DOI: 10.5061/dryad.gn4p4
title: Data from: Into and out of the tropics: global diversification patterns in a hyper-diverse clade of ectomycorrhizal fungi

description: Ectomycorrhizal (ECM) fungi, symbiotic mutualists of many dominant tree
 and shrub species, exhibit a biogeographic pattern counter to the
 established latitudinal diversity gradient of most macroflora and fauna.
 However, an evolutionary basis for this pattern has not been explicitly
 tested in a diverse lineage. In this study, we reconstructed a
 mega-phylogeny of a cosmopolitan and hyper-diverse genus of ECM fungi,
 Russula, sampling from annotated collections and utilizing publically
 available sequences deposited in GenBank. Metadata from molecular
 operational taxonomic unit cluster sets were examined to infer the
 distribution and plant association of the genus. This allowed us to test
 for differences in patterns of diversification between tropical and
 extratropical taxa, as well as how their associations with different plant
 lineages may be a driver of diversification. Results show that Russula is
 most species-rich at temperate latitudes and ancestral state
 reconstruction shows that the genus initially diversified in temperate
 areas. Migration into and out of the tropics characterizes the early
 evolution of the genus, and these transitions have been frequent since
 this time. We propose the ‘generalized diversification rate’ hypothesis to
 explain the reversed latitudinal diversity gradient pattern in Russula as
 we detect a higher net diversification rate in extratropical lineages.
 Patterns of diversification with plant associates support host switching
 and host expansion as driving diversification, with a higher
 diversification rate in lineages associated with Pinaceae and frequent
 transitions to association with angiosperms.
description: Russula mega-phylogeny
 alignmentNexus 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.Russula mega-phylogeny
 ML constrained treeMaximum likelihood
 phylogenetic reconstruction of clustered global GenBank sequences using a
 constraint tree implemented in RaXML.Russula mega-phylogeny
 ultrametric treeMegaphylogeny
 ultrametricized using a nonparametric rate smoothing method implemented in
 r8s.Russula multigene
 alignmentMultigene 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).Russula multigene
 Bayesian treeBayesian multigene
 phylogeny inferred in MrBayes version 3.2.2. for 1,000,000 generations
 with default priors.Russula multigene ML
 treeMaximum likelihood
 reconstruction of mutigene alignment inferred in raxmlGUI 1.2 executing
 1000 rapid ML bootstrapped replicates.Russulaceae BEAST
 alignmentMultigene 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.Russulaceae BEAST
 treeChronogram 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.Russulaceae BEAUTi
 fileBEAUTi file used for
 BEAST runs to infer the chronogram of Russulales. Partitions and models
 were inferred using PartitionFinder 1.1.1.Clustertree
 1.0File 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.Accession numbers and
 metadata of GenBank RussulaA 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.GenBank_metadata.txt