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Updated: Jun 3, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Parametric analysis of alignment and phylogenetic uncertainty.
Anna-Sapfo Malaspinas1, Nicholas Eriksson, Peter Huggins
1Department of Integrative Biology, University of California at Berkeley, CA 94720-3140, USA.
Bulletin of Mathematical Biology
|March 17, 2011
Summary
Phylogenetic tree inference is sensitive to DNA alignment methods. This study introduces parametric alignment to analyze alignment parameter robustness and improve phylogenetic accuracy, particularly for Drosophila intronic sequences.
Area of Science:
- Computational Biology
- Bioinformatics
- Phylogenetics
Background:
- Phylogenetic tree inference relies on accurate multiple DNA sequence alignment.
- The choice of alignment parameters significantly impacts the reliability of inferred phylogenies.
- Existing methods lack robust analysis of alignment parameter sensitivity.
Purpose of the Study:
- To develop tools for assessing the robustness of phylogenetic inference to variations in alignment parameters.
- To introduce novel improvements in parametric alignment for general parametric inference.
- To elucidate the relationship between alignment parameters and reconstructed phylogenetic trees.
Main Methods:
- Development of parametric alignment tools with novel improvements.
- Application of a Gaussian distribution on alignment parameters.
- Derivation of probabilities for optimal alignment summaries and inferred phylogenies.
- Analysis of intronic sequences from Drosophila using the developed method.
Main Results:
- Phylogeny estimates demonstrate sensitivity to the selection of alignment parameters.
- Parametric alignment effectively reveals the complex relationship between alignment parameters and tree reconstruction.
- The developed tools provide a quantitative measure of phylogenetic robustness.
Conclusions:
- Robust phylogenetic inference requires careful consideration of alignment parameter choices.
- Parametric alignment offers a powerful approach to understanding and mitigating alignment-induced biases in phylogenetics.
- This method enhances the reliability of evolutionary relationship reconstructions from DNA sequence data.
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