10.5061/DRYAD.6M20J
Pease, James B.
Wake Forest University
Brown, Joseph W.
University of Michigan-Ann Arbor
Walker, Joseph F.
University of Michigan-Ann Arbor
Hinchliff, Cody E.
University of Idaho
Smith, Stephen A.
University of Michigan-Ann Arbor
Data from: Quartet Sampling distinguishes lack of support from conflicting
support in the green plant tree of life
Dryad
dataset
2018
branch support
quartet sampling
lineage sorting
discordance
Phylogenetic methods
bootstrap
plant tree of life
Viridiplantae
National Science Foundation
https://ror.org/021nxhr62
1208809
2018-09-07T00:00:00Z
2018-09-07T00:00:00Z
en
https://doi.org/10.1002/ajb2.1016
379368248 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Premise of the Study—Phylogenetic support has been difficult to evaluate
within the green plant tree of life partly due to a lack of specificity
between conflicted versus poorly informed branches. As datasets continue
to expand in both breadth and depth, new support measures are needed that
are more efficient and informative. Methods— We describe the Quartet
Sampling (QS) method, a quartet-based evaluation system that synthesizes
several phylogenetic and genomic analytical approaches. QS characterizes
discordance in large-sparse and genome-wide datasets, overcoming issues of
alignment sparsity and distinguishing strong conflict from weak support.
We test QS with simulations and recent plant phylogenies inferred from
variously sized datasets. Key Results— QS scores demonstrate convergence
with increasing replicates and are not strongly affected by branch depth.
Patterns of QS support from different phylogenies lead to a coherent
understanding of ancestral branches defining key disagreements, including
the relationships of Ginkgo to cycads, magnoliids to monocots and
eudicots, and mosses to liverworts. The relationships of ANA grade
angiosperms, major monocot groups, bryophytes, and fern families are
likely highly discordant in their evolutionary histories, rather than
poorly informed. QS can also detect discordance due to introgression in
phylogenomic data. Conclusions— Quartet Sampling is an efficient synthesis
of phylogenetic tests that offers more comprehensive and specific
information on branch support than conventional measures. The QS method
corroborates growing evidence that phylogenomic investigations that
incorporate discordance testing are warranted when reconstructing complex
evolutionary histories, in particular those surrounding ANA grade
angiosperms, monocots, and non-vascular plants.
Quartet Sampling Results/Data: Cannon, et al. 2015A gzipped tar archive
containing the input alignment and tree, and results of various Quartet
Sampling analyses for the Cannon et al 2015
study.Pease_etal_2017_QuartetSampling_Empirical_Cannon2015.tar.gzQuartet
Sampling Results/Data: Hinchliff and Smith 2014A gzipped tar archive
containing the input alignment and tree, and results the concatenated
200-replicate Quartet Sampling analyses for the Hinchliff and Smith 2014
study.Pease_etal_2017_QuartetSampling_Empirical_Hinchliff2014.tar.gzQuartet Sampling Results/Data: Pryer, et al. 2016A gzipped tar archive containing the input alignment and tree, and results of various Quartet Sampling analyses for the Pryer, et al. 2016Pease_etal_2017_QuartetSampling_Empirical_Pryer2016.tar.gzQuartet Sampling Results/Data: Walker, et al. 2017A gzipped tar archive containing the input alignment and tree, and results of various Quartet Sampling analyses for the Walker, et al. 2017 study.Pease_etal_2017_QuartetSampling_Empirical_Walker2017.tar.gzQuartet Sampling Results/Data: Xi, et al. 2014A gzipped tar archive containing the input alignment and tree, and results of various Quartet Sampling analyses for the Xi, et al. 2014 study.Pease_etal_2017_QuartetSampling_Empirical_Xi2014.tar.gzQuartet Sampling Branch Replicate SimulationsA gzipped tar archive containing the results of the effect of number of replicates on QC values.Pease_etal_2017_QuartetSampling_Simulation_BranchRep.tar.gzQuartet Sampling ILS/Introgression SimulationsA gzipped tar archive containing the results of the effect of ILS and introgression on QC/QC values.Pease_etal_2017_QuartetSampling_Simulation_ILSIntrog.tar.gzQuartet Sampling Results/Data: Zanne, et al. 2014A gzipped tar archive containing the input alignment and tree, and results of various Quartet Sampling analyses for the Zanne, et al. 2014 study.Pease_etal_2017_QuartetSampling_Empirical_Zanne2014.tar.gzQuartet Sampling Results/Data: Pease, et al. 2016A gzipped tar archive containing the input alignment and tree, and results of various Quartet Sampling analyses for the Pease, et al. 2016 study.Pease_etal_2017_QuartetSampling_Empirical_Pease2016.tar.gz