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Updated: May 19, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Detecting phylogenetic signals in eukaryotic whole genome sequences
1School of Computer Science, Tel-Aviv University, Israel.
Summary
Whole genomes contain phylogenetic signals, but these signals degrade over long evolutionary times. The average common subsequence (ACS) method effectively extracts this signal from both DNA and proteome data, aligning well with established taxonomy.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Whole genome sequences offer vast molecular data for evolutionary insights.
- Challenges exist in whole genome evolution modeling and identifying conserved regions.
- Limited phylogenetic reconstructions have utilized whole genome data.
Purpose of the Study:
- To investigate the feasibility of whole genome-based phylogenetic reconstruction across diverse eukaryotes.
- To compare the performance of different phylogenetic methods using whole genome data.
- To assess the reliability of phylogenetic signals in whole genomes over evolutionary timescales.
Main Methods:
- Applied K(r), feature frequency profile (FFP), and average common subsequence (ACS) methods to 24 multicellular eukaryotic genomes.
- Utilized ACS on both DNA and proteome sequences (ACS(DNA) and ACS(AA)).
- Compared resulting phylogenetic trees against the National Center for Biotechnology Information (NCBI) taxonomy tree.
Main Results:
- ACS(AA) proteome-based trees showed complete agreement with the NCBI taxonomy.
- ACS(DNA) genome-based trees demonstrated excellent agreement up to 800 million years ago (MYA).
- Phylogenetic signal quality decreased for divergence times of 1 billion years ago and beyond, indicating signal saturation.
Conclusions:
- Whole genomes contain a discernible phylogenetic signal.
- The ACS method is superior for detecting phylogenetic signals in whole genome data.
- Phylogenetic signal derived from whole genomes saturates at deeper evolutionary divergences.
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