||Bacteria Escherichia coli
||Ochman H, Elwyn S, Moran NA. Calibrating bacterial evolution. Proc Natl Acad Sci U S A. 1999 Oct 26 96(22):12638-43. Table - link PubMed ID10535975
||To examine relative evolutionary rates over different classes of
sites (synonymous, nonsynonymous, and 16S rRNA), researchers compared
homologous sequences from species sufficiently closely
related that they are not in saturation for any class of sites.
Bacterial species differing by more than 5% in their 16S rRNA
sequences are typically at or near saturation at synonymous
sites of protein coding regions. After limiting the dataset to
include only those pairs of species with 16S rRNAs that were
more than more 95% identical, all available coding regions for
each pair were extracted from GenBank. In the event that homologous genes were assigned different names in the sister
species, homology initially was established through BLAST
similarity searches of all of the coding regions for each species.
The resulting pairs of sequences, tentatively assigned as homologs,
were aligned by using SEQUENCHER 3.0 (Gene Codes,
Ann Arbor, MI) and their coding frames were assigned with
MACCLADE 3.01 (23). Only those pairs of species having five or
more sequenced homologs of more than 100 aa in length were
considered for subsequent analysis. The phylogenetic relationships
of the taxa included in this study are presented in Fig. 1.
(Most of the completely sequenced bacterial genomes currently
available in the databases are too distantly related to one
another, and to other bacteria for which coding sequences are
available, to be useful for this study.) Sequence divergence at
synonymous (Ks) and nonsynonymous (Ka) sites were calculated
with DIVERGE (GCG), which uses the method of Li (24).
Estimates of Ks and Ka for Buchnera spp. (5, 17) and E. coli/S.
enterica (25, 26) were obtained from the literature. Calculated from values in table. [Genome size] ×[Substitution Rate]/[Generations per year]=[substitutions/generation].
[4.7×10^6 nucleotides]× [4.5×10^-9 substitutions/(nucleotide×year)]/[range of 100–300 generations/year]= 7.05×10^-5 - 2.115×10^-4 substitutions per generation. Substitution rates are calculated per synonymous site per year based on externally calibrated divergence times. These divergence times relate to known geologic events such as diversification of cyanobacteria diversification 1.3 Billion Years ago or host evolution (warm blooded vertebrates, mammals) ~100 MYa in the case of E. coli and S. enterica (Ochman and Wilson, 1987 PUBMED ID 3125340).
coli and S. enterica diverge at a synonymous substitution rate
of 0.90% per million years (25, 26), which corresponds to a
within lineage rate of 0.0045 mutations per site per million
years. Natural populations of E. coli have an estimated 100–
300 generations per year (37–39), implying a rate of about
0.0001 to 0.0002 mutations per genome per generation (Table
1). Drake et al.’s estimate (20–22), based on laboratory derived
mutation rates, was 0.003 mutations per genome BNID 102008,103918, more
than an order of magnitude higher. Similar calculations for
Buchnera, whose generation times can be estimated from the number of replications within the host insect and the number
of host generations per year (19, 40–42), result in 0.0001 to
0.0002 mutations per genome per generation, a rate identical
to that estimated for E. coli. Hence, the genomic
mutation rate may well be constant across bacterial species on
an evolutionary time scale, but it is not compatible with the
rate based on laboratory studies.