Evolution__3rd_Edition

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Biologists came to accept, through
the 1980s, that most molecular
evolution is by drift
CHAPTER 7 / Natural Selection and Random Drift 179
in the 1970s. It was keenly discussed, but did not win widespread acceptance, nor did it
inspire a big research program that assumed its validity. Indeed the neutral theory is
controversial still for protein evolution. Natural selection may play a big part in the
evolutionary change of, and genetic variation in, proteins a though this is far from
confirmed.
Through the 1980s, DNA sequence data began to accumulate. The neutral theory
was more, and the selectionist theory less, successful at predicting and explaining the
patterns of evolution in DNA, particularly in synonymous and non-coding sites. Moreover,
much of the DNA is non-coding. Perhaps 95% of human DNA does not code
for genes. The nature of “non-coding” DNA has only slowly become clear a indeed
biologists are still uncertain why non-coding DNA exists. During the 1970s, things
were more uncertain than now and biologists could argue that the apparently excessive
DNA could be informational in some way. Then selection would work on it. But much
of the non-coding DNA is now generally accepted to have no function, though its
nucleotide sequence may be partially constrained. It is difficult to see how selection
could drive many changes in this sort of “junk” DNA. Most evolution in non-coding,
non-genic DNA is thought to be neutral, though not pan-neutral. Therefore most of
the substitutions that occur in the DNA as a whole are thought to be neutral too,
because most of the DNA is non-coding. The conclusion is a little different from
Kimura’s original claim. He made it for proteins, that is for non-synonymous changes
in the DNA. He “won” the argument, but not for the kind of evidence he originally
discussed. It has turned out that most evolution is not in amino acid-changing parts
of the DNA.
The idea that most evolution in synonymous and non-coding DNA is neutral is now
inspiring a huge research program: the reconstruction of the history of life using
molecular evidence. Parts 4 and 5 of this book look at this kind of research. The
research could have been built on the theory of natural selection, but it follows more
easily from the neutral theory. Most of the biologists who are doing the work probably
assume that the molecular changes they are studying occur by random drift.
As an interim conclusion, we can say that the neutral explanation for molecular
evolution in synonymous sites within genes, and in non-coding parts of DNA, is widely
accepted. This being so, the majority of molecular evolution proceeds by random drift
rather than selection.
Natural selection is still evolutionarily important. It drives adaptive evolution, and
we now turn to ways of looking for signs of adaptive evolution a or the signature of
selection a in DNA sequence data.
7.8 Genomic sequences have led to new ways of studying
molecular evolution
Genomic sequences have become available in large amounts recently, and they can
be used to look for signs of selection and drift. We shall look at five examples of this
current research trend, beginning with a classic result. They mainly make use of the
distinction between synonymous and non-synonymous nucleotide changes.