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Supplementary material 7 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure S2e
Supplementary material 8 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure S2f
Supplementary material 4 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure S2b
Supplementary material 6 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure S2d
Supplementary material 1 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Tables S1–S6
Figure 9 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 9 Box plots of a length (bases) and b GC (%) content of ITS1 and ITS2 sequences for each one of the main lineages (Clades/Clusters) of the genus Ganoderma. The size of each box represents 50% of the values, the black horizontal line within each box indicates the median, the 'x' represents the average value, the error bars represent interquartile ranges and circles indicate outliers.
Supplementary material 5 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure S2c
Figure 8 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 8 Box plots of aITS sequence similarity (%) and b genetic distances (p-values) within (intra) and between (inter) Ganoderma species for each one of the main lineages (Clades/Clusters) of the genus, as well as pairwise comparisons between selected species. The size of each box represents 50% of the values, the black horizontal line within each box indicates the median, the 'x' represents the average value, the error bars represent interquartile ranges and circles indicate outliers. The red-dotted horizontal line, transversing the plots, represents the value levels accepted in this study for proposing new phylogenetic species.
Figure 6 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 6 Detail from Fig. 3. Phylogenetic reconstruction of the genus Ganoderma inferred from ML analysis, based on ITS sequence data (main dataset, DS; Table 2) for Clades B, C and D. ML bootstrap values (BS) ≥ 65% and Bayesian Posterior Probabilities (BPP) ≥ 0.95 are shown. Sequences names on the left appear as initially labelled and are followed by the respective GenBank/ENA/DDBJ or UNITE accession number, while the total number of identical entries corresponding to a particular sequence is placed in parentheses, followed by the type of host plant (legend for the coloured shapes is found at the lower left side of the tree) and geographic origin of the respective material (the latter appears in different fonts colour depending on the continent of provenance; see also Table 1 and Suppl. material 1: Table S2). Species names on the right correspond to those inferred in this study evaluated in conjunction with literature data. Sequences generated in the present work appear in bold typeface, while underlined sequences are those originating from type material. Scale bar: 0.01 nucleotide substitutions per site.
Figure 5 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 5 Detail from Fig. 3. Phylogenetic reconstruction of the genus Ganoderma inferred from ML analysis, based on ITS sequence data (main dataset, DS; Table 2) for Clade A, Cluster A.3. ML bootstrap values (BS) ≥ 65% and Bayesian Posterior Probabilities (BPP) ≥ 0.95 are shown. Sequences names on the left appear as initially labelled and are followed by the respective GenBank/ENA/DDBJ or UNITE accession number, while the total number of identical entries corresponding to a particular sequence is placed in parentheses, followed by the type of host plant (legend for the coloured shapes is found at the lower left side of the tree) and geographic origin of the respective material (the latter appears in different fonts colour depending on the continent of provenance; see also Table 1 and Suppl. material 1: Table S2). Species names on the right correspond to those inferred in this study evaluated in conjunction with literature data. Sequences generated in the present work appear in bold typeface, while underlined sequences are those originating from type material. Scale bar: 0.01 nucleotide substitutions per site.
Figure 7 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 7 Detail from Fig. 3. Phylogenetic reconstruction of the genus Ganoderma inferred from ML analysis, based on ITS sequence data (main dataset, DS; Table 2) for Clade E. ML bootstrap values (BS) ≥ 65% and Bayesian Posterior Probabilities (BPP) ≥ 0.95 are shown. Sequences names on the left appear as initially labelled and are followed by the respective GenBank/ENA/DDBJ or UNITE accession number, while the total number of identical entries corresponding to a particular sequence is placed in parentheses, followed by the type of host plant (legend for the coloured shapes is found at the lower left side of tree) and geographic origin of the respective material (the latter appears in different fonts colour depending on the continent of provenance; see also Table 1 and Suppl. material 1: Table S2). Species names on the right correspond to those inferred in this study evaluated in conjunction with literature data. Sequences generated in the present work appear in bold typeface, while underlined sequences are those originating from type material. Scale bar: 0.01 nucleotide substitutions per site.
Figure 4 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 4 Detail from Fig. 3. Phylogenetic reconstruction of the genus Ganoderma inferred from ML analysis, based on ITS sequence data (main dataset, DS; Table 2) for Clade A, Clusters A.1 and A.2. ML bootstrap values (BS) ≥ 65% and Bayesian Posterior Probabilities (BPP) ≥ 0.95 are shown. Sequences names on the left appear as initially labelled and are followed by the respective GenBank/ENA/DDBJ or UNITE accession number, while the total number of identical entries corresponding to a particular sequence is placed in parentheses, followed by the type of host plant (legend for the coloured shapes is found at the lower left side of tree) and geographic origin of the respective material (the latter appears in different font colour depending on the continent of provenance; see also Table 1 and Suppl. material 1: Table S2). Species names on the right correspond to those inferred in this study evaluated in conjunction with literature data. Sequences generated in the present work appear in bold typeface, while underlined sequences are those originating from type material. Scale bar: 0.01 nucleotide substitutions per site.
Figure 3 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 3 Summary tree of the genus Ganoderma inferred from ML analysis, based on ITS sequence data (main dataset, DS; Table 2). Thick lines represent ML bootstrap values (BS) ≥ 65% and Bayesian Posterior Probabilities (BPP) ≥ 0.95. Clades and Clusters within the tree appear as presented in Table 1 and Suppl. material 1: Table S2. Species names correspond to those inferred in this study. Scale bar: 0.01 nucleotide substitutions per site.
Figure 2 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 2 Basidiomes of Ganoderma spp. amongst those collected and analysed in this study (specimens codes appear in parantheses; Suppl. material 1: Table S1) aG. lucidum (A1180) bG. carnosum (DD1243) cG. resinaceum (2012-0077) dG. adspersum (2010-0015) eG. applanatum (DD2119) fG. pfeifferi (DD2118).
Figure 1 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure 1 a Initial labelling of 3908 Ganoderma sequences analysed in the present study: numbers in parentheses correspond to sequences deposited under the particular name in GenBank/ENA/DDBJ and UNITE, while species names appear underlined when ITS sequences derive from type material b final assigment of 3908 Ganoderma sequences to 80 species and six distinct groups as a result of the phylogenetic analyses performed in this study: numbers in parentheses correspond to the number of sequences grouped within each taxon (data deriving from Table 1 and Suppl. material 1: Tables S2, S4).
Supplementary material 2 from: Fryssouli V, Zervakis GI, Polemis E, Typas MA (2020) A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 75: 71-143. https://doi.org/10.3897/mycokeys.75.59872
Figure S1
Data from: Contrasting responses of nitrogen: phosphorus stoichiometry in plants and soils under grazing: a global meta-analysis
<p>1. Grazing by ungulate herbivores can greatly alter nitrogen ([N]) and phosphorus ([P]) concentrations in plants and soils. It is not clear, however, how grazing might affect N:P co-limitation in grasslands depending on soil N and P availability.</p> <p>2. Here we selected 173 peer-reviewed studies, which measured 12 key variables associated with changes in [N], [P] and N:P ratios (i.e. N:P stoichiometry) in soils and plants in the presence or absence of herbivore grazing. Subsequently, we addressed the magnitude and direction of grazing effects on these variables using a meta-analysis approach.</p> <p>3. Grazing increased leaf [N] and [P] but decreased total and available soil [N] and [P]. Grazing also increased leaf N:P ratios while decreasing root and total soil N:P ratios.</p> <p>4. The response ratio (RR) of leaf N:P was negatively correlated with RR of plant-available soil [P] and positively correlated with RR of available soil N:P ratio (rather than with RR of total soil N:P).</p> <p>5. Intensive grazing (e.g., heavy grazing or long-term grazing) had in general more positive effects on plant N:P stoichiometry and negative effects on soil N:P stoichiometry than light grazing. Responses of plant-soil N:P stoichiometry to grazing greatly varied depending on plant functional group identity, plant organizational level (i.e. species and community) and grassland type.</p> <p>6. Synthesis and applications. Our study suggests that understanding changes in available soil N:P stoichiometry (rather than total soil N:P) in response to grazing is crucial to predict nutrient co-limitation in grassland biomes. Our findings show that P is more important for plant growth than generally thought due to greater reduction of plant-available soil [P] under grazing. A better mechanistic understanding of the relationships between plant and available soil N:P stoichiometry under grazing will greatly help improve the sustainability of natural and semi-natural grassland ecosystems.</p>
Data from: Prevalence of sleep-disordered breathing after stroke and TIA: a meta-analysis
Objective: To perform a systematic review and meta-analysis on the prevalence of sleep-disordered breathing (SDB) after stroke. Methods: We searched PubMed, Embase (Ovid), the Cochrane Library, and CINAHL (from their commencements to 7th of April 2017) for clinical studies reporting prevalence and/or severity of SDB after stroke or transitory ischemic attack (TIA). Only sleep apnea tests performed with full polysomnography and diagnostic devices of the AASM categories I-IV were included. We conducted random-effects meta-analysis. PROSPERO registration number: CRD42017072339. Results: The initial search identified 5211 publications. 89 studies (including 7096 patients) met inclusion criteria. 54 studies were performed in the acute phase after stroke (after less than 1 month), 23 studies in the subacute phase (after 1-3 months) and 12 studies in the chronic phase (after more than 3 months). Mean apnea-hypopnea index (AHI) was 26.0/h (SD 21.7-31.2). Prevalence of SDB with AHI greater than 5/h and greater than 30/h was found in 71% (95% CI 66.6-74.8) and 30% (95% CI 24.4-35.5) of patients, respectively. Severity and prevalence of SDB were similar in all examined phases after stroke, irrespective of the type of sleep apnea test performed. Heterogeneity between studies (I2) was mostly high. Conclusion: The high prevalence of SDB after stroke and TIA, which persists over time, is important in light of recent studies reporting the a) feasibility and b) efficacy of SDB treatment in this clinical setting.
Data from: Use of isotretinoin and risk of depression in patients with acne: a systematic review and meta-analysis
Objective: This study aimed to investigate the association between the use of isotretinoin and the risk of depression in patients with acne. Design: This was a meta-analysis in which the standardized mean difference (SMD) and the relative risk (RR) were used for data synthesis employed the random-effects model. Setting: Studies were identified via electronic searches of PubMed, Embase, and the Cochrane Library up to December 28, 2017. Participants: Patients with acne. Interventions: Studies comparing isotretinoin with other interventions in patients with acne were included. Results: Twenty studies were selected. The analysis of 17 studies showed a significant association of the use of isotretinoin with improved symptoms compared with the baseline before treatment [SMD = −0.33, 95% confidence interval (CI) −0.51 to −0.15, P < 0.05; I2 = 76.6%, P < 0.05)]. Four studies were related to the analysis of the risk of depression. The pooled data indicated no association of the use of isotretinoin with the risk of depressive disorders (RR = 1.15, 95% CI 0.60–2.21, P = 0.14). The association of the use of isotretinoin with the risk of depressive disorders was statistically significant on pooling retrospective studies (RR = 1.39, 95% CI 1.05–1.84, P = 0.02), but this association was not evident on pooling prospective studies (RR = 0.85, 95% CI 0.60–2.21, P = 0.86). Conclusions: This study suggested an association of the use of isotretinoin in patients with acne with significantly improved depression symptoms. Future randomized controlled trials are needed to verify the present findings.
Data from: High-dose methylprednisolone for acute traumatic spinal cord injury: A meta-analysis
Objective Due to the continuing debates on the utility of high-dose methylprednisolone (MP) early after acute spinal cord injury (ASCI), we aim to evaluate the therapeutic and adverse effects of high-dose MP according to NASCIS-2 dosing protocol in comparison to no steroids on patients with ASCI, by performing a meta-analysis on the basis of the current available clinical trials. Methods We searched PubMed and Cochrane Library (to May 22 2018) for studies comparing neurological recoveries, adverse events and in-hospital costs between ASCI patients who underwent high-dose MP treatment or not. Data were synthesized with corresponding statistical models according to the degree of heterogeneity. Results We enrolled 16 studies (1863 participants) including 3 RCTs and 13 observational studies. Pooled results indicated that MP was not associated with an increase in motor score improvement (RCTs: p = 0.84; Observational studies: p = 0.44) and incidence of recovery by at least one grade on the ASIA Impairment Scale (AIS) or Frankel (p=0.53). Meanwhile, MP did not lead to better sensory recovery (p=0.07). However, MP was associated with a significant higher incidence of gastrointestinal hemorrhage (p=0.04) and respiratory tract infection (p=0.01). The difference in the overall in-hospital costs between MP and control groups was not statistically significant (p=0.78). Conclusions Based on the current evidence, high-dose MP treatment, in comparison to controls, does not contribute to better neurological recoveries but may increase the risk of adverse events in patients with ASCI. Therefore, we recommend against routine use of high-dose MP early after ASCI.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.