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Figure 2 in Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life
No full textFigure 2. Summary of data quality. A, distribution of alignment lengths for 208 loci after GBlocks processing. B, correlation of assembly quality (N50) and percent alignment coverage.Published as part of Dentinger, BTM, Gaya, E, O'Brien, H, Suz, LM, Lachlan, R, Diaz-Valderrama, JR, Koch, RA & Aime, MC, 2016, Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life, pp. 11-32 in Biological Journal of the Linnean Society 117 on page 19, DOI: 10.1111/bij.12553, http://zenodo.org/record/784860
Figure 1 in Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life
No full textFigure 1. Bioinformatic pipeline used for the identification and phylogenetic analysis of 210 single copy genes from Illumina short-read sequence data. The box with the dashed line indicates a pre-processing step that was necessary prior to assembly when sequence quality was low.Published as part of Dentinger, BTM, Gaya, E, O'Brien, H, Suz, LM, Lachlan, R, Diaz-Valderrama, JR, Koch, RA & Aime, MC, 2016, Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life, pp. 11-32 in Biological Journal of the Linnean Society 117 on page 17, DOI: 10.1111/bij.12553, http://zenodo.org/record/784860
Figure 3 in Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life
No full textFigure 3. Phylogenetic analysis of the order Agaricales based on a 208 single copy loci combined dataset. Chronogram is based on a partitioned analysis using RAXML with branch lengths transformed to reflect time using correlated penalized likelihood. Numbers next to branches indicate percent support from 50 nonparametric bootstraps.Published as part of Dentinger, BTM, Gaya, E, O'Brien, H, Suz, LM, Lachlan, R, Diaz-Valderrama, JR, Koch, RA & Aime, MC, 2016, Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life, pp. 11-32 in Biological Journal of the Linnean Society 117 on page 20, DOI: 10.1111/bij.12553, http://zenodo.org/record/784860
Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life
No full textDentinger, BTM, Gaya, E, O'Brien, H, Suz, LM, Lachlan, R, Diaz-Valderrama, JR, Koch, RA, Aime, MC (2016): Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life. Biological Journal of the Linnean Society 117: 11-32, DOI: 10.1111/bij.1255
Figure 5. A, topological similarities between gene trees. A in Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life
No full textFigure 5. A, topological similarities between gene trees. A non-metric multidimensional ordination plot, based on the Robinson–Foulds (RF) distance between each pair of genes, is used to visualize the topological similarity among the 208 single gene trees. Pairs of gene trees with similar topologies are closer together in the two-dimensional space. Colours represent RF distances between individual gene trees and the extended majority-rule consensus (MRE) phylogeny. B, identifying optimal subsets of genes with the least topological incongruence. The graph shows the Tree Certainty (TC) values from Salichos & Rokas (2013). Information theory approach using the MRE phylogeny as a reference tree, where higher values represent greater congruency between the gene trees and the MRE tree. The x-axis represents the number of genes sampled, following an iterative procedure beginning with the first two genes in the respective ranking and progressively adding genes according to their order in the list. The five ranking criteria all outperformed random gene orders.Published as part of Dentinger, BTM, Gaya, E, O'Brien, H, Suz, LM, Lachlan, R, Diaz-Valderrama, JR, Koch, RA & Aime, MC, 2016, Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life, pp. 11-32 in Biological Journal of the Linnean Society 117 on page 22, DOI: 10.1111/bij.12553, http://zenodo.org/record/784860
Figure 4 in Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life
No full textFigure 4. Consensus trees of individual gene trees. Left: extended majority-rule consensus (MRE) tree based on bootstrap replicates of individual gene analyses for all genes with no missing taxa (N = 175). Numbers above branches are internode certainty (IC) and internode certainty all (ICA) values for all individual bootstrap trees compared to the MRE tree. Numbers in bold represent nodes that are not present in the ASTRAL tree (right). Right: coalescentbased consensus tree recovered by ASTRAL using 208 single gene maximum likelihood trees from RAXML analysis. Numbers in bold above branches are IC, ICA values for all individual bootstrap trees that are not present in the MRE tree (left). Numbers below branches are bootstrap supports based on single gene bootstrap analysis (100 replicates each).Published as part of Dentinger, BTM, Gaya, E, O'Brien, H, Suz, LM, Lachlan, R, Diaz-Valderrama, JR, Koch, RA & Aime, MC, 2016, Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life, pp. 11-32 in Biological Journal of the Linnean Society 117 on page 21, DOI: 10.1111/bij.12553, http://zenodo.org/record/784860
Pleurotineae Dentinger & Gaya & O'Brien & Suz & Lachlan & Diaz-Valderrama & Koch & Aime 2016, subord. nov.
No full textPleurotineae Aime, Dentinger & Gaya subord. nov. Name registration: IF551136 Type family: Pleurotaceae K uhner €, Bull. mens. Soc. linn. Lyon 49: 184 (1980). Basidiomata primarily clavarioid to pleurotoid, occasionally agaricoid, often tough textured. Hyphae often dimitic, hyaline, non-amyloid; clamp connections often present. Basidia clavate, 2–4 spored, and, in some species, interspersed with thick-walled encrusted cystidia; basidiospores hyaline. Representative families: Pleurotaceae, Pterulaceae Corner. Notes: Pleurotineae is equivalent to Pleurotaceae (ex-Pluteoid clade) + Pterulaceae (ex-Hygrophoroid clade) fide Matheny et al. (2006). We did not sample exemplars of Typhulaceae, Sarcomyxa or Xeromphalina, which were recovered with Pterulaceae by Matheny et al. (2006), although they might also belong here. This lineage can be characterized by the development of dimitic hyphae in many members and thick-walled encrusted hymenial cystidia. Although most members of this group are saprobic, a diverse range of symbiotic lifestyles is present, including nematophagy (Pleurotus), ant mutualisms (Pterula velohorta, P. nudihorta), and a plant pathogen (e.g. Pterulicium xylogenum).Published as part of Dentinger, BTM, Gaya, E, O'Brien, H, Suz, LM, Lachlan, R, Diaz-Valderrama, JR, Koch, RA & Aime, MC, 2016, Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life, pp. 11-32 in Biological Journal of the Linnean Society 117 on page 26, DOI: 10.1111/bij.12553, http://zenodo.org/record/784860
Schizophyllineae Dentinger, Gaya, O'Brien, Suz, Lachlan, Diaz-Valderrama, Koch & Aime, 2016, subord. nov.
No full textSchizophyllineae Aime, Dentinger & Gaya subord. nov. Name registration: IF551137 Type family: Schizophyllaceae Quel., Fl. mycol. France (Paris): 365 (1888). Basidiomata typically astipitate with a tubular or cupulate hymenophore. Hyphae are monomitic, usually presenting clamp connections, non-amyloid, and often gelatinous. Basidia four spored and basidiospores hyaline. Cystidia absent. Representative families: Fistulinaceae Lotsy, Schizophyllaceae. Notes: Schizophyllineae is equivalent to schizophylloid clade of Moncalvo et al. (2002). The Lachnellaceae, which was recovered as the sister group to Schizophyllaceae by Matheny et al. (2006) and Binder et al. (2010), might also belong here. Species are readily distinguished by the unusual tubular or cupulate hymenophore that predominates in members of this group. Ecologically, this group is characterized by saprotrophy, with both white- (Schizophyllum) and brown- (Fistulina) rot capacity.Published as part of Dentinger, BTM, Gaya, E, O'Brien, H, Suz, LM, Lachlan, R, Diaz-Valderrama, JR, Koch, RA & Aime, MC, 2016, Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life, pp. 11-32 in Biological Journal of the Linnean Society 117 on page 26, DOI: 10.1111/bij.12553, http://zenodo.org/record/784860
Agaricaceae Fr.
No full textAgaricineae Fr., emend. Aime, Dentinger & Gaya Fries, EM. 1825. Systema orbis vegetabilis, p. 65. Type family: Agaricaceae Chevall., Fl. gen. env. Paris (Paris): 121 (1826). Basidiomata predominantly agaricoid or gasteroid; agaricoid development various, including several hemiangiocarpic lineages, but not angiocarpic. Hyphae monomitic, clamp connections present or absent. Basidia 2–4 spored; basidiospores typically pigmented some shade of brown with exception of members formerly placed in Lepiotaceae. Representative families: Agaricaceae, Psathyrellaceae Vilgalys, Moncalvo & Redhead, Strophariaceae Singer & A.H. Sm., Crepidotaceae Singer, Hydnangiaceae G aum €. & C.W. Dodge, Hymenogastraceae Vittad., Inocybaceae J ulich €, Tubariaceae Vizzini. Notes: This corresponds to previously recognized ‘Agaricoid’ clade, which has been consistently recovered as monophyletic in recent studies (Matheny et al., 2006, 2015; Garnica et al., 2007; Binder et al., 2010; Kohler et al., 2015). Many species in this lineage have basidiospores with a thickened, darkly pigmented wall (Matheny et al., 2006; Garnica et al., 2007). Although species producing dark-pigmented basidiospores do occur in a few other lineages (e.g. Melanomphalia), the vast majority of these have diversified within Agaricineae. The present study does not include exemplars from Nidulariaceae Dumort, Cortinariaceae R. Heim ex Pouzar, Inocybaceae J ulich €, or Bolbitiaceae Singer but other studies support their placement here (Matheny et al., 2006, 2015; Binder et al., 2010).Published as part of Dentinger, BTM, Gaya, E, O'Brien, H, Suz, LM, Lachlan, R, Diaz-Valderrama, JR, Koch, RA & Aime, MC, 2016, Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life, pp. 11-32 in Biological Journal of the Linnean Society 117 on page 27, DOI: 10.1111/bij.12553, http://zenodo.org/record/784860
Pluteineae Dentinger & Gaya & O'Brien & Suz & Lachlan & Diaz-Valderrama & Koch & Aime 2016, subord. nov.
No full text<p> <b>Pluteineae</b> Aime, Dentinger & Gaya <i>subord. nov.</i></p> <p> <i>Name registration</i>: IF551140</p> <p> <i>Type family</i>: Pluteaceae Kotl. & Pouzar, Ceska Mykol. 26: 218 (1972).</p> <p>Basidiomata agaricoid, mostly fleshy, the majority with angiocarpic development and free lamellae. Hyphae monomitic; clamp connections present or absent; non-amyloid. Basidia 2–4 spored; basidiospores hyaline or with pink pigmentation, the vast majority smooth, some amyloid. Cystidia often present. Hymenophoral tramal regular, bilateral or inverse.</p> <p> <i>Representative families</i>: Amanitaceae R. Heim ex Pouzar, Pluteaceae.</p> <p> <i>Notes</i>: Pluteineae contains most angiocarpic species of Agaricales, although some species (primarily members of <i>Pluteus</i>) do not develop veils. Most Amanitaceae are ectomycorrhizal, except <i>Aspidella</i> spp., and most Pluteaceae are saprobes. This lineage was first recovered with bootstrap support in Moncalvo <i>et al.</i> (2002) but without a formal clade designation. Limnoperdonaceae may also belong here (Matheny <i>et al.</i>, 2006). This group was not supported in the ASTRAL tree (Fig. 4) and the tree based on ranked genes using RF distances (see Supporting information, Fig. S2C), and some previous studies have not recovered Pluteaceae with Amanitaceae (Bodensteiner <i>et al.</i>, 2004) or <i>Volvariella</i> within Pluteaceae (Justo <i>et al.</i>, 2011), and further investigation is warranted.</p>Published as part of <i>Dentinger, BTM, Gaya, E, O'Brien, H, Suz, LM, Lachlan, R, Diaz-Valderrama, JR, Koch, RA & Aime, MC, 2016, Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life, pp. 11-32 in Biological Journal of the Linnean Society 117</i> on page 27, DOI: 10.1111/bij.12553, <a href="http://zenodo.org/record/7848603">http://zenodo.org/record/7848603</a>
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