TreeBASE Search-Analyses for study 25936

@ARTICLE{TreeBASE2Ref30581, author = {Gislaine C.S. Melanda and Thiago Accioly and Renato Juciano Ferreira and Ana C.M. Rodrigues and Tiara Sousa Cabral and Gilberto Coelho and Marcelo A Sulzbacher and Vagner G. Cortez and Tine Grebenc and Paulo Marinho and Maria P. Mart?n and Iuri E Baseia}, title = {Diversity trapped in cages: revision of Blumenavia M?ller (Clathraceae, Basidiomycota) reveals three hidden species}, year = {2020}, keywords = {Multigenic analyses; Clathraceae; Gasteroid fungi; Systematics; Taxonomy.}, doi = {}, url = {http://doi.org/10.1371/journal.pone.0232467}, pmid = {}, journal = {PLoS ONE }, volume = {15}, number = {5}, pages = {e0232467}, abstract = {Basidiomata of Phallales have a diversified morphology with adhesive gleba that exudes an odor, usually unpleasant that attracts mainly insects, which disperse the basidiospores. The genus Blumenavia belongs to the family Clathraceae and, based on morphological features, only two species are currently recognized: B. rhacodes and B. angolensis. However, the morphological characters adopted in species delimitations within this genus are inconsistent, and molecular data are scarce. The present study aimed to review and identify informative characters that contribute to the delimitation of Blumenavia species. Exsiccates from America and Africa were analyzed morphologically, and molecularly, using ITS, LSU, ATP6, RPB2 and TEF-1α markers for Maximum Parsimony, Bayesian and Maximum likelihood analyses, and also for coalescent based species delimitations (BP&P), as well as for bPTP, PhyloMap, Topo-phylogenetic and Geophylogenetic reconstructions. According to our studies, seven species can be considered in the genus: B. rhacodes and B. angolensis are maintained, B. usambarensis and B. toribiotalpaensis are reassessed, and three new species are proposed, B. baturitensis Melanda, M.P. Mart?n & Baseia, sp. nov., B. crucis-hellenicae G. Coelho, Sulzbacher, Grebenc & Cortez, sp. nov., and B. heroica Melanda, Baseia & M.P. Mart?n, sp. nov. Morphological characters considered informative to segregate and delimit the species through integrative taxonomy include color, width and presence of grooves on each arm, and glebifer position and shape. These must be clearly observed while the basidiomata are still fresh. Since most materials are usually analyzed after dehydration and deposit in collections, field techniques and protocols to describe fugacious characters from fresh specimen are demanded, as well as the use of molecular analysis, in order to better assess recognition and delimitation of species in Blumenavia.} }

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Analyses for Study 25936

Citation title: "Diversity trapped in cages: revision of Blumenavia M?ller (Clathraceae, Basidiomycota) reveals three hidden species".

Study name: "Diversity trapped in cages: revision of Blumenavia M?ller (Clathraceae, Basidiomycota) reveals three hidden species".

This study is part of submission 25936 (Status: Published).

Analyses

Analysis 1

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Bayesian analysis --

Step details

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Notes

Software used

Name
Version
URL
Algorithm
Commands
Ten million generations were used, and trees were sampled each 5,000 generations. Convergence and sampling were checked by Potential Scale Reduction Factor (PSRF) and Estimated Sample Size (ESS) as recommended by MrBayes developers. Convergence was also visualized in Tracer v.1.7.1 [34]. Stationarity of MCMC were assessed in Tracer v.1.7.1 software and also manually in MCMC output from MrBayes v.2.3.6 when Average Standard Deviation of Split Frequencies (AvgStdDev) dropped below 0.01. five partitions (ITS1-5.8S-ITS2/LSU/ATP6/RPB2/TEF-1a),

Output data

1 Output object(s)

Analysis 2

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Maximum parsimony --

Output data

1 Output object(s)

Analysis 3

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Bayesian analysis --

Step details

Name
Notes

Software used

Name
Version
Algorithm
Commands
Ten million generations were used, and trees were sampled each 5,000 generations. Convergence and sampling were checked by Potential Scale Reduction Factor (PSRF) and Estimated Sample Size (ESS) as recommended by MrBayes developers. Convergence was also visualized in Tracer v.1.7.1 [34]. Stationarity of MCMC were assessed in Tracer v.1.7.1 software and also manually in MCMC output from MrBayes v.2.3.6 when Average Standard Deviation of Split Frequencies (AvgStdDev) dropped below 0.01. Seven partitions (ITS1/5.8S/ITS2/LSU/ATP6/RPB2/TEF-1a).

Output data