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Does a tree-like phylogeny only exist at the tips in the prokaryotes?
Christopher J Creevey1, David A Fitzpatrick, Gayle K Philip
1Bioinformatics and Pharmacogenomics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland.
Proceedings. Biological Sciences
|December 24, 2004
Summary
Prokaryotic evolution is complex, with horizontal gene transfer (HGT) potentially creating a network rather than a tree. Phylogenetic signal is strong in gamma-proteobacteria but weak at deeper evolutionary levels.
Area of Science:
- Evolutionary Biology
- Microbial Phylogenetics
- Genomics
Background:
- The evolutionary history of prokaryotes is debated, with horizontal gene transfer (HGT) challenging traditional tree-like models.
- Understanding prokaryotic phylogeny is crucial for deciphering microbial evolution and relationships.
Purpose of the Study:
- To investigate the existence and inferability of a definitive prokaryotic phylogenetic tree using supertree methods.
- To assess the impact of horizontal gene transfer (HGT) on prokaryotic evolutionary patterns.
- To determine the reliability of orthologous genes for reconstructing deep prokaryotic relationships.
Main Methods:
- Analysis of three datasets (11, 10, and 61 taxa) spanning different prokaryotic divisions using complete genomes.
- Application of supertree methods to infer phylogenetic relationships.
- Evaluation of phylogenetic signal congruence among gene trees at various evolutionary depths.
Main Results:
- Phylogenetic signal congruence among gene trees was no better than random for deep prokaryotic relationships.
- A strong and highly accurate phylogenetic signal was detected within gamma-proteobacteria genes.
- Difficulties in inferring deep-level prokaryotic relationships are attributed to signal erosion, bias, hidden paralogy, and HGT.
Conclusions:
- Deep-level prokaryotic phylogeny is challenging to resolve due to factors including significant HGT.
- While a cohesive genomic signal exists within specific clades like gamma-proteobacteria, a universal prokaryotic tree remains difficult to confidently establish.
- The findings support the possibility of HGT levels inconsistent with a simple tree model for prokaryotic evolution.