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Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria
Chih-Horng Kuo1, Howard Ochman
1Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA. chkuo@email.arizona.edu
Biology Direct
|October 1, 2009
Summary
Bacterial molecular clock studies reveal that substitution rates vary significantly across genes and lineages, challenging universal clock assumptions. However, relative-rate tests can establish reliable local clocks for accurate bacterial evolutionary dating.
Area of Science:
- Microbial evolutionary biology
- Molecular evolution
- Bioinformatics
Background:
- Bacteria lack a robust fossil record, necessitating molecular sequence comparisons for evolutionary history inference.
- Molecular clock dating relies on assumptions of constant substitution rates across time and taxa, which are often violated.
- Inconsistent substitution rates can lead to significant inaccuracies in evolutionary timescale estimates.
Purpose of the Study:
- To investigate the consistency of substitution rates in conserved bacterial genes.
- To assess the validity of molecular dating methods in bacterial evolution.
- To identify factors influencing substitution rate variation in bacterial lineages.
Main Methods:
- Analysis of 16S ribosomal RNA (rRNA) gene evolution in endosymbionts calibrated with host fossil records.
- Genome-wide estimation of nonsynonymous and synonymous substitution rates.
- Comparison of divergence estimates derived from 16S rRNA genes and universally conserved protein-coding genes.
Main Results:
- Substitution rates were consistent within bacterial clades but varied widely across different lineages.
- Nonsynonymous and synonymous substitution rates demonstrated high variability across bacterial taxa.
- Genetic drift significantly influences substitution accumulation in 16S rRNA genes and at nonsynonymous sites.
- Divergence estimates from protein-coding genes showed poor agreement with those from 16S rRNA genes.
Conclusions:
- A wide range of substitution rates exists across bacterial genes and taxa, cautioning against universal molecular clock assumptions.
- The assumption of a universal molecular clock for inferring bacterial divergence times is unreliable.
- Relative-rate tests on homologous genes can establish dependable local clocks for calibrating bacterial evolution.
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