Data from: Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

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.