Data from: Into and out of the tropics: global diversification patterns in a hyper-diverse clade of ectomycorrhizal fungi

Looney BP, Ryberg M, Hampe F, Sánchez-García M, Matheny PB

Date Published: December 2, 2015

DOI: http://dx.doi.org/10.5061/dryad.gn4p4

 

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Title Russula mega-phylogeny alignment
Downloaded 31 times
Description Nexus file of global clustered MOTU's from GenBank and sequences generated for this study for 4 loci (ITS 1-845, LSU 846-1800, rpb1 1801-3114, and rpb2 3115-3927). Note: in a mega-phylogeny approach multigene loci are taken from clustered sets based on sequence similarity and are not necessarily sequences from identified voucher sequence.
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Title Russula mega-phylogeny ML constrained tree
Downloaded 20 times
Description Maximum likelihood phylogenetic reconstruction of clustered global GenBank sequences using a constraint tree implemented in RaXML.
Download Russula mega-phylogeny ML constrained tree.tre (93.60 Kb)
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Title Russula mega-phylogeny ultrametric tree
Downloaded 15 times
Description Megaphylogeny ultrametricized using a nonparametric rate smoothing method implemented in r8s.
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Title Russula multigene alignment
Downloaded 14 times
Description Multigene alignment of sequences from vouchered specimens identified by taxonomic experts for 4 loci (ITS 1-953, LSU 954-1902, rpb1 (intron 1903-2559, exon 2560-3267), and rpb2 3268-4049).
Download Russula multigene alignment.nexus (445.7 Kb)
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Title Russula multigene Bayesian tree
Downloaded 13 times
Description Bayesian multigene phylogeny inferred in MrBayes version 3.2.2. for 1,000,000 generations with default priors.
Download Russula multigene Bayesian tree.tre (57.51 Kb)
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Title Russula multigene ML tree
Downloaded 8 times
Description Maximum likelihood reconstruction of mutigene alignment inferred in raxmlGUI 1.2 executing 1000 rapid ML bootstrapped replicates.
Download Russula multigene ML tree.tre (7.885 Kb)
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Title Russulaceae BEAST alignment
Downloaded 31 times
Description Multigene alignment of GenBank sequences and sequences generated for this study for 4 loci (ITS 1-434, LSU 435-1271, rpb1 (intron 1272-2054, exon 2055-2762), rpb2 3458). Ambiguous site alignments in ITS were excluded using gblocks.
Download Russulaceae BEAST alignment.nex (728.3 Kb)
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Title Russulaceae BEAST tree
Downloaded 10 times
Description Chronogram of members of Agaricomycetidae and Russulales inferred from three independent runs in BEAST 2 with 50,000,000 generations and a 10% burn-in. Calibrations used mean age estimates of Russulales, Boletales, Agaricales, Agaricomycetidae, and the ancestral node of all three orders from Floudas et al. 2012.
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Title Russulaceae BEAUTi file
Downloaded 37 times
Description BEAUTi file used for BEAST runs to infer the chronogram of Russulales. Partitions and models were inferred using PartitionFinder 1.1.1.
Download Russulaceae BEAUTi file.xml (805.5 Kb)
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Title Clustertree 1.0
Downloaded 22 times
Description File package for a command line program for the unreleased phylommand software package. This algorithm clusters sequence sets based on branch length cutoffs from a phylogeny.
Download Clustertree 1.0.zip (35.88 Kb)
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Title Accession numbers and metadata of GenBank Russula
Downloaded 39 times
Description A list of sequences of putative Russula species extracted using the bioinformatics program emerencia (http://www.emerencia.org) in July of 2012. Associated metadata including identification, strain number, publication information, host, tissue type, and location is also provided.
Download GenBank_metadata.txt (1.346 Mb)
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When using this data, please cite the original publication:

Looney BP, Ryberg M, Hampe F, Sánchez-García M, Matheny PB (2016) Into and out of the tropics: global diversification patterns in a hyper-diverse clade of ectomycorrhizal fungi. Molecular Ecology 25(2): 630–647. http://dx.doi.org/10.1111/mec.13506

Additionally, please cite the Dryad data package:

Looney BP, Ryberg M, Hampe F, Sánchez-García M, Matheny PB (2015) Data from: Into and out of the tropics: global diversification patterns in a hyper-diverse clade of ectomycorrhizal fungi. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.gn4p4
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