Calibrating bacterial evolution

Abstract

Attempts to calibrate bacterial evolution have relied on the assumption that rates of molecular sequence divergence in bacteria are similar to those of higher eukaryotes, or to those of the few bacterial taxa for which ancestors can be reliably dated from ecological or geological evidence. Despite similarities in the substitution rates estimated for some lineages, comparisons of the relative rates of evolution at different classes of nucleotide sites indicate no basis for their universal application to all bacteria. However, there is evidence that bacteria have a constant genomewide mutation rate on an evolutionary time scale but that this rate differs dramatically from the rate estimated by experimental methods. Rates of molecular evolution in higher eukaryotes can be resolved through comparisons of homologous molecules in species for which divergence times have been inferred from fossil and geologic evidence. But without a robust fossil record, how is it possible to establish the age of bacterial species and to calibrate their rates of sequence divergence over an evolutionary time scale? In lieu of direct fossil evidence, divergence times for bacteria have been obtained by three approaches.Age Inferred by Association with Ecological Events. By linking the appearance of several bacterial lineages to large-scale events that occurred at known times in the geologic past, Ochman and Wilson (1, 2) constructed a time scale for bacterial evolution. Applying these dates, they calculated the absolute rates of 5S rRNA and 16S rRNA divergence; these were fairly uniform across bacterial species and similar to those observed for the homologous molecules in eukaryotes. Based on an estimated rate of 16S rRNA divergence of nearly 1% per 50 million years, they calculated that Escherichia coli and Salmonella enterica sv. Typhimurium (hereafter referred to as S. enterica)-the most closely related pair of bacterial species for which appreciable genetic information was available at the time-shared a common ancestor between 120 million and 160 million years ago. Comparisons of homologous protein-coding regions from E. coli and S. enterica indicated an average rate of sequence divergence at synonymous sites of 0.90% per million years. (Note that divergence between lineages is twice the substitution rate, and that this yields a substitution rate for E. coli and S. enterica of 0.45% per million years.) Ochman and Wilson (2) could not establish the synonymous substitution rates for bacterial taxa other than E. coli and S. enterica because of insufficient availability of protein-coding sequences for other pairs of closely related bacterial species.Age Inferred from Host Fossil Record. The unique association between bacterial endosymbionts and their insect hosts allowed Moran et al. (3) to estimate the dates of divergence for members of the genus Buchnera in the Proteobacteria. Buchnera live within specialized cells of aphids and are essential to the growth and reproduction of their hosts, which inherit the endosymbionts cytoplasmically....

Host-microbial symbiosis in the vertebrate gastrointestinal tract and the Lactobacillus reuteri paradigm

“…Because of their slow evolution, 16S rRNA sequences have a significant limitation in such studies. The average substitution rate of bacterial 16S rRNA genes has been calculated as ≈1% per 50 million y, and the closely related species Escherichia coli and Salmonella enterica are predicted to have separated more than 100 million y ago (36,37). Although such estimates have to be taken with caution, it is likely that most of the lineages detected in contemporary vertebrates have diversified before they became associated with their vertebrate hosts.…”

Transposable elements as genomic diseases

“…The time resolution of molecular clocks is limited by the time needed to accumulate a single (synonymous) nucleotide substitution, the elementary time unit of molecular evolution. For E. coli in the wild, for example, synonymous nucleotide substitutions accumulate at a rate of circa K s =0.009 per gene pair and per 10 8 -3×10 8 generations 50 . For a transposable element of approximately 1 kilo basepair in length, one would expect of the order of 9 substitutions in this amount of time.…”

Global distribution of cyanobacterial ecotypes in the cold biosphere

“…Molecularclock analysis of several bacterial taxa suggests that a 1% divergence in 16S rRNA gene sequence corresponds to an evolutionary time span of approximately 50 million years (Moran et al, 1993;Ochman et al, 1999). This would imply that the Arctic and Antarctic ribotypes described here have been isolated or subject to reduced genetic exchange for less than 10 million years.…”