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Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms
1Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
Molecular Phylogenetics and Evolution
|May 24, 2015
Summary
Phylogenetic analyses using shortcut coalescent methods may produce errors with divergent gene trees. Concatenation methods may be more reliable for ancient angiosperm divergences, highlighting the need for careful method selection.
Area of Science:
- Phylogenomics
- Molecular Evolution
- Computational Biology
Background:
- Recent phylogenomic studies suggest (Amborellales, Nymphaeales) form a sister clade to other angiosperms.
- Shortcut coalescent phylogenetic methods were reported to outperform concatenation for these data.
Purpose of the Study:
- To falsify the conclusions from recent phylogenomic analyses.
- To investigate the robustness of coalescent and concatenation methods to gene tree discordance.
Main Methods:
- Re-analysis of phylogenomic data from 310 nuclear genes.
- Comparison of coalescent methods (MP-EST, STAR, ASTRAL) and concatenation.
- Evaluation of character subsampling procedures (Observed Variability, TIGER).
Main Results:
- Discrepancies between coalescent and concatenation methods stem from coalescent method (MP-EST, STAR) non-robustness to divergent and mis-rooted gene trees.
- ASTRAL demonstrated greater robustness to mis-rooted gene trees compared to MP-EST and STAR.
- Character subsampling methods OV and TIGER showed bias towards asymmetrical character distributions.
Conclusions:
- Methodological artifacts in gene tree reconstruction can be more problematic for shortcut coalescent methods than concatenation assumptions for ancient divergences.
- Novel phylogenetic tools require rigorous application of fundamental principles to avoid systematic errors.
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