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Updated: May 21, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Surprising results on phylogenetic tree building methods based on molecular sequences.
1Department of Computer Science, ETH Zurich, Zurich, Switzerland. gonnet@inf.ethz.ch
BMC Bioinformatics
|June 29, 2012
Summary
Minimal evolution distance methods outperform maximum likelihood methods for phylogenetic tree building from molecular sequences. This study introduces new tree quality measures, Intra and Taxon, to reliably evaluate 176 methods.
Area of Science:
- Bioinformatics
- Computational Biology
- Evolutionary Biology
Background:
- Phylogenetic tree building from molecular sequences (PTMS) methods rely solely on DNA or amino acid sequences.
- Evaluating the accuracy and reliability of these PTMSs is crucial for understanding evolutionary relationships.
Purpose of the Study:
- To statistically evaluate 176 PTMSs using novel tree quality measures.
- To compare the performance of different PTMS components and identify superior methods.
- To investigate evolutionary differences between Metazoa and other species based on molecular data.
Main Methods:
- Developed and applied the Intra measure for statistically significant evaluation of 176 PTMSs across 193,138 orthologous protein groups.
- Utilized the Taxon measure to compare PTMS-derived trees against established NCBI taxonomic classifications.
- Ranked components of PTMSs, including Multiple Sequence Alignments (MSAs), substitution matrices, and tree builders (Maximum Likelihood vs. Distance methods).
Main Results:
- The Intra measure demonstrated high consistency across species and strong discriminatory power among PTMSs.
- A high correlation was observed between the Intra and Taxon measures, validating both metrics.
- Maximum Likelihood methods performed poorly, while minimal evolution distance methods using MSA-induced alignments showed superior performance.
Conclusions:
- Minimal evolution distance methods consistently outperform Maximum Likelihood methods for phylogenetic tree construction.
- The study provides a ranking of PTMS components, highlighting the effectiveness of MSA-induced alignments.
- Distinct molecular traces in Metazoa suggest unique evolutionary patterns, and the developed quality measures will drive the design of new, more reliable PTMSs.
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