Dryad

In the folder “Dryad” you will find 4 subfolders: 1) “Alignment”, which includes the alignment used to reconstruct the molecular phylogeny, and the Partition Finder analyses; 2) “ASR”, which includes one hundred random trees obtained from the posterior distribution of the BEAST analyses, and the files used for the ancestral state reconstruction; 3) “BAMM v2.5”, which includes the raw results from the BAMM analysis and a subfolder "topological uncertainty BAMM v.2.5" which includes 100 random trees and their respective BAMM results; 4) “BiSSE”, which includes the tree, character state table and R script used to run the BiSSE analyses, and a subfolder “topological uncertainty BiSSE” with 100 random trees and their respective R scripts

Russula multigene ML tree

Maximum likelihood reconstruction of mutigene alignment inferred in raxmlGUI 1.2 executing 1000 rapid ML bootstrapped replicates

Russulaceae BEAST alignment

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

Russula mega-phylogeny ML constrained tree

Maximum likelihood phylogenetic reconstruction of clustered global GenBank sequences using a constraint tree implemented in RaXML

Russula multigene alignment

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)

Clustertree 1.0

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

Russula mega-phylogeny alignment

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

Russulaceae BEAST tree

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

Russula multigene Bayesian tree

Bayesian multigene phylogeny inferred in MrBayes version 3.2.2. for 1,000,000 generations with default priors

Russula mega-phylogeny ultrametric tree

Megaphylogeny ultrametricized using a nonparametric rate smoothing method implemented in r8s