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12.3.3 The Neutral (or Nearly Neutral) Theory of Evolution
Another controversy involves the mechanism(s) of molecular evolution. At the
core of the dispute is the neutral theory of molecular evolution ( Kimura 1968,
1983, 1987, Ohta 1996, 2000b ). The neutrality theory (or the modified “nearly
neutral” theory) recognizes that for any gene a large proportion of all possible
mutations (alleles) are deleterious and that these are eliminated or maintained
at a very low frequency by natural selection. The evolution of morphologi-
cal, behavioral, and ecological traits is governed largely by natural selection,
because selection occurs on favorable alleles and against deleterious alleles.
However, many mutations can result in alleles which are equivalent, or nearly
so, to each other. Neutral mutations are not subject to selection because they
do not affect the fitness of the individual carrying them. Neither do they affect
their morphology, physiology, or behavior. The neutrality theory states that the
majority of nucleotide substitutions in the course of evolution are the result of
the gradual, random fixation of neutral changes, rather than the result of posi-
tive Darwinian selection. Neutral mutations can spread in a population because
only a relatively small number of gametes are sampled each generation (random
genetic drift). By chance, they can be transmitted to the next generation at a
higher frequency ( Kimura 1968, 1983 ).
Ohta (1996) concluded that the “strictly neutral theory has not held up as
well as the nearly neutral theory, yet remains invaluable as a null hypothesis for
detecting selection.” The main difference between the nearly neutral theory
and the traditional selection theory is that “the nearly neutral theory predicts
rapid evolution in small populations, whereas the latter predicts rapid evolution
in large populations” ( Ohta 1996 ). Kreitman (1996) noted that the neutral the-
ory has been useful for organizing thinking about the nature of evolutionary
forces acting on variation at the DNA level and has provided a set of testable
predictions (acting as a useful null hypothesis). However, Kreitman (1996) argues
“the neutral theory cannot explain key features of protein evolution nor pat-
terns of biased codon usage in certain species.” Despite this, he concludes the
neutral theory “is likely to remain an integral part of the quest to understand
molecular evolution.” Finally, both Ohta (1996) and Kreitman (1996) agree that
the “nearly neutral theory” is more compatible with the current data in explain-
ing synonymous changes and the evolution of codon bias.
Why be concerned about neutrality or nearly neutral theories? The neu-
trality theory is a basic assumption of some methods of estimating phylogeny
and also affects the molecular-clock hypothesis ( Ohta 1996, 2000b, Kreitman
1996 ). Data indicate that many protein, chromosome, and DNA variations are
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