Evolution__3rd_Edition

156 PART 2 / Evolutionary Genetics
Molecular evolution is studied in
substitutions between species and
polymorphisms within species
Molecular evolution may be driven
by selection or drift
7.1 Random drift and natural selection can both
hypothetically explain molecular evolution
Evolution, at the molecular level, is observable as nucleotide (or base) changes in the
DNA and amino acid changes in proteins. The word substitution is often used to refer to
an evolutionary change. In particular, a gene (or a nucleotide) substitution means that
one form of a gene (or a nucleotide) increases in frequency from being rare in the population
to being common. Evolutionary substitutions are studied by comparing different
species. If one species has nucleotide A at a certain site and another species has nucleotide
G, then at least one substitution must have occurred in the evolutionary lineage
connecting the two species. Molecular evolution is also studied by looking at polymorphisms
within a species. A polymorphism exists if, for example, some individuals of
a species have nucleotide A at a certain site while other individuals have G. A complete
substitution has not occurred, because both A and G are in fairly high frequency, but
some process must have driven up the frequency of one or both nucleotides in the past.
Polymorphism within a species, and evolutionary change between species, can be
explained by two processes: natural selection and drift. This chapter will be looking at
the contributions of drift and selection in molecular evolution. The subject hardly
existed before the 1960s. Then gel electrophoresis (Section 4.5, p. 83) started to be
used to study polymorphism, and the amino acid sequences of some proteins (such as
cytochrome c and hemoglobin) became available for several species. The early evidence
led Kimura (1968) and King & Jukes (1969) to suggest what Kimura called the neutral
theory of molecular evolution. Motoo Kimura (who lived from 1924 to 1994) was a
Japanese geneticist, and it was particularly him and his followers who promoted the
neutral theory in the two decades after those original publications in 1968 and 1969.
The neutral theory does not suggest that random drift explains all evolutionary
change. Natural selection is still needed to explain adaptation. It is, however, possible
that the adaptations we observe in organisms required only a small proportion of all the
evolutionary changes that have actually taken place in the DNA. The neutral theory
states that evolution at the level of DNA and proteins, but not of adaptation, is dominated
by random processes; most evolution at the molecular level would then be nonadaptive.
We can contrast the neutral theory with its opposite: the idea that almost all
molecular evolution has been driven by natural selection.
The difference between the two ideas can be understood in terms of the frequency
distribution for the selection coefficients of mutations, or genetic variants. (It does not
matter here whether we talk about new mutations or the set of genetic variants existing
in a population at a genetic locus. “Genetic variant” could be substituted for “mutation”
throughout this paragraph.) Given a mutation of a certain selection coefficient, the theory
of random drift or selection (as described in Chapters 5 and 6) applies in a mathematically
automatic way. If the selection coefficient is positive, the mutation increases in
frequency; if it is negative, it is eliminated; if it is zero, the gene frequencies drift. 1
1 This chapter uses a slightly different notation for selection coefficients from Chapter 5. In Chapter 5, the
genotype with the highest fitness was given a fitness of 1 and the other genotypes were given fitnesses like (1 − s).
Here we shall be interested in whether one form of a molecule has a higher, lower, or equal, fitness with another
form, and it will be more convenient to talk about selection coefficients that are +, 0, or –. A +ve selection
coefficient means natural selection favors the variant; –ve means it is selected against; 0 means it is neutral.
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