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Model selection may not be a mandatory step for phylogeny reconstruction.

Shiran Abadi¹, Dana Azouri^1,2, Tal Pupko³

¹School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv, Tel-Aviv, 69978, Israel.

Nature Communications

|February 27, 2019

Summary

Model selection for phylogeny reconstruction is often debated, but this study shows different criteria yield similar results. Skipping this step and using the GTR+I+G model is also effective for evolutionary studies.

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Area of Science:

Evolutionary biology
Computational biology
Bioinformatics

Background:

Phylogeny reconstruction is crucial for evolutionary studies.
Model selection is a standard but debated step in this process.
Various criteria exist for selecting evolutionary models.

Purpose of the Study:

To investigate the necessity and impact of model selection in phylogeny reconstruction.
To compare inferences from different model selection criteria.
To assess the utility of skipping model selection.

Main Methods:

Analysis of empirical and simulated phylogenetic datasets.
Application of various established model selection criteria.
Comparison of resulting phylogenetic topologies and ancestral sequence reconstructions.
Evaluation of using the GTR+I+G model without prior selection.

Main Results:

Incongruency in selected models is common across datasets.
Different model selection criteria consistently produce similar phylogenetic inferences.
Skipping model selection and using the GTR+I+G model also yields comparable results.
Topological and ancestral sequence reconstructions are robust to model choice.

Conclusions:

The choice of model selection criterion is not critical for topology and ancestral sequence reconstruction.
Model selection may be a non-essential step in current phylogeny reconstruction strategies.
Using the GTR+I+G model directly offers a time-efficient alternative.