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Updated: Jul 23, 2025

Development of an Individual-Tree Basal Area Increment Model using a Linear Mixed-Effects Approach

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Parameter Estimation and Species Tree Rooting Using ALE and GeneRax.

Tom A Williams¹, Adrián A Davín², Benoit Morel^3,4

¹School of Biological Sciences, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TH, United Kingdom.

Genome Biology and Evolution

|July 18, 2023

Summary

This summary is machine-generated.

Gene tree-species tree reconciliation tools like ALE and GeneRax accurately infer gene evolution events and root species trees. Despite recent criticisms, these methods prove reliable for studying genome evolution across diverse life forms.

Keywords:

comparative genomics gene tree–species tree reconciliation microbial evolution phylogenetics

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Area of Science:

Phylogenetics
Computational Biology
Evolutionary Genomics

Background:

Probabilistic gene tree-species tree reconciliation methods, including ALE and GeneRax, are used to infer gene duplication, transfer, and loss events.
These methods are foundational for mapping gene family origins and rooting species trees, with prior applications across Archaea, Bacteria, and eukaryotes.
Recent concerns questioned the reliability of ALE/GeneRax model-based estimates for duplication and transfer events, potentially impacting species tree rooting.

Purpose of the Study:

To rigorously assess criticisms regarding the accuracy of ALE/GeneRax reconciliation methods.
To validate the reliability of these tools for inferring gene duplication, transfer, and loss events.
To evaluate the impact of these methods on species tree rooting across different domains of life.

Main Methods:

Utilized simulated datasets to test the accuracy of ALE/GeneRax under controlled conditions.
Compared ALE/GeneRax results with alternative methodological approaches using empirical biological data.
Analyzed gene duplication and transfer frequencies across various lineages to assess biological consistency.

Main Results:

ALE and GeneRax demonstrated accuracy on simulated data.
Results from ALE/GeneRax showed good agreement with alternative methods on empirical data.
ALE successfully captured biologically relevant variation in gene duplication and transfer rates across lineages.
ALE-consistently recovered established species tree roots in plants and opisthokonts.
In Bacteria, ALE's root predictions aligned with other methods in regions of uncertainty.

Conclusions:

The ALE/GeneRax model and reconciliation-based approaches are validated as accurate tools for studying genome evolution.
These methods reliably infer gene duplication, transfer, and loss events and aid in species tree rooting.
ALE's ability to recover biologically consistent patterns reinforces its utility in evolutionary genomics research.