RT Journal Article
SR Electronic
T1 Quartet Sampling distinguishes lack of support from conflicting support in the plant tree of life
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 148536
DO 10.1101/148536
A1 James B. Pease
A1 Joseph W. Brown
A1 Joseph F. Walker
A1 Cody E. Hinchliff
A1 Stephen A. Smith
YR 2017
UL http://biorxiv.org/content/early/2017/06/10/148536.1.abstract
AB Premise of the Study Phylogenetic support has been difficult to evaluate within the plant tree of life partly due to the inability of standard methods to distinguish conflicted versus poorly informed branches. As phylogenomic and broad-scale datasets continue to grow, support measures are needed that are more efficient and informative.Methods We describe the Quartet Sampling (QS) method that synthesizes several phylogenetic and genomic analytical approaches into a quartet-based evaluation system. QS rapidly characterizes discordance in large-sparse and genome-wide datasets, overcoming issues of sparse alignment and distinguishing strong conflict from weak support. We test this method with simulations and recent plant phylogenies inferred from variously sized datasets.Key Results QS scores decrease in variance with increasing replicates and are not strongly affected by branch depth. Patterns of QS support from different phylogenies leads to a coherent understanding of ancestral branches defining key disagreements, including Ginkgo+cycad, magnoliids+eudicots (excluding monocots), and mosses+liverworts. The relationships of ANA grade angiosperms, major monocot groups, and bryophytes and fern families are found to likely be the result of discordant evolutionary histories, rather than poor information. Also, analyses of phylogenomic data show QS can detect discordance due to introgression.Conclusions The QS method represents an efficient and effective synthesis of phylogenetic tests that offer 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 to reconstruct the complex evolutionary histories surrounding in particular ANA grade angiosperms, monocots, and non-vascular plants.