presence of [CD₃]-methionine resulted in the incorporation of two deuterium atoms into the C-24 methyl group of these sterols demonstrating that a 24-methylene intermediate was produced as occurs in other fungi. The phycobiont, T. decolorans contained predominantly poriferasterol with lower levels of clionasterol, ergost-5-en-3β-ol, brassicasterol and cholesterol. Two other Trebouxia spp. (213/3 and 219/2) contained similar sterol mixtures.     

Phytophthora Species Infecting Hardy Ornamentals in Nurseries and the Managed Environment in Scotland

Between 2002 and the end of 2009, more than 4000 samples from hardy ornamental plants, collected in surveys for Phytophthora ramorum, were examined to establish the occurrence and diversity of Phytophthora species in Scotland. The samples were gathered from more than 77 plant genera in nurseries, gardens and amenity landscapes. Fifteen different Phytophthora spp. were isolated and identified either by polymerase chain reaction (PCR) or by sequencing of the ITS1, 5.8S subunit and ITS2 region of the ribosomal RNA gene. The most widespread Phytophthora spp. were P. ramorum and P. syringae, followed by P. cactorum, P. kernoviae, P. plurivora, P. cambivora, P. citrophthora, P. taxon ‘Pgchlamydo’, P. pseudosyringae and some single isolates of P. cinnamomi, P. cryptogea, P. gonapodyides, P. nicotianae and P. hibernalis. One isolate did not match any known species. In relation to the number of samples, Phytophthora was found more frequently in trade premises than in gardens or amenity landscapes and the species diversity was higher, highlighting the risks involved in plant trade.     

ULTRASTRUCTURE OF THE PYRENOID OF TREBOUXIA IN RAMALINA MENZIESII TUCK.1,2

Trebouxia sp., the phycobiont of the lichen Ramalina menziesii Tuck., was examined with the electron microscope. Its pyrenoid is characterized structurally as being permeated by interconnected vesiculate membrane systems associated with osmiophilic globules termed pyrenoglobuli. The variety of membrane structure associated with the pyrenoid has been documented with electron micrographs. A model based on serial sections was constructed to show the extent of vesiculation, to demonstrate that the pyrenoglobuli within the pyrenoid matrix are invariably adjacent to the thylakoid membranes within that, matrix, and to emphasize the recurrent thylakoid membrane to pyrenoglobuli relationship. A comparison of the glutaraldehyde-osmium fixation image of the pyrenoglobuli and pyrenoid matrix with the permanganate fixation image has been included. The structure of the pyrenoid matrix in thin section was examined and appears essentially granular.     

Systematics and phylogeny of Vasseuromys (Mammalia,Rodentia, Gliridae) with a description of a new species from the late Miocene of eastern Europe

Vasseuromys is a species‐rich genus of small‐ to medium‐sized glirids spanning the latest Oligocene to late Miocene of Europe and western Asia. Despite extensive discoveries over the past 50 years, little phylogenetic work has been done on Vasseuromys. This study presents the first phylogenetic analysis of the genus that includes all the described species and a new taxon Vasseuromys tectus sp. nov. from the late Miocene of eastern Europe, providing the first insights into the evolutionary relationships within the clade. Results suggest that the genus is clearly paraphyletic. Two strongly supported genus‐level clades are recognized within ‘Vasseuromys’: a restricted Vasseuromys clade (containing the three species, V. pannonicus, V. rugosus and V. tectus) and the Glirulus clade that includes ‘Vasseuromys’ duplex. The remaining ‘Vasseuromys’ species are found to constitute a set of paraphyletic taxa, with the polyphyletic ‘Ramys’ nested within it. The genus Gliruloides is synonymized with Glirulus. Vasseuromys tectus sp. nov. is the most derived member of the genus in having a greater number of cheek teeth ridges including constantly present anterotrope, centrotrope, second prototrope on M1–2, third metatrope on M2, two to three posterotropids on p4 and strong ectolophids on lower molars. The results of the study confirm a European origin for Vasseuromys while suggesting that the late Miocene species of the genus dispersed from the east in the early Turolian.     

The ultrastructure of the symbionts ofRhizocarpon geographicum,Parmelia conspersa andUmbilicaria pustulata growing under dryness conditions

Summary The dryness-induced ultrastructural changes of both myco- and phycobiont of three lichen species (R. geographicum, P. conspersa, andU. pustulata) have been studied over three months and half, period of time. During this time other ecological factors, such as rock substratum, temperature, light and gas interchange were unaltered compared to the natural conditions. A large number of ultrastructural changes were observed in the mycobiont as well as in the phycobiont (Trebouxia) and often, cells showed a highly disorganized morphology. The most important ultrastructural modifications were: 1. pyrenoglobuli of the algae were peripheral, 2. new and unknown structures were observed in the phycobionts of bothR. geographicum andU. pustulata as well as in the mycobiont of the latter species.