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Relative Model Fit Does Not Predict Topological Accuracy in Single-Gene Protein Phylogenetics.

Stephanie J Spielman¹

¹Department of Biological Sciences, Rowan University, Glassboro, NJ.

Molecular Biology and Evolution

|March 20, 2020

Summary

Model selection in protein phylogenetics may not improve accuracy. Studies show consistent tree topologies and similar false-positive rates across models, suggesting current models may be misspecified. Model fit is not a reliable proxy for phylogenetic accuracy.

Keywords:

maximum likelihood phylogenetics protein models relative model selection

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A Protocol for Computer-Based Protein Structure and Function Prediction

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Published on: November 3, 2011

Area of Science:

Phylogenetics
Computational Biology
Evolutionary Biology

Background:

Phylogenetic reconstruction relies on selecting appropriate evolutionary models.
Model selection typically uses information-theoretic criteria to rank model fit.
It's assumed better model fit enhances phylogenetic accuracy.

Purpose of the Study:

To investigate the relationship between model fit and topological accuracy in protein phylogenetics.
To assess the impact of model misspecification on phylogenetic inference.
To evaluate the utility of relative model selection for protein evolutionary analyses.

Main Methods:

Utilized simulations with site-heterogeneous codon models, distinct from protein-level models.
Analyzed real protein sequences to assess phylogenetic inference across various models.
Compared topologies and false-positive rates inferred by models with different goodness-of-fit scores.

Main Results:

Phylogenetic trees showed high topological consistency despite significant differences in model fit.
All tested models inferred similar proportions of false-positive splits, indicating potential widespread model misspecification.
The general time reversible (GTR) model performed comparably to models with fixed exchangeabilities.

Conclusions:

Relative model selection may not hinder protein phylogenetic analysis but offers no predictable accuracy improvements.
Model fit is not a reliable indicator of phylogenetic inference accuracy in protein evolution.
Current protein evolution models might be fundamentally misspecified for real sequence data.