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

• Published in: American journal of botany Vol. 105; no. 3; pp. 385 - 403
• Main Authors: Pease, James B., Brown, Joseph W., Walker, Joseph F., Hinchliff, Cody E., Smith, Stephen A.
• Format: Journal Article
• Language: English
• Published: United States John Wiley and Sons, Inc 01-03-2018; Botanical Society of America, Inc
• Subjects: Angiosperms; Biological Evolution; bootstrap; branch support; Branches; Bryophyta - genetics; Bryophytes; Computer Simulation; Cycadopsida - genetics; Datasets; Discordance; DNA, Plant - analysis; Ferns; Ferns - genetics; Genome, Plant; Genomes; Genomics; Genomics - methods; Ginkgo biloba - genetics; Hepatophyta - genetics; introgression; INVITED SPECIAL ARTICLE: For the Special Issue: Using and Navigating the Plant Tree of Life; likelihood; lineage sorting; Magnoliopsida - genetics; Phylogenetics; phylogenomics; Phylogeny; Reproducibility of Results; Sampling; Trees; Viridiplantae; Viridiplantae - genetics; branch support; likelihood; lineage sorting; discordance; phylogenetics; bootstrap; introgression; Viridiplantae; phylogenomics
• ISSN: 0002-9122; 1537-2197
• DOI: 10.1002/ajb2.1016

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 data sets 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 data sets, overcoming issues of alignment sparsity and distinguishing strong conflict from weak support. We tested QS with simulations and recent plant phylogenies inferred from variously sized data sets.
Key Results
QS scores demonstrated convergence with increasing replicates and were not strongly affected by branch depth. Patterns of QS support from different phylogenies led 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 (Amborella, Nymphaeales, Austrobaileyales), 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, monocots, and nonvascular plants.