Sampling distinguishes lack of support from conflicting support in the plant tree of 1 life 1 2 3

14 Premise of the Study— Phylogenetic support has been difficult to evaluate within the plant 15 tree of life partly due to the difficulty of distinguishing conflicted versus poorly informed 16 branches. As datasets continue to expand in both breadth and depth, new support measures are 17 needed that are more efficient and informative. 18 Methods— We describe the Quartet Sampling (QS) method, a quartet-based evaluation 19 system that synthesizes several phylogenetic and genomic analytical approaches. QS 20 characterizes discordance in large-sparse and genome-wide datasets, overcoming issues of 21 alignment sparsity and distinguishing strong conflict from weak support. We test QS with 22 simulations and recent plant phylogenies inferred from variously sized datasets. 23 Key Results— QS scores demonstrate convergence with increasing replicates and are not 24 strongly affected by branch depth. Patterns of QS support from different phylogenies leads to a 25 coherent understanding of ancestral branches defining key disagreements, including the 26 relationships of Ginkgo to cycads, magnoliids to monocots and eudicots, and mosses to 27 liverworts. The relationships of ANA grade angiosperms, major monocot groups, bryophytes, and 28 fern families are likely highly discordant in their evolutionary histories, rather than poorly 29 informed. QS can also detect discordance due to introgression in phylogenomic data. 30 Conclusions— The QS method represents an efficient and effective synthesis of phylogenetic 31 tests that offer more comprehensive and specific information on branch support than conventional 32 measures. The QS method corroborates growing evidence that phylogenomic investigations that 33 2 . CC-BY-NC 4.0 International license not peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/148536 doi: bioRxiv preprint first posted online Jun. 10, 2017;