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The tree and net components of prokaryote evolution.
Pere Puigbò1, Yuri I Wolf, Eugene V Koonin
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
Genome Biology and Evolution
|October 5, 2010
Summary
Prokaryote evolution is complex, with gene transfer creating a "net of life." However, a consistent tree-like pattern emerges from nearly universal genes, suggesting a combination of tree and net models is needed to understand evolution.
Area of Science:
- Evolutionary biology
- Genomics
- Phylogenetics
Background:
- Prokaryotic gene phylogenies often differ due to horizontal gene transfer (HGT), challenging the traditional Tree of Life (TOL) model.
- The concept of a
- net of life
- has been proposed to better represent prokaryotic evolution.
Purpose of the Study:
- To quantitatively assess the relative contributions of tree-like and net-like evolutionary signals in prokaryotes.
- To investigate whether a single tree can represent prokaryotic genome evolution or if a combined model is necessary.
Main Methods:
- Analysis of approximately 7,000 phylogenetic trees from the "Forest of Life" (FOL) dataset.
- Quantitative measurement of tree and net evolutionary signals using quartet analysis.
- Examination of nearly universal trees (NUTs) for consistent evolutionary trends.
- Evolutionary simulations to test hypotheses about HGT patterns.
Main Results:
- While diverse net-like evolutionary routes are prevalent in the FOL, a prominent tree-like signal exists, particularly in NUTs.
- The balance between tree-like and net-like evolution varies significantly across bacterial and archaeal lineages and gene functional classes.
- Evolutionary simulations suggest that biased HGT alone cannot fully explain the observed central tree-like signal.
Conclusions:
- Prokaryotic evolution is best represented by a combination of tree and net models, not solely a net.
- Nearly universal genes provide a strong tree-like signal that is a dominant coherent evolutionary trend.
- Understanding prokaryotic evolution requires considering both vertical gene transfer (tree-like) and horizontal gene transfer (net-like) processes.
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