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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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MoleRate: comparing molecular relative evolutionary rates to detect convergent evolution.

Avery G Selberg^1,2, Nathan Clark³, Anton Nekrutenko⁴

¹Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, United States.

Evolution; International Journal of Organic Evolution

|December 12, 2025

Summary

MoleRate is a new phylogenetic rate test that identifies accelerated or reduced evolutionary rates in genes. This tool helps uncover the molecular basis of adaptation and functional importance across species, revealing significant selective pressures related to phenotypes.

Keywords:

convergent evolution molecular evolution phylogenetic comparative methods

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Area of Science:

Evolutionary Genomics
Phylogenetics
Molecular Evolution

Background:

Evolutionary rates of genes can indicate conservation, functional importance, or adaptation.
Large-scale genomic data offer opportunities to study evolutionary rate shifts linked to phenotypes.
Convergent phenotypic adaptation can be reflected in repeated rate shifts across lineages.

Purpose of the Study:

Introduce MoleRate, a novel phylogenetic rate test for detecting evolutionary rate shifts.
Provide a likelihood-based hypothesis testing framework for evolutionary rate analysis.
Enable the detection and filtering of aberrant signals from single lineages.

Main Methods:

Developed an explicit phylogenetic rate test (MoleRate).
Applied MoleRate to simulated and empirical data, including mammalian phenotypes.
Utilized visualization tools for result exploration and communication.

Main Results:

MoleRate detects biologically significant enrichments in selective pressure related to phenotypes.
Identified accelerated or reduced evolutionary rates in protein-coding genes associated with specific phenotypes.
Demonstrated MoleRate's superior performance compared to existing methods, including robust signal detection.

Conclusions:

MoleRate is an effective tool for identifying molecular adaptations underlying phenotypic evolution.
The method reveals significant selective pressures associated with specific phenotypes.
MoleRate enhances the study of evolutionary genomics and the discovery of adaptive evolution.