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.
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.
Russula mega-phylogeny ML constrained tree
Maximum likelihood phylogenetic reconstruction of clustered global GenBank sequences using a constraint tree implemented in RaXML.
Russula mega-phylogeny ultrametric tree
Megaphylogeny ultrametricized using a nonparametric rate smoothing method implemented in r8s.
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).
Russula multigene Bayesian tree
Bayesian multigene phylogeny inferred in MrBayes version 3.2.2. for 1,000,000 generations with default priors.
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.
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.
Russulaceae BEAUTi file
BEAUTi file used for BEAST runs to infer the chronogram of Russulales. Partitions and models were inferred using PartitionFinder 1.1.1.
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.
Accession numbers and metadata of GenBank Russula
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.
GenBank_metadata.txt