Calibrating bacterial evolution - PubMed (original) (raw)

Calibrating bacterial evolution

H Ochman et al. Proc Natl Acad Sci U S A. 1999.

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 genome-wide mutation rate on an evolutionary time scale but that this rate differs dramatically from the rate estimated by experimental methods.

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Figures

Figure 1

Figure 1

Phylogenetic tree of bacterial taxa used in this study based on 16S rRNA sequences. Only terminal branch lengths are proportional to sequence divergence. Colors indicate chromosomal G+C content as follows: green, <45% G+C; red, 45–55% G+C; blue, >55% G+C.

Figure 2

Figure 2

Relative extent of sequence divergence among pairs of bacterial species. Only pairs of species that differ by less than 5% in 16S rRNA sequences and for which sequence information is available for at least five homologous genes are included. Colors correspond to chromosomal G+C contents as in Fig. 1. (A) Divergence at synonymous sites (_K_s) vs. divergence at 16S rRNA (_K_16S). (B) Divergence at synonymous (_K_s) vs. nonsynonymous (_K_a) sites.

Figure 3

Figure 3

Rates of 16S rRNA sequence divergence in bacterial endosymbionts of insects. Divergence times are estimated from fossil evidence of insect hosts and were obtained from the literature (, –36). Shaded area denotes a rate of 16S rRNA divergence of 1–2% per 50 million years. Insect and bacterial taxa are follows (host/symbiont): aphids (Schizaphis graminum/Buchnera aphidicola, Schlechtendalia chinesis/Buchnera aphidicola); cockroach-termite (Blattaria germanica/symbiont, Mastotermes darwiniensis/symbiont); cockroach (Blattaria germanica/symbiont_, Periplaneta americana_/symbiont); whitefly (Trialeurodes vaporariorum/P-endosymbiont, Siphoninus phillyreae/P-endosymbiont); tsetse fly (Glossinia brevipalis/Wigglesworthia glossinidia, Glossinia morsitans/Wigglesworthia glossinidia).

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