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7 results for “sorediate lichens”
Bacidia fuscoviridis, another overlooked sorediate crustose lichen widely distributed in temperate eastern North America
<p>To evaluate the generic relationships of <em>Bacidia fuscovirdis </em>within Ramalinaceae we carried out BLASTn searches of the existing reference sequences of <em>B. fuscoviridis</em> in NCBI which recovered representatives of <em>Biatora </em>Ach., <em>Lecania </em>A.Massal. and <em>Mycobilimbia</em> Rhem, as the closest hits for ITS and the lone sequence of rpb2. Based on these results we used the published phylogeny of Ramalinaceae from Kistenich et al. (2018) as a guide and constructed a multi-locus dataset that mirrored their sampling of the clade containing <em>Bilimbia</em>, <em>Lecania</em> and <em>Mycobilimbia</em> with <em>Biatora</em> as an outgroup. We downloaded the mtSSU, ITS, nucLSU and RPB2 sequences used by those authors (see Table 1) and manually aligned each dataset in Mesquite 3.31 (Maddison & Maddison 2017. We then added the available reference sequences of<em> B. fuscoviridis </em>(three ITS sequences, one rpb2 sequence) to the relevant alignment, manually adjusted them, and defined all ambiguously aligned regions and gap-rich terminal regions in an exclusion set. The excluded regions were then manually deleted, terminal gaps transformed to missing data, and uncertainties and polymorphisms transformed to missing data. The alignments were then concatenated in Mesquite and exported a single PHYLIP file. The concatenated alignment was partitioned and RAxML v8.2x (Stamatakis 2006) was used to infer a maximum likelihood (ML) topology and bootstrapping was performed with 500 pseudoreplicates and implementing the model GTRGAMMA across all partitions. The results were visualized in FigTree 1.4.3 (Rambaut 2016).</p> <p>This data deposit includes the underlying files for the phylogeny presented in the published study (Curtis et al., Journal of the Torrey Botanical Society). It includes a translation table for GenBank accessions and terminal names used in the dataset, individual alignments for ITS, mtSSU, nucLSU and rpb2 all in NEXUS format, concatenated alignment in NEXUS and PHYLIP format as well as partitions file for RAxML, and the final tree figure presented in the publication.</p>
Data from: Lecanora caperatica (Lecanoraceae, lichenized ascomycetes) a new sorediate species widespread in eastern North America
Lecanora caperatica is described based on collections from throughout temperate eastern North America. It is a crustose sorediate species in the L. subfusca group which has pulcaris-type apothecia, and produces atranorin and caperatic acid often with accessory roccellic/angardianic acid. The species is chemically similar to the European L. mugosphagneti which differs in ecology, thallus morphology and in having albella-type apothecia. The generic placement of L. caperatica, and its affinity to the L. subfusca group, are confirmed by molecular phylogenetic analysis.
Data from: Lecanora caperatica (Lecanoraceae, lichenized ascomycetes) a new sorediate species widespread in eastern North America
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Japewia aliphatica (Lecanoraceae, lichenized Ascomycota), a new acidophilous sorediate-blastidiate lichen from Europe
<p>final concatenated ITS and mtSSU alignment for Bayesian and ML analysis</p>
FIGURE 1A–D in Lecania sessilisoraliata, a new sorediate lichen species from limestone in Turkey
FIGURE 1A–D. Lecania sessilisoraliata (holotype): A, habitus. Scale =2mm, B. marginal zone of thallus. Scale= 2 mm, C. soralia. Scale= 1 mm, D. apothecium and soredia. Scale= 0.5 mm. E. Soredia. Scale= 50 μm. F. hymenium. Scale= 50 μm.
Figure 2 from: Malíček J, Palice Z, Vondrák J, Łubek A, Kukwa M (2018) Bacidia albogranulosa (Ramalinaceae, lichenized Ascomycota), a new sorediate lichen from European old-growth forests. MycoKeys 44: 51-62. https://doi.org/10.3897/mycokeys.44.30199
Figure 2 Phylogeny of selected members of Bacidia s.str. This is a Bayesian phylogenetic reconstruction based on nrITS and mtSSU sequences. The new species, Bacidiaalbogranulosa, is indicated in bold. Branches with > 0.95 Bayesian posterior probability values are indicated by thicker lines. Bayesian posterior probabilities (first value) and maximum likelihood bootstrap percentages (second value) are indicated.
Figure 1 from: Malíček J, Palice Z, Vondrák J, Łubek A, Kukwa M (2018) Bacidia albogranulosa (Ramalinaceae, lichenized Ascomycota), a new sorediate lichen from European old-growth forests. MycoKeys 44: 51-62. https://doi.org/10.3897/mycokeys.44.30199
Figure 1 Morphology of Bacidiaalbogranulosa. A Holotype (PRA/Vondrák 11888) B Common phenotype (Malíček 10802) C Typical growth form on old beech trees (Malíček 8166) D Phenotype with abundant soredia forming a seemingly leprose thallus (Malíček 8013) E Detail of soredia (Malíček 8166) F Soredia arising from granules (PRA/Vondrák 11888). Scale bars: 1 mm (A−C), 0.5 mm (D), 0.2 mm (E, F). Photos by J. Malíček (A, B) and J. Machač (C−F).
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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OpenNeuro
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