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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Measuring Phylogenetic Information of Incomplete Sequence Data.

Tae-Kun Seo^1,2, Olivier Gascuel^2,3, Jeffrey L Thorne⁴

¹Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea.

Systematic Biology

|September 1, 2021

Summary

This summary is machine-generated.

We introduce effective sequence length (ESL) to quantify phylogenetic information loss from sequence alignment gaps. A new model adequacy test helps disentangle the impact of gaps and evolutionary model misspecification on phylogenetic inference.

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Area of Science:

Phylogenetics
Computational Biology
Molecular Evolution

Background:

Phylogenetic analysis commonly uses probabilistic models of molecular evolution.
Sequence alignments with gaps (insertions/deletions) reduce phylogenetic information.
Existing methods are sensitive to both gaps and model misspecification.

Purpose of the Study:

To develop methods for assessing phylogenetic information loss due to gaps and model misspecification.
To introduce the concept of effective sequence length (ESL) for quantifying information content.
To create a goodness-of-fit test for evaluating the adequacy of evolutionary models.

Main Methods:

Proposed calculation of effective sequence length (ESL) accounting for alignment gaps.
Developed a novel test for model adequacy by comparing Fisher information between actual and simulated sequence data.
Utilized theoretical frameworks and empirical data analysis.

Main Results:

Demonstrated that ESL differs from the actual column count due to gaps.
Showed how to disentangle the effects of gaps and model misspecification on phylogenetic information.
Identified specific alignment sites and tree branches most impacted by these factors using Fisher information.

Conclusions:

Effective sequence length (ESL) provides a robust measure of phylogenetic information content.
The new model adequacy test effectively distinguishes between information loss from gaps and evolutionary model misspecification.
This work enhances the reliability of phylogenetic inference from molecular sequence data.