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Evolution of genomes
Descent with modification
At the most abstract level, evolution can be defined as
descent with modification. We have seen how DNA
replication ensures a mostly faithful passing of the genome
to progeny. But if this replication were 100% accurate, no
modification whatsoever could occur in asexual species,
the variability in sexually reproducing organisms would be
limited to the possible recombinations of a fixed number of
alleles.
Descent with modification
However, the variety we see in nature is MUCH greater
than what could be achieved by recombination alone.
Most modifications in the course of evolution are due to
copying errors in the process of DNA replication called
mutations. These copying errors provide the raw material
that natural selection acts on. Deleterious mutations tend
to be eliminated by selection, favorable mutations tend to
spread through the population and eventually replace the
original (wildtype) allele.
Descent with modification
Many mutations appear to be neither deleterious nor
favorable. The change in frequency of individuals that
carry such neutral mutations is largely determined by
genetic drift.
It is not always clear whether a mutation is deleterious,
favorable, or neutral. Due to epistatic interactions of
different loci in the genome, a mutation on one locus can
confer a selective advantage when in the company of one
set of alleles and can confer a disadvantage when in the
company of a different set of alleles.
Types of mutations
For the development of good models of molecular
evolution it is useful to distinguish between different types
of mutations. I will make here the major distinction
between mutations on a local scale and mutations on
a global scale, the former being ones that can be described
by looking at a stretch of a few thousand base pairs, the
latter being ones on the scale of the whole genome. It
should be pointed out that the distinction is made for
modeling purposes only and is clear cut in some and
artificial in other cases.
Mutations on a local scale
On a local scale, there are for types of mutations:
 Point mutations
 Insertions of a stretch of DNA
 Deletions of a stretch of DNA
 Inversions of a stretch of DNA
It is often difficult to decide whether a deletion or an
insertion has occurred relative to the genome of a common
ancestor. Insertions and deletions are therefore often
lumped together under the name indels.
Tandem repeats
Another effect of local mutations (most likely due to
DNA-slippage or to unequal crossover) is the frequent
occurrence of tandem repeats, where the same fragment
of DNA is repeated in tandem, often many times.
Dependent upon the length of the repeated stretch and
the number of repeats, geneticists distinguish satellite
DNA, minisatellites, and microsatellites.
Point mutations
Point mutations are the replacement of one nucleotide by
another. We distinguish transitions (the replacement of
one purine by another or one pyrymidine by another) from
transversions (the replacement of a pyrymidine by a purine
or vice versa). Transitions occur much more frequently
than transversions.
Point mutations
If point mutations occur in a coding region, due to the
degeneracy of the genetic code, the mutation may or may
not alter the sequence of amino acids that is being coded.
We distinguish between silent or synonymous mutations
and non-synonymous mutation. In the case of the former,
a codon for an amino acid is being mutated to another
codon for the same amino acid (or one STOP codon for
another STOP codon); in the case of the latter, the
translation of the codon changes.
Mutations on a global scale
On the scale of the whole genome, several types of
mutations are known to have occurred. For our purposes,
the most interesting phenomena are gene duplications
and genome rearrangements.
Another important effect of evolution on a global scale is
the existence of highly repetitive non-coding DNA
produced by transposable elements.
Genome rearrangements
Over the course of evolution, many large-scale genome
rearrangements are known to have occurred. This involve
such processes as large-scale inversions and transpositions
(often involving the movement of genetic material from
one chromosome to another) as well as linking or breaking
up chromosomes.
Gene duplications
Gene duplication is a process by which two copies of a
parental gene get passed on to the progeny. This process
leads to several important phenomena. Some genes simply
persist in several copies. Other genes form gene families
with each gene having somewhat different functions. In
other cases, one copy of the duplicated gene ceases to
be expressed and becomes a pseudogene.
Orthologous vs paralogous genes
In bioinformatics, we often study genes from different
organisms that have evolved from a common ancestral
gene. Such genes are called homologous genes. If the
genes have all evolved from the same copy of the
ancestral gene since the most recent duplication of this
gene, we speak of orthologous genes, otherwise we
speak of paralogous genes.