Evolution__3rd_Edition

180 PART 2 / Evolutionary Genetics
The higher rate of synonymous than
non-synonymous evolution ...
. . . is evidence that natural
selection acts against nonsynonymous
mutations
7.8.1 DNA sequences provide strong evidence for natural selection
on protein structure
When, in Chapter 4, we considered the evidence for biological variation, we noticed
that many DNA sequence variants can be uncovered if proteins are sequenced at the
DNA level (Section 4.5, p. 84). This observation has important implications for molecular
evolution. At the alcohol dehydrogenase (Adh) locus in the fruitfly (Drosophila
melanogaster), two alleles (fast and slow) are present. Kreitman (1983) sequenced the
DNA of 11 different copies of the gene. He found that the proteins were uniform within
each allelic class. He found only two amino acid sequences, corresponding to the two
alleles. But he found a number of DNA sequences coding for each allele. Within an
allelic class, he found synonymous, but not non-synonymous, variation. The combination
of a fixed amino acid sequence and variable silent sites provides, as Lewontin
(1986) emphasized, evidence that natural selection has been operating to maintain the
enzyme structure.
There are two possible reasons why the enzyme sequence, at the amino acid level,
should be fixed within each allelic class. One is “identity by descent”: all the copies of
each allele may be descended from an ancestral mutation, which had that sequence and
has been passively passed from generation to generation. Eventually another amino
acid-altering mutation may arise within one allelic class, and that allele will (at least
temporarily) have become two alleles. The constant sequence within current fruitfly
populations only means that not enough time has passed for such a mutation to occur.
Alternatively, the gene copies that make up an allelic class may all have the same
sequence because that sequence is maintained by natural selection; when a mutation
arises, selection removes it.
The observed variability distinguishes between these two hypotheses. The variability
in the synonymous sites means that there has been time for mutations to arise in the
molecule. If mutations have arisen in synonymous sites, they will surely have arisen in
non-synonymous sites too. Therefore, we can reason that the identity in amino acid
sequence is unlikely to be identity by descent. Mutations in non-synonymous sites have
presumably not been retained because natural selection eliminated them.
If it had turned out that the Adh-f allele was fixed for one DNA sequence at all sites,
synonymous and non-synonymous, we should not know whether the uniformity was
due to selection or identity by descent. We should be in the same position as we were
in before Kreitman’s DNA-level study. The uniformity might mean only that no mutations
had occurred. Kreitman’s DNA sequencing thus provides evidence for selection
that could not have been obtained with amino acid sequences alone.
The absence of amino acid sequence variation within the Adh-f (and Adh-s) allelic class
is particularly striking because 30% of the enzyme is made up of isoleucine and valine,
which are biochemically very similar (and indistinguishable by gel electrophoresis). A
neutralist might have predicted that some of the valines could be changed to isoleucines,
or vice versa. The only amino acid sequence variant is the one that causes the Adh-f /
Adh-s polymorphism. That polymorphism is known to be maintained by natural selection.
Therefore, none of the amino acids in the 255 amino acid alcohol dehydrogenase
enzyme of the fruitfly can be changed neutrally. Interestingly, that means that we could
almost construct Figure 7.1 for alcohol dehydrogenase at the amino acid level. The
graph would be like Figure 7.1a for mutations that change an amino acid, but like
..