Molecular Biology and Evolution, Vol 16, 1586-1598, Copyright © 1999 by Society for Molecular Biology and Evolution
MA Clark, NA Moran and P Baumann
A major limitation on ability to reconstruct bacterial evolution is the
lack of dated ancestors that might be used to evaluate and calibrate
molecular clocks. Vertically transmitted symbionts that have cospeciated
with animal hosts offer a firm basis for calibrating sequence evolution in
bacteria, since fossils of the hosts can be used to date divergence events.
Sequences for a functionally diverse set of genes have been obtained for
bacterial endosymbionts (Buchnera) from two pairs of aphid host species,
each pair diverging 50-70 MYA. Using these dates and estimated numbers of
Buchnera generations per year, we calculated rates of base substitution for
neutral and selected sites of protein-coding genes and overall rates for
rRNA genes. Buchnera shows homogeneity among loci with regard to synonymous
rate. The Buchnera synonymous rate is about twice that for low-codon-bias
genes of Escherichia coli-Salmonella typhimurium on an absolute timescale,
and fourfold higher on a generational timescale. Nonsynonymous
substitutions show a greater rate disparity in favor of Buchnera, a result
consistent with a genomewide decrease in selection efficiency in Buchnera.
Ratios of synonymous to nonsynonymous substitutions differ for the two
pairs of Buchnera, indicating that selection efficiency varies among
lineages. Like numerous other intracellular bacteria, such as Rickettsia
and Wolbachia, Buchnera has accumulated amino acids with codons rich in A
or T. Phylogenetic reconstruction of amino acid replacements indicates that
replacements yielding increased A + T predominated early in the evolution
of Buchnera, with the trend slowing or stopping during the last 50 Myr.
This suggests that base composition in Buchnera has approached a limit
enforced by selective constraint acting on protein function.
ORIGINAL ARTICLE
Sequence evolution in bacterial endosymbionts having extreme base compositions
Microbiology Section, University of California, Davis, USA.
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