Evolution__3rd_Edition

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Evidence shows that synonymous
codons are not used randomly
Figure 7.8
Relative frequencies of codons
match tRNA abundances.
(a) The green columns (above)
are the relative frequencies
of six leucine codons in
Escherichia coli; the gray
columns (below) are the
relative frequencies of the
corresponding tRNA molecules
in the cell. The two sets of
codons joined by a + sign are
recognized by a single tRNA
molecule. (b) The same
relation, but in Saccharomyces
cerevisiae. Notice the different
bias in codon usage in the two
species, which reillustrates the
point of Table 7.7. From
Kimura (1983). Redrawn with
permission of Cambridge
University Press © 1983.
to a common environment. In this case, convergence is good evidence that selection
has been at work on the lysozyme gene. The case can be strengthened in two ways. One
is that a third species, the South American bird called the hoatzin (Opisthocomus hoazin)
has also independently evolved cellulose digestion. It also uses a lysozyme, secreted in
its stomach, to digest cellulose-digesting bacteria. The hoatzin’s lysozyme is a related
but different gene from the one redeployed in ruminants and langurs, but it shows the
same set of amino acid changes. Secondly, the evolution of lysozyme in ruminants and
cows shows an elevated dN/dS ratio, which is suggestive of selection-powered adaptive
evolution, as we saw in the previous section (Messier & Stewart 1997).
7.8.5 Codon usages are biased
CHAPTER 7 / Natural Selection and Random Drift 187
The top part (green columns) of Figure 7.8 shows the relative frequency of the six
leucine codons in two single-celled organisms, the bacterium Escherichia coli and
the eukaryotic yeast Saccharomyces cerevisiae. The six codons are synonymous, and we
expect them to evolve by random drift. Notice two features of the figure: one is that the
codon frequencies are unequal within a species. The other is that the species differ in
which codons are abundant, and which rare. E. coli has more CUG; yeast has more
UUG.
What is the explanation for codon biases? Two hypotheses have been suggested:
selective constraint or mutation pressure. The mutation pressure hypothesis suggests
that mutation is biased toward certain nucleotides (Section 4.8, p. 89). If A tended to
mutate to G in E. coli, for instance, that might produce the excess of CUG and paucity
of CUA codons.
Alternatively, some codon changes may be disadvantageous and selected against.
Two possible reasons are the strength of DNA bonds and the relative abundance of
transfer RNAs. The GC bond is stronger than the AT bond, because GC has three
(a) Bacteria (b) Yeast
Codon
frequencies
tRNA
frequencies
CUG CUA CUC + CUU UUG + UUA GUG + CUA CUC CUU UUG UUA