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A Spatially Explicit Model of Stabilizing Selection for Improving Phylogenetic Inference.

Jeremy M Beaulieu¹, Brian C O'Meara², Michael A Gilchrist²

¹Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA.

Molecular Biology and Evolution

|December 11, 2020

Summary

Ultraconserved elements (UCEs) contain deep evolutionary information. A new model, SelON, better explains UCE sequence evolution by including spatially varying selection, improving phylogenetic accuracy.

Keywords:

Wright–Fisher mutation stabilizing selection ultraconserved elements

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Area of Science:

Evolutionary biology
Genomics
Phylogenetics

Background:

Ultraconserved elements (UCEs) are highly conserved DNA sequences critical for understanding evolutionary history.
Current phylogenetic methods often assume uniform evolutionary rates across UCEs, potentially overlooking complex selective pressures.

Purpose of the Study:

To develop and evaluate a novel model, SelON (selection on nucleotides), that explicitly incorporates spatially varying stabilizing selection within UCEs.
To assess the performance of SelON against traditional models using empirical vertebrate UCE data.

Main Methods:

Introduction of the Wright-Fisher model of selection on nucleotides (SelON).
SelON models mutation, drift, and position-dependent Gaussian stabilizing selection.
Comparison of SelON with the GTR+Γ model using 400 vertebrate UCEs for turtle phylogeny.

Main Results:

SelON demonstrated significantly improved model fit compared to the GTR+Γ model.
The analysis supported the placement of turtles as sister to lepidosaurs.
UCE-specific parameters from SelON quantify selection strength and variation effectively.

Conclusions:

The SelON model provides a more accurate representation of evolutionary processes within UCEs.
Explicitly modeling selection on UCEs enhances understanding of their deep conservation.
This approach improves phylogenetic inference and sheds light on UCE evolutionary mechanisms.