Nov 21, 2019

PHYLOGENETIC CONFLICTS, COMBINABILITY, AND DEEP PHYLOGENOMICS IN PLANTS

Systematic Biology
Stephen A SmithJoseph W Brown

Abstract

Studies have demonstrated that pervasive gene tree conflict underlies several important phylogenetic relationships where different species tree methods produce conflicting results. Here, we present a means of dissecting the phylogenetic signal for alternative resolutions within a dataset in order to resolve recalcitrant relationships and, importantly, identify what the dataset is unable to resolve. These procedures extend upon methods for isolating conflict and concordance involving specific candidate relationships and can be used to identify systematic error and disambiguate sources of conflict among species tree inference methods. We demonstrate these on a large phylogenomic plant dataset. Our results support the placement of Amborella as sister to the remaining extant angiosperms, Gnetales as sister to pines, and the monophyly of extant gymnosperms. Several other contentious relationships, including the resolution of relationships within the bryophytes and the eudicots, remain uncertain given the low number of supporting gene trees. To address whether concatenation of filtered genes amplified phylogenetic signal for relationships, we implemented a combinatorial heuristic to test combinability of genes. We found that nested c...Continue Reading

Mentioned in this Paper

Study
Genes
Trees (plant)
Phylogenetic Analysis
Angiosperms
Pine, Bach Flower Essence
Amborella
Analysis
Lymphatic Tree
Drug Combinations

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