DOI: 10.5061/dryad.6m20j
title: Data from: Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

description: 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.
description: 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