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08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L.
Yasin Bakış1, Hasan H Otu, Nivart Taşçı
1Department of Biology, Abant İzzet Baysal University, Bolu 14280, Turkey. bakis_y@ibu.edu.tr
BMC Bioinformatics
|January 18, 2013
Summary
The Relative Complexity Measure (RCM) offers a robust alternative to traditional multiple sequence alignment for phylogenetic tree reconstruction. This non-alignment based method proves more reliable, especially for highly variable DNA sequences.
Area of Science:
- Molecular Biology
- Bioinformatics
- Phylogenetics
Background:
- Phylogenetic tree accuracy heavily relies on multiple sequence alignment (MSA) quality, which is sensitive to parameter choices.
- Varying alignment parameters can lead to divergent phylogenetic outcomes.
- The Relative Complexity Measure (RCM) is a novel, non-alignment based approach designed to address MSA limitations.
Purpose of the Study:
- To apply the RCM method for reconstructing robust phylogenetic trees.
- To analyze phylogenetic relationships within the genus Galanthus using sequence data from Turkey.
- To compare the robustness of phylogenies derived from nuclear and chloroplast DNA.
Main Methods:
- Application of the Relative Complexity Measure (RCM) for phylogenetic tree construction.
- Analysis of nuclear ribosomal RNA gene sequences.
- Analysis of chloroplast DNA sequences.
Main Results:
- The RCM method was successfully applied to reconstruct phylogenetic trees for the genus Galanthus.
- Phylogenetic trees derived from nuclear ribosomal RNA gene sequences exhibited greater robustness.
- Phylogenetic trees derived from chloroplast DNA sequences showed a higher degree of variation.
Conclusions:
- Phylogenies generated using RCM demonstrated robustness and reliability compared to other methods.
- RCM presents a viable alternative to overcome challenges associated with MSA-based phylogenetic analyses.
- RCM is particularly suitable for highly variable sequence families where MSA accuracy is parameter-dependent.
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