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 disagreeme...