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Phylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants.

Stephen A Smith¹, Nathanael Walker-Hale^1,2, Joseph F Walker^1,3

¹Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Biological Sciences Building, Ann Arbor, MI 48109-1085, USA.

Systematic Biology

|November 21, 2019

Summary

Gene tree conflict complicates species tree reconstruction. This study introduces a method to dissect phylogenetic signal, resolving some relationships and identifying data limitations in phylogenomic plant data.

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Area of Science:

Evolutionary Biology
Genomics
Phylogenetics

Background:

Gene tree conflict is a common issue in phylogenetics, leading to conflicting results from different species tree inference methods.
Resolving deep phylogenetic relationships requires methods that can effectively handle and interpret conflicting evolutionary signals within genomic data.

Purpose of the Study:

To develop and apply a method for dissecting phylogenetic signal to resolve recalcitrant relationships and identify data limitations.
To investigate the impact of gene tree conflict on species tree inference and evaluate methods for data filtering and gene combinability.

Main Methods:

Developed a procedure to dissect phylogenetic signal within a dataset, extending methods for isolating conflict and concordance.
Applied combinatorial heuristics to test gene combinability and assess the amplification of phylogenetic signal.
Utilized a large phylogenomic plant dataset for demonstration and analysis.

Main Results:

Supported key phylogenetic relationships: Amborella sister to angiosperms, Gnetales sister to pines, and monophyly of extant gymnosperms.
Identified persistent uncertainty in relationships within bryophytes and eudicots due to insufficient supporting gene trees.
Found that nested conflicts limit data filtering effectiveness and that broad concatenation of genes is not supported by the underlying conflicting signal.

Conclusions:

The developed approach effectively dissects datasets to address deep phylogenetic relationships and ascertain inferential boundaries.
Gene tree conflict necessitates careful data analysis rather than broad gene concatenation for accurate species tree inference.
The study highlights the importance of identifying what data cannot resolve, in addition to what it can.