| 1. |
- Boluda, C. G., et al.
(författare)
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Evaluating methodologies for species delimitation : the mismatch between phenotypes and genotypes in lichenized fungi (Bryoria sect. Implexae, Parmeliaceae)
- 2019
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Ingår i: Persoonia. - : RIJKSHERBARIUM. - 0031-5850 .- 1878-9080. ; 42, s. 75-100
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Tidskriftsartikel (refereegranskat)abstract
- In many lichen-forming fungi, molecular phylogenetic analyses lead to the discovery of cryptic species within traditional morphospecies. However, in some cases, molecular sequence data also questions the separation of phenotypically characterised species. Here we apply an integrative taxonomy approach - including morphological, chemical, molecular, and distributional characters - to re-assess species boundaries in a traditionally speciose group of hair lichens, Bryoria sect. Implexae. We sampled multilocus sequence and microsatellite data from 142 specimens from a broad intercontinental distribution. Molecular data included DNA sequences of the standard fungal markers ITS, IGS, GAPDH, two newly tested loci (FRBi15 and FRBi16), and SSR frequencies from 18 microsatellite markers. Datasets were analysed with Bayesian and maximum likelihood phylogenetic reconstruction, phenogram reconstruction, STRUCTURE Bayesian clustering, principal coordinate analysis, haplotype network, and several different species delimitation analyses (ABGD, PTP, GMYC, and DISSECT). Additionally, past population demography and divergence times are estimated. The different approaches to species recognition do not support the monophyly of the 11 currently accepted morphospecies, and rather suggest the reduction of these to four phylogenetic species. Moreover, three of these are relatively recent in origin and cryptic, including phenotypically and chemically variable specimens. Issues regarding the integration of an evolutionary perspective into taxonomic conclusions in species complexes, which have undergone recent diversification, are discussed. The four accepted species, all epitypified by sequenced material, are Bryoria fuscescens, B. glabra, B. kockiana, and B. pseudofuscescens. Ten species rank names are reduced to synonymy. In the absence of molecular data, they can be recorded as the B. fuscescens complex. Intraspecific phenotype plasticity and factors affecting the speciation of different morphospecies in this group of Bryoria are outlined.
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| 2. |
- Divakar, Pradeep K., et al.
(författare)
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Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi
- 2015
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 208:4, s. 1217-1226
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 3. |
- Schneider, K. M., et al.
(författare)
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Gut microbiota depletion exacerbates cholestatic liver injury via loss of FXR signalling
- 2021
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Ingår i: Nature Metabolism. - : Springer Science and Business Media LLC. - 2522-5812. ; 3:9, s. 1228-1241
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Tidskriftsartikel (refereegranskat)abstract
- Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease of unknown aetiology for which there are no approved therapeutic options. Patients with PSC display changes in gut microbiota and in bile acid (BA) composition; however, the contribution of these alterations to disease pathogenesis remains controversial. Here we identify a role for microbiota-dependent changes in BA synthesis that modulates PSC pathophysiology. In a genetic mouse model of PSC, we show that loss of microbiota-mediated negative feedback control of BA synthesis results in increased hepatic BA concentrations, disruption of bile duct barrier function and, consequently, fatal liver injury. We further show that these changes are dependent on decreased BA signalling to the farnesoid X receptor, which modulates the activity of the rate-limiting enzyme in BA synthesis, CYP7A1. Moreover, patients with advanced stages of PSC show suppressed BA synthesis as measured by serum C4 levels, which is associated with poor disease prognosis. Our preclinical data highlight the microbiota-dependent dynamics of BA metabolism in cholestatic liver disease, which could be important for future therapies targeting BA and gut microbiome interactions, and identify C4 as a potential biomarker to functionally stratify patients with PSC and predict disease outcomes. Patients with primary sclerosing cholangitis (PSC), a chronic cholestatic liver disease, display changes in the gut microbiota and in bile acid composition. Schneider, Candels and colleagues identify a role for microbiota-dependent regulation of bile acid synthesis through farnesoid X receptor signalling, which is relevant for PSC disease progression.
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| 4. |
- Hajra, Rajkumar, et al.
(författare)
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Cometary plasma response to interplanetary corotating interaction regions during 2016 June-September : a quantitative study by the Rosetta Plasma Consortium
- 2018
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 480:4, s. 4544-4556
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Tidskriftsartikel (refereegranskat)abstract
- Four interplanetary corotating interaction regions (CIRs) were identified during 2016 June-September by the Rosetta Plasma Consortium (RPC) monitoring in situ the plasma environment of the comet 67P/Churyumov-Gerasimenko (67P) at heliocentric distances of similar to 3-3.8 au. The CIRs, formed in the interface region between low- and high-speed solar wind streams with speeds of similar to 320-400 km s(-1) and similar to 580-640 km s(-1), respectively, are characterized by relative increases in solar wind proton density by factors of similar to 13-29, in proton temperature by similar to 7-29, and in magnetic field by similar to 1-4 with respect to the pre-CIR values. The CIR boundaries are well defined with interplanetary discontinuities. Out of 10 discontinuities, four are determined to be forward waves and five are reverse waves, propagating at similar to 5-92 per cent of the magnetosonic speed at angles of similar to 20 degrees-87 degrees relative to ambient magnetic field. Only one is identified to be a quasi-parallel forward shock with magnetosonic Mach number of similar to 1.48 and shock normal angle of similar to 41 degrees. The cometary ionosphere response was monitored by Rosetta from cometocentric distances of similar to 4-30 km. A quiet time plasma density map was developed by considering dependences on cometary latitude, longitude, and cometocentric distance of Rosetta observations before and after each of the CIR intervals. The CIRs lead to plasma density enhancements of similar to 500-1000 per cent with respect to the quiet time reference level. Ionospheric modelling shows that increased ionization rate due to enhanced ionizing (>12-200 eV) electron impact is the prime cause of the large cometary plasma density enhancements during the CIRs. Plausible origin mechanisms of the cometary ionizing electron enhancements are discussed.
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| 5. |
- Myllys, L, et al.
(författare)
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High cyanobiont selectivity of epiphytic lichens in old growth boreal forest of Finland
- 2007
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Ingår i: New Phytologist. - : Wiley. - 1469-8137 .- 0028-646X. ; 173:3, s. 621-629
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Tidskriftsartikel (refereegranskat)abstract
- • Here, cyanobiont selectivity of epiphytic lichen species was examined in an old growth forest area in Finland. • Samples of the eight lichen species were collected from the same aspen (Populus tremula) and adjacent aspens in the same stand. The cyanobionts of these samples were compared with free and symbiotic Nostoc obtained from other habitats and geographic regions. • Our results, based on the phylogenetic analysis of a partial small subunit of the ribosomal DNA (16S rDNA) and the rbcLX gene complex did not show any correlation with the geographic origin of the samples at any spatial scale. Instead, there was a correlation between the cyanobionts and the alleged taxonomy of their mycobionts. • The results indicate that the lichen species examined are highly selective towards their cyanobiont partners. Only Lobaria pulmonaria proved to be more flexible, being able to associate with a wide range of Nostoc. A same Nostoc strain was found to form associations with taxonomically unrelated lichens indicating that the cyanobiont–mycobiont associations as a whole were not highly specific in the examined species.
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| 6. |
- Myllys, L, et al.
(författare)
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New genes for phylogenetic studies of lichenized fungi: glyceraldehyde-3-phosphate dehydrogenase and beta-tubulin genes
- 2002
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Ingår i: Lichenologist. - : Cambridge University Press (CUP). - 0024-2829. ; 34:3, s. 237-246
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Tidskriftsartikel (refereegranskat)abstract
- Primers for amplification and sequencing of partial glyceraldehyde-3-phosphate dehydrogenase (gpd) gene were designed for lichenized fungi. The 5' gpd primer is most probably fungal specific, since a BLAST search in GenBank found identical sequences only from ascomycetous taxa, whereas the 3' gpd primer was more universal. Utility of the gpd primers and previously designed beta-tubulin primers was tested in nine lichen taxa. Both the gpd and beta-tubulin primer pairs amplified in most of the taxa examined: the gpd primers generated a c. 1100 nucleotide fragment, whereas the PCR product obtained from the beta-tubulin primers was c. 900 nucleotides long. The gpd amplification products of Cladonia arbuscula and C. rangiferina were sequenced and both were found to contain three introns, the length of which varied between 49 to 83 nucleotides. To examine the applicability of gpd sequences in resolving relationships within Ascomycota, trees were calculated from 22 fungal gpd sequences obtained from GenBank together with the two Cladonia sequences using parsimony jackknifing. The gpd tree was compared with the SSU rDNA tree of the respective species (or genera). A similar analysis of the beta-tubulin gene was not performed, because only a few beta-tublin sequences from the same taxa were available in GenBank. The gpd tree was well resolved but in conflict with the SSU rDNA tree. In contrast to the SSU rDNA tree, the gpd tree did not support the monophyly of the Ascomycota. Analysis of the combined data set produced a tree very similar to that of the SSU rDNA data. However, the relationship of Lecanorales to the other orders remained unresolved. Even though gpd and beta-tubulin are highly conserved proteins, the third codon positions and introns are variable and both genes have the potential for inferring phylogenetic relationships at the lower taxonomic levels in the lichenized fungi. The two genes may be useful even below species level, depending on the species investigated.
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| 7. |
- Myllys, L, et al.
(författare)
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Phylogenetic relationships of Stereocaulaceae based on simultaneous analysis of beta-tubulin, GAPDH and SSU rDNA sequences
- 2005
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Ingår i: Taxon. - 0040-0262. ; 54:3, s. 605-618
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Tidskriftsartikel (refereegranskat)abstract
- The phylogenetic relationships of the lichenised ascomycete family Stereocaulaceae were investigated with partial beta-tubulin, partial glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and SSU rDNA sequence data. Due to the marked length variation in the SSU rDNA sequences, the analyses were performed with direct optimization. The combined analysis of the beta-tubulin, GAPDH and SSU rDNA sequences as well as the separate analyses of beta-tubulin and GAPDH data recognized the monophyletic group comprising Lepraria, Muhria and Stereocaulon. In the combined analysis Stereocaulon tornense appears as a basal taxon in the Stereocaulon clade, suggesting that the crustose growth form and the absence of cephalodia are primitive features within the genus. Muhria is nested in Stereocaulon and groups with the crustose S. cumulatum and S. leucophaeopsis. The genus Lepraria is monophyletic if Leproloma is included, but species that were represented by several specimens in our study, i.e., Lepraria jackii and Leproloma membranaceun, do not appear as monophyletic entities. The genus Pilophorus is included in Cladoniaceae. Combined analysis of the three data-sets clearly led to an increase in support values compared to the separate analyses, showing high support for the monophyly of families Cladoniaceae and Stereocaulaceae and for the sistergroup relation for the two families. The relationships between higher groupings did not reach high support values probably due to the incongruencies among the three datasets.
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| 8. |
- Myllys, L, et al.
(författare)
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Phylogeny of bipolar Cladonia arbuscula and Cladonia mitis (Lecanorales, Euascomycetes)
- 2003
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Ingår i: Molecular Phylogenetics and Evolution. - 1095-9513. ; 27:1, s. 58-69
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic relationships and levels of geographic differentiation of two closely related bipolar taxa, Cladonia arbuscula and Cladonia mitis, were cladistically examined with ITS regions, SSU rDNA introns, partial P-tubulin, and partial glyceraldehyde 3-phosphate dehydrogenase (GAPDH) genes. In the combined analysis of the four genes, C arbuscula was paraphyletic, while C mitis, nested within C arbuscula, formed a strongly supported monophyletic group. C arbuscula samples were divided into three separate clades: "arbuscula I," appearing as basal to the other ingroup taxa, "arbuscula II," and "arbuscula III" (the latter represented by only one specimen), which were not correlated with any morphological trait. Only C mitis specimens formed a morphologically and chemically distinct group. None of the main clades was correlated with geographic origin. The separate analyses were poorly resolved, and in most cases samples from "arbuscula I,'' ''arbuscula, II," and "arbuscula III" clades were intermixed. An incongruence test revealed conflict among the four gene regions in almost all cases. Only ITS regions and introns were not significantly incongruent, suggesting lack of recombination within the ribosomal DNA locus. Incomplete lineage sorting and recombination were considered to be the main reasons accounting for the incongruencies. The high proportion of shared polymorphisms between the "arbuscula F and "arbuscula II" clades, especially found from the beta-tubulin gene and from the ITS regions, and the lack of corroborating morphological characters both indicate a short history of reproductive isolation among the groups. The lack of genetic differentiation among the northern and southern samples within the main clades indicates a relatively recent gene flow, which may have resulted from migrations during the Pleistocene glaciations or from more recent long-distance dispersal. (C) 2002 Elsevier Science (USA). All rights reserved.
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| 9. |
- Myllys, M., et al.
(författare)
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Plasma properties of suprathermal electrons near comet 67P/Churyumov-Gerasimenko with Rosetta
- 2019
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Ingår i: Astronomy and Astrophysics. - : EDP SCIENCES S A. - 0004-6361 .- 1432-0746. ; 630
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Tidskriftsartikel (refereegranskat)abstract
- Context: The Rosetta spacecraft escorted comet 67P/Churyumov-Gerasimenko from 2014 to September 2016. The mission provided in situ observations of the cometary plasma during different phases of the cometary activity, which enabled us to better understand its evolution as a function of heliocentric distance.Aims: In this study, different electron populations, called warm and hot, observed by the Ion and Electron Sensor (IES) of the Rosetta Plasma Consortium (RPC) are investigated near the comet during the escorting phase of the Rosetta mission.Methods: The estimates for the suprathermal electron densities and temperatures were extracted using IES electron data by fitting a double-kappa function to the measured velocity distributions. The fitting results were validated using observations from other RPC instruments. We give upgraded estimates for the warm and hot population densities compared to values previously shown in literature.Results: The fitted density and temperature estimates for both electron populations seen by IES are expressed as a function of heliocentric distance to study their evolution with the cometary activity. In addition, we studied the dependence between the electron properties and cometocentric distance.Conclusions: We observed that when the neutral outgassing rate of the nucleus is high (i.e., near perihelion) the suprathermal electrons are well characterized by a double-kappa distribution. In addition, warm and hot populations show a significant dependence with the heliocentric distance. The populations become clearly denser near perihelion while their temperatures are observed to remain almost constant. Moreover, the warm electron population density is shown to be strongly dependent on the radial distance from the comet. Finally, based on our results we reject the hypothesis that hot electron population seen by IES consists of solely suprathermal (halo) solar wind electrons, while we suggest that the hot electron population mainly consists of solar wind thermal electrons that have undergone acceleration near the comet.
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| 10. |
- Stenroos, S, et al.
(författare)
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High selectivity in symbiotic associations of lichenized ascomycetes and cyanobacteria
- 2006
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Ingår i: Cladistics. - 1096-0031. ; 22:3, s. 230-238
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Tidskriftsartikel (refereegranskat)abstract
- The selectivity of mycobionts and cyanobionts in lichen symbioses were examined. We analyzed symbiotic cyanobionts, collected from different sample sites, and compared them to free-living cyanobacteria Nostoc. Cyanobionts were obtained from lichens assigned to the genera Pseudocyphellaria and Sticta, in particular. Multiple gene loci were screened and direct optimization was used in the phylogenetic analyses. We show that many lichen fungi are strongly selective towards their cyanobionts. Lichenized ascomycetes seem to be able to identify and choose a specific strain, species or a species group of Nostoc with which to associate. The present analyses also suggest that some of the Nostoc taxa may be specialized in symbiotic life with only lichenized ascomycetes. Despite the selectivity observed in fungi, there appears to be no coevolution between the partners. We have also discussed the problems of using the tRNA(Leu) intron as a marker in phylogenetic analyses.
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| 11. |
- Stenroos, S, et al.
(författare)
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Phylogeny of the genus Cladonia s.lat. (Cladoniaceae, Ascomycetes) inferred from molecular, morphological, and chemical data
- 2002
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Ingår i: Cladistics. - 1096-0031. ; 18:3, s. 237-278
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Forskningsöversikt (refereegranskat)abstract
- Phylogenetic relationships within the genus Cladonia, including Cladina (Cladoniaceae, Lecanoromycetes), were reconstructed based upon simultaneous analyses of DNA sequences and morphological and chemical data. We used sequences from the internal transcribed spacer 1 (ITS1), the 5.8 rDNA gene, and the internal transcribed spacer 2 (ITS2) of the nuclear rDNA gene cluster, and partial sequences from the protein-coding beta-tubulin gene. The analyses included 235 specimens of 168 taxa representing all currently recognized sections of Cladonia and Cladina and the outgroup genera Cladia, Pycnothelia, and Rainalea. Analyses were performed using optimization alignment with three different parameter values. The results of all analyses support the inclusion of Cladina in Cladonia. The current sectional division of Cladonia was not supported, and a new provisional classification for the genus is proposed.
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| 12. |
- Thell, Arne, et al.
(författare)
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Monophyletic groups within the Parmeliaceae identified by ITS rDNA, beta-tubulin and GAPDH sequences
- 2004
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Ingår i: Mycological Progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 3:4, s. 297-314
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic relationships within the Parmeliaceae are analysed cladistically on the basis of DNA characters from partial beta-tubulin, partial glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and ITS sequences. 100 taxa representing 73 of the 88 genera currently recognised are included in the analyses. Eight monophyletic groups including two or more genera were identified in the tree calculated from the combined data matrix. Three of the groups cover almost half of the species of the family. The largest and strongest supported group includes seven genera with their distribution centres in the Southern Hemisphere: Almbornia, Chondropsis, Karoowia, Namakwa, Neofuscelia, Xanthomaculina and Xanthoparmelia. The second group is a clade of four essentially tropical genera: Concamerella, Flavoparmelia, Parmotrema and Rimelia. The third large group with strong support is the core of cetrarioid lichens, distributed primarily in cold areas of the Northern Hemisphere. The genus Parmelia sensu Hale is not closely related with most of its segregates. One new combination, Cetrariella commixta, is proposed. Coelopogon abraxas is reported from South America for the first time.
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| 13. |
- Thell, Arne, et al.
(författare)
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Phylogeny and ecology of Cetraria obtusata, Coelopogon epiphorellus, and related taxa (Parmeliaceae, lichenized ascomycetes).
- 2002
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Ingår i: Mitteilungen aus dem Institut fuer Allgemeine Botanik Hamburg. - 0344-5615. ; 30-32, s. 283-296
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The phylogeny of two lichens, Cetraria obtusata from the Alps and Coelopogon epiphorellus occurring in the southern hemisphere is studied. A DNA-matrix based on ITS 1 and ITS 2 sequences of the rDNA is compared with a data set composed of morphology and secondary chemistry characters in phylogeny analyses using PAUP 4.0. The two data sets were entirely congruent. Neither Cetraria obtusata nor Coelopogon epiphorellus, both earlier segregated from the Cetraria aculeata group (Coelocaulon), are closely related with Cetraria s. str. Ecology notes of the two species are added and their phylogenetic affinities are discussed.
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| 14. |
- Thell, Arne, et al.
(författare)
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Phylogeny of cetrarioid lichens (Parmeliaceae) inferred from ITS and beta-tubulin sequences, morphology, anatomy and secondary chemistry.
- 2002
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Ingår i: Mycological Progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 1:4, s. 335-354
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic relationships within the family Parmeliaceae (lichenized ascomycetes) with emphasis on the heterogeneous group of cetrarioid lichens are reconstructed. The results are based on cladistic analyses of DNA-sequences, morphological and chemical data. Almost all currently recognized cetrarioid genera were included in the analyses together with parmelioid and alectorioid members of the presumably monophyletic family Parmeliaceae. We tried to sample taxonomic diversity of the family as widely as possible. The ITS1-5.8S-ITS2 region of the rDNA and a partial beta-tubulin gene from 126 samples representing 82 species were analysed. Cetrarioid lichens were identified as a monophyletic group, supported by both ITS and beta-tubulin characters. This group was reanalysed using 47 morphological, anatomical and secondary chemistry characters combined with the DNA data matrix. ITS and beta-tubulin sequences provide congruent information, and a clear correlation between DNA-data and conidial shape is observed. The current taxonomy of the cetrarioid lichens is discussed and compared with the phylogenetic trees obtained here. A comprehensive study of the phylogeography of some bipolar or subcosmopolitic species with representatives from both hemispheres was performed. Cetraria aculeata is the only taxon where correlation between DNA-data and geographic origin is observed.
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| 15. |
- Wellbrock, A., et al.
(författare)
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Observations of a Solar Energetic Particle Event from Inside and Outside the Coma of Comet 67P
- 2022
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Ingår i: Journal of Geophysical Research - Space Physics. - : John Wiley & Sons. - 2169-9380 .- 2169-9402. ; 127:12
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Tidskriftsartikel (refereegranskat)abstract
- We analyze observations of an SEP event at Rosetta’s target comet 67P/Churyumov-Gerasimenko during March 6th-10th 2015. The comet was 2.15AU from the Sun, with the Rosetta spacecraft approximately 70km from the nucleus placing it deep inside the comet’s coma and allowing us to study its response. The Eastern flank of an ICME also encountered Rosetta on March 6th and 7th. Rosetta’s RPC data indicate increases in ionization rates, and cometary water group pickup ions exceeding 1keV. Increased charge exchange reactions between solar wind ions and cometary neutrals also indicate increased upstream neutral populations consistent with enhanced SEP induced surface activity. In addition, the most intense parts of the event coincide with observations interpreted as an infant cometary bow shock, indicating that the SEPs may have enhanced the formation and/or intensified the observations. These solar transient events may also have pushed the cometopause closer to the nucleus.We track and discuss characteristics of the SEP event using remote observations by SOHO, WIND and GOES at the Sun, in-situ measurements at STEREO A, Mars and Rosetta, and ENLIL modeling. Based on its relatively prolonged duration, gradual and anisotropic nature and broad angular spread in the heliosphere, we determine the main particle acceleration source to be a distant ICME which emerged from the Sun on March 6th 2015 and was detected locally in the Martian ionosphere but was never encountered by 67P directly. The ICME’s shock produced SEPs for several days which traveled to the in-situ observation sites via magnetic field line connections.
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