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Introductory article
Article Contents
Molecular evolution is the process by which molecules of living forms diverge from one
another over time. The study of molecular evolution embraces the evolution of the
molecules themselves, their origins, how they change from taxon to taxon, the effects of
these changes on function, and the integration of the molecules in the biochemical
pathways of an organism. It also infers phylogenetic relationships and contributes to the
formulation of general principles of evolution at the molecular level.
Introduction
For evolution to take place, changes must occur and they
must then be handed on further. In the case of biological
evolution, the changes (mutations) occur in the molecules
of the hereditary (genetic) material, the nucleic acids, and
their transmission from ancestor to descendant is guaranteed by the replication of these molecules. The changes may
remain conned to the nucleic acids or they may be
translated into an alteration of proteins encoded in the
genetic material; the modied proteins may then eect the
alteration of other molecules, sugars for example, and so
on, until, at the end of the causal chain, changes aecting
an observable character may take place. Ultimately, a
molecular change in the genetic constitution (genotype)
may thus be transliterated into altered appearance,
physiology or behaviour the organisms phenotype. To
become an evolutionary change, however, the mutation
must spread through a group of individuals, the population. There are thus two principal levels at which evolution
can be studied the molecular and the population levels.
Corresponding to a population at the molecular level is the
gene pool the total genetic material of an interbreeding
population at a given time (in a more restricted sense, a
gene pool is an assemblage of all alleles at a given locus in a
population in a given generation; here a gene is a unit of
inheritance, a sequence of nucleotides to which a specic
function can be assigned; alternative forms of a gene are
alleles and the position a gene or allele occupies on a
chromosome is a locus). Evolutionary changes at the
molecular level constitute molecular evolution.
The study of molecular evolution embraces three broad
areas. First, it is concerned with the evolution of the
molecules themselves, primarily sequences of nucleic acids
and proteins their origin, the manner in which they
change from taxon to taxon, the eects of these changes on
function, and the integration of the molecules in the
biochemical pathways of an organism. Although almost
any molecule or molecular segment can be selected for
evolutionary analysis, certain molecules have become
biologists favourites. These include haemoglobins, lysozymes, colour-sensitive pigment proteins, eye-lens crystal-
. History
. Principle
. Methods
. Molecular Clock
. The Neutral Theory of Evolution
. Evolution of the Genome
History
Molecules are not visible to the naked eye; although the
large molecules of nucleic acids and proteins can be
visualized with the aid of an electron microscope, the
Molecular Evolution
discernible detail is insucient to spot changes in microstructure. The study of molecular evolution therefore only
became possible after methods for detecting structural
changes in macromolecules were developed. The rst
methods were indirect: they revealed that structural change
occurred but provided no information about the nature of
the change, nor about its location in the molecule. One
indirect method took advantage of the immune systems
ability to distinguish foreign substances from those of the
organisms own. For example, the inoculation of human
serum albumin into a rabbit leads to the production of
antibodies, which react strongly with human, less strongly
with chimpanzee and gorilla, and do not react with rhesus
macaque serum albumin at all. This immunological
reaction, which, if positive, results in the formation of a
visible precipitate, indicates that human serum albumin is
structurally somewhat dierent from the serum albumin of
a chimpanzee or a gorilla, and quite distinct from the
monkey protein. The ability of antibodies to dierentiate
between structurally distinct proteins and carbohydrates
was already recognized at the turn of the century and was
exploited in attempts to classify plants and animals. Later
the method fell into disuse, only to be resurrected in the
1960s and 1970s.
Three other methods protein electrophoresis, DNA
DNA hybridization and restriction enzyme analysis were
also developed to detect dierences between biological
macromolecules without being able to ascertain the
chemical nature of the changes. Electrophoresis distinguishes proteins according to their overall charge. DNA
DNA hybridization takes advantage of the observation
that the two complementary strands of a DNA molecule
dissociate (melt) on heating and then reanneal again on
cooling. If radioactively labelled, melted DNA of one
species is mixed with melted DNA of another species and
the mixture is cooled, the strands derived from the two
species form hybrid duplexes. The extent of this DNA
DNA hybridization depends on the similarity of the DNA
of the two species and it can be determined by heating the
hybrid molecules: the greater the similarity, the higher the
melting temperature of the hybrids. The third method puts
to use restriction enzymes, proteins that have evolved in
various bacteria as a means of providing protection from
an invasion of foreign DNA. The enzymes attack the
foreign DNA and hack it into pieces, each enzyme
recognizing specic regions of the molecule. Because of
the dierences in structure, each DNA molecule yields a
distinct set of fragments when digested with one or more
restriction enzymes. The fragments can be separated and
visualized, and their length can be determined by electrophoresis.
Ultimately, advances in biochemistry led to the development of direct methods by which the nature of
mutational changes could be established. Biochemical
investigations revealed proteins and nucleic acids to be
strings of amino acid and nucleotide residues, respectively,
2
Principle
From the point of view of evolution, the simplest structural
change (mutation) in a DNA molecule is the substitution of
a nucleotide of one kind by another nucleotide during
replication. The substitution may or may not eect a
replacement of an amino acid residue in a protein,
depending on the region and the site of its occurrence. A
mutation generates a new allele that falls into one of three
broad categories. An allele with the same chance of
contributing its own copy to the next generation is said
to be neutral. An allele that eects its own preferential
transmission, increasing the chance of survival of its bearer
or of producing a larger number of ospring (i.e. increases
its tness), is said to be selectively advantageous. Finally,
an allele that decreases the chance of survival and
Molecular Evolution
Methods
Molecular evolution begins with allele-frequency changes
in a population. To study these initial changes, researchers
sample a population and test all individuals in the sample
Molecular Evolution
Molecular Clock
Phenotypic evolutionary changes are highly erratic. Some
lineages may change rapidly within a short time, while
others appear not to have changed their phenotypes for
many millions of years. Early protein sequence comparisons suggested that, at the molecular level, amino acid
replacements might accumulate at a much more regular
pace. Indeed, if a large proportion of nondeleterious
mutations were neutral in terms of their eect on tness,
their fate in the gene pool would be determined by random
genetic drift and xations could be expected to occur at
more or less regular intervals. It would, however, be a
stochastic regularity, rather like that leading to the
expectation of obtaining 50% heads in coin ipping: the
more times you ip a coin, the closer the match between the
observed and the expected result. The supposition that
molecules evolve at an approximately constant rate is
termed the molecular clock. According to the molecular
clock hypothesis, the number of amino acid replacements
(and by extension also the number of nucleotide substitutions) found between proteins (nucleic acid segments) of
two species is proportional to the time elapsed since the
divergence of these species from their common ancestor. If
4
Molecular Evolution
Molecular Evolution
Further Reading
Gillespie JH (1991) The Causes of Molecular Evolution. Oxford: Oxford
University Press.
Kimura M (1983) The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
Li W-H (1997) Molecular Evolution. Sunderland, MA: Sinauer
Associates.
Li W-H and Graur D (1991) Fundamentals of Molecular Evolution.
Sunderland, MA: Sinauer Associates.
Nei M (1987) Molecular Evolutionary Genetics. New York: Columbia
University Press.
Ridley M (1996) Evolution, 2nd edn. Cambridge: Blackwell Science.