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Phylogenetic reconstruction and lateral gene transfer.
Eric Bapteste1, Yan Boucher, Jessica Leigh
1Canadian Institute for Advanced Research and Genome Atlantic, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada. eric.bapteste@dal.ca
Trends in Microbiology
|September 1, 2004
Summary
Lateral gene transfer (LGT) can obscure evolutionary history. Re-analyzing a study on gammaproteobacteria, we found its core genes are not entirely free from LGT, challenging tree-based evolutionary models.
Area of Science:
- Evolutionary biology
- Genomics
- Phylogenetics
Background:
- Lateral gene transfer (LGT) complicates the reconstruction of evolutionary history and the Tree of Life.
- A conserved gene core is hypothesized to be refractory to LGT, preserving phylogenetic signals.
Purpose of the Study:
- To re-analyze a study claiming the core of single-copy orthologs in gammaproteobacteria is LGT-free.
- To assess the validity of the conserved gene core concept in phylogenetic reconstruction.
Main Methods:
- Re-analysis of existing data on gammaproteobacteria genomes.
- Examination of single-copy orthologs.
- Assessment of lateral gene transfer (LGT) impact on phylogenetic signal.
Main Results:
- The conclusion that the core of single-copy orthologs in gammaproteobacteria is free of LGT is premature.
- It is difficult to determine the extent of LGT within this core gene set.
- The conserved gene core concept faces significant challenges.
Conclusions:
- Phylogenetic relationships are not exclusively tree-like and are influenced by LGT.
- The conserved gene core, while important, should not be the sole basis for defining phylogenetic relationships.
- A more complex framework, the Synthesis of Life, is proposed for a more natural classification.