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Updated: Jun 2, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

multistrap: boosting phylogenetic analyses with structural information.

Athanasios Baltzis¹, Luisa Santus^1,2, Björn E Langer¹

¹Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.

Nature Communications

|January 15, 2025

Summary

This summary is machine-generated.

Improving phylogenetic tree reliability is crucial. Combining protein sequence and structural data enhances bootstrap branch support values, leading to more accurate evolutionary insights.

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Last Updated: Jun 2, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Area of Science:

Computational Biology
Bioinformatics
Evolutionary Biology

Background:

Reliable branch support estimates are critical for accurate phylogenetic trees.
Traditional bootstrapping methods using only sequence data can be limited by saturation.

Purpose of the Study:

To improve the reliability of phylogenetic branch support estimates.
To integrate both sequence and structural information for enhanced phylogenetic analysis.

Main Methods:

Developed a novel approach named multistrap.
Systematically compared homologous intra-molecular structural distances.
Computed tree-like distance matrices using combined sequence and structure data.

Main Results:

Structural distance variations show less saturation than sequence-based Hamming distances.
Phylogenetic trees derived from combined data show strong similarities to sequence-only trees.
Combined sequence and structure bootstrap support values improve discrimination between correct and incorrect branches.

Conclusions:

The multistrap approach effectively enhances bootstrap branch support values.
Utilizing predicted and experimental 3D protein structures improves phylogenetic accuracy.
This method offers a more robust way to infer evolutionary relationships.