Encyclopedia of Evolution.pdf - Online Reading Center

will eventually be separated by crossing over; meanwhile
they are in linkage disequilibrium. Over time, the markers
approach greater equilibrium as more crossing over events
separate them. How far away they are from equilibrium can
be used to estimate how long it has been since one of the
markers originated. For example, there are two markers that
are very close to the CCR5 allele that confers resistance to
HIV (see AIDS, evolution of). Geneticists estimate that
the observed degree of disequilibrium between the markers
and the allele would have developed in about 28 generations,
or just under 700 years. The evolutionary importance
of this result is that the CCR5 mutation may have arisen as
a defense against bacteria during the Black Death, which
occurred about 700 years ago.
Molecular clocks are a widely accepted method of evolutionary
study but are not accepted without thorough calibration.
Further Reading
Ho, Simon Y. W., et al. “Accuracy of rate estimation using relaxedclock
models with a critical focus on the early metazoan radiation.”
Molecular Biology and Evolution 22 (2005): 1,355–1,363.
Langley, C. H., and Walter Fitch. “An estimation of the constancy of
the molecular rate of evolution.” Journal of Molecular Evolution
3 (1974): 161–177.
Zuckerkandl, Emile, and Linus Pauling. “Molecular disease, evolution,
and genic heterogeneity.” In M. Kash and B. Pullman, eds.,
Horizons in Biochemistry. New York: Academic Press, 1962.
mutations Mutations are alterations in DNA. They create
new genetic variation that allows evolutionary innovation
(see DNA [raw material of evolution]).
Most mutations are neutral—that is, they have no effect
on the evolutionary process:
• Most mutations occur in cells that will die when the organism
dies. For example, a mutation in a muscle cell of an
animal will be lost when that cell dies. Some of these
somatic mutations may induce cancer, if the mutation
causes the cell to lose control of cell division. Some somatic
mutations in plants may persist if the part of the plant that
contains the mutation is used for vegetative propagation.
This is how the mutation for seedless oranges has persisted:
The original mutation produced a branch with seedless
oranges, and pieces of the branch were grafted onto other
orange trees, from which further grafts were propagated,
until there are now many thousands of orange trees that
produce fruit without seeds. But usually the only mutations
that will be passed into future generations are the germ line
mutations, which occur in eggs or sperm, or in the cells
that produce eggs and sperm. Such a mutation may end up
in a fertilized egg, from which an organism develops, and
will be found in every cell, including the germ line cells, of
the offspring.
• Most germ line mutations are also neutral in their effect.
This is because most of the DNA in eukaryotic cells does
not encode genetic information. Mutations in the noncoding
DNA usually do not matter, since the information in this
DNA is not used to construct proteins. Mutations may accu-
mutations
mulate in noncoding DNA, acting as a measure of evolutionary
divergence (see DNA [evidence for evolution]).
• Even within genes, many mutations are neutral. DNA
encodes genetic information in codons. There are 64 possible
codons but only 20 kinds of amino acids which these
codons can specify. That is, in DNA language, there are 64
different words to specify only 20 different meanings. If a
mutation occurs that changes one codon to another, without
changing the amino acid that it specifies, the resulting
protein will not be changed. This often occurs when a
mutation changes the third base in the codon. Chloroplast
DNA extracted from 20-million-year-old leaves of Taxodium
and Magnolia and compared to modern chloroplast
DNA indicate that most of the mutations of Magnolia, and
all of the mutations in Taxodium, that occurred during the
past 20 million years were in the third bases of codons (see
fossils and fossilization). Mutations in the third base
of a codon are not always neutral. If a mutation changes
a codon from one that matches a common transfer RNA
to one that matches an uncommon one, the efficiency of
translation may be reduced.
• Many mutations are almost neutral. If a mutation in a gene
causes a different amino acid to be placed in a certain position
in a protein, the protein will be changed—but perhaps
not significantly. If one amino acid substitutes for another
amino acid that is chemically similar (for example, if leucine
substitutes for isoleucine), the protein shape may be
almost identical to what it had previously been. Even a
major amino acid change may have no effect on a protein
if it occurs someplace out of the way—in a position that
is on the outside of the protein and away from the active
site, which is the location on the protein where the chemical
reaction occurs. Many proteins exist in a great variety
of forms known as isozymes. For example, cells of all
organisms contain the protein cytochrome c. In all organisms,
cytochrome c does the same job, but its structure is
different in many different species. It therefore exists in
hundreds of different forms, due to mutations. Often an
isozyme from even a distantly related species can function
well if inserted in place of an organism’s normal enzyme.
For example, many human genes work well when inserted
into other animals such as mice.
Some mutations, however, can cause major changes in
the protein specified by a gene:
• If a major amino acid substitution occurs inside of a protein,
it may alter the entire shape of the protein. If a major amino
acid substitution occurs near the active site of the protein,
the function of the protein may be altered. This is what happened
with the hemoglobin mutation that causes sickle-cell
anemia. A mutation in the DNA caused a valine to substitute
for a glutamic acid in the resulting protein, in position
6 out of 146 amino acids. This change was enough to cause
the hemoglobin to crystallize under acidic conditions. This
mutation can cause severe medical problems but also confers
resistance to malaria (see balanced polymorphism).
• In most cases, such a mutation will disrupt the function of
the protein, but in some cases a mutation may improve the