10.5061/DRYAD.GN4P4
Looney, Brian P.
University of Tennessee at Knoxville
Ryberg, Martin
Uppsala University
Hampe, Felix
Ghent University
Sánchez-García, Marisol
University of Tennessee at Knoxville
Matheny, P. Brandon
University of Tennessee at Knoxville
Data from: Into and out of the tropics: global diversification patterns in
a hyper-diverse clade of ectomycorrhizal fungi
Dryad
dataset
2015
latitudinal diversity gradient
Russulaceae
Phyloinfomatics
2015-12-02T18:17:44Z
2015-12-02T18:17:44Z
en
https://doi.org/10.1111/mec.13506
8511072 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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 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