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8 results for “Bacidia”
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: The faces of Bacidia schweinitzii: molecular and morphological data reveal three new species including a widespread sorediate morph
Bacidia schweinitzii is a common crustose lichen that is widespread in eastern North America. It is comprised of three distinct morphotypes differing in apothecial pigmentation. Here we show that molecular data from the mtSSU region affirms the distinctiveness of these morphotypes, prompting the recognition of three species: B. schweinitzii s.str., B. ekmaniana sp. nov. and B. purpurans sp. nov. We also show that a common sorediate crustose lichen, sympatric with B. schweinitzii, represents a monophyletic lineage whose relationship with B. schweinitzii s.str. could not be resolved with certainty using analyses of ITS and mtSSU sequence data. We recognize this sorediate lineage as a distinct species, B. sorediata sp. nov. All four taxa are described, illustrated and mapped.
FIGURE 1 in Taxonomy and nomenclature of seven names in Bacidia (Ramalinaceae, Lecanorales) described from Russia
FIGURE 1. Lecania graminum and Bacidia subabbrevians, thalli with apothecia. A. L. graminum (TUR-V 20778, isolectotype). B. B. subabbrevians (H-NYL 17446, isolectotype).—Scales = 1.0 mm.
Data from: The faces of Bacidia schweinitzii: molecular and morphological data reveal three new species including a widespread sorediate morph
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Phylogenetic data for the lichen genus Bacidia originally used to describe a new species, Bacidia gigantensis
<p><i>Bacidia gigantensis</i>, a green to greenish-brown, sorediate, crustose to microsquamulose lichen is described a new to science. It is corticolous on mature <i>Thuja occidentalis</i> trees throughout Sleeping Giant Provincial Park on the Sibley Peninsula along the north shore of Lake Superior, Ontario. The species is unusual within <i>Bacidia</i> due to the production of asexual propagules and homosekikaic acid. Placement in <i>Bacidia</i> is based on the characters of the sexual reproductive structures (biatorine apothecia with a true exciple, <i>Bacidia</i>-type asci, sigmoid, acicular, ascospores), ITS sequence data and molecular phylogenetic analyses of mtSSU sequence data. The latter also inferred a relationship to <i>Bacidiopsora</i>, a tropical genus that has been proposed for synonymy with <i>Bacidia</i> and includes other species with similar chemistries.</p>
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).
Phylogenetic data for the lichen genus Bacidia originally used to describe a new species, Bacidia gigantensis
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