Mutation and genetic
variation


Mutations are raw material of
evolution.
No variation means no evolution and
mutations are the ultimate source of
variation.
Where do new alleles
come from?

DNA made up of sequence of
nucleotides. Each nucleotide includes
a sugar, phosphate and one of four
possible nitrogenous bases (adenine
and guanine [both purines], and
thymine and cytosine [both
pyrimidines]).
4.1a
4 + 4.1d
4.1b
.
Where do new alleles
come from?


The opposite strands of the DNA molecule
are complementary because the strands are
held together by bonds between the
opposing bases and adenine bonds only
with thymine and cytosine only with
guanine.
Thus, knowing the sequence on one strand
enables one to construct the sequence on
the other strand.
4.2
Where do new alleles
come from?


Sequence of bases in DNA codes for
protein structure as each three base
sequence codes for one amino acid in
the protein chain.
[To refresh yourself on basic DNA
structure and protein synthesis see
any Introductory Biology textbook]
4.3a
Where do new alleles
come from?


When DNA is synthesized an enzyme
called DNA polymerase reads one
strand of DNA molecule and constructs
a complementary strand.
If DNA polymerase makes a mistake
and it is not repaired, a mutation has
occurred.
4.2
Types of mutations


A mistake that changes one base on a DNA
molecule is called a point mutation.
Two forms:
– Transition: one pyrimidine (T or C) substituted
for the other pyrimidine or one purine
substituted for the other purine (A or G).
– Transversion: purine substituted for pyrimidine
or vice versa
Fig 4.4
Types of mutations

Transitions more common than
transversions. Perhaps because
transitions cause less disruption to the
DNA molecule and so are less likely to
be noticed by DNA repair molecules.
Types of mutations


Not all mutations cause a change in
amino acid coded for. These are called
silent mutations.
Mutations that do cause a change in
amino acid are called replacement
mutations.
Types of mutations


Another type of mutation occurs when
bases are inserted or deleted from the
DNA molecule.
This causes a change in how the
whole DNA strand is read (a frame
shift mutation) and produces a nonfunctional protein.
Mutation rates



Most data on mutations comes from
analysis of loss-of-function mutations.
Loss-of-function mutations cause gene
to produce a non-working protein.
Examples of loss-of-function mutations
include: insertions and deletions,
mutation to a stop codon and insertion
of jumping genes.
Mutation rates


Some mutations cause readily
identified phenotypic changes.
E.g. Achrondoplastic dwarfism is a
dominant disorder. An Achrondoplastic
individual’s condition must be the
result of a mutation, if his parents do
not have the condition.
Mutation rates


Human estimate is 1.6
mutations/genome/generation.
In Drosophila rate is only 0.14 m/g/g, but
when corrected for number of cell divisions
needed to produce sperm (400 in humans
25 in Drosophila) mutation rates per cell
division are very similar.
Mutation rates


These rates are underestimates as
they are based on loss-of-function
mutations.
Direct estimate of number of
mutations of all kinds made for
roundworm Caenorhabditis elegans by
sequencing mitochondrial DNA.
Mutation rates


Roundworms can self-fertilize so researchers
tracked 74 family lines derived from one
female and followed each for 214
generations.
At end sequenced 771,672 base pairs of
mitochondrial DNA. Found 26 mutations
giving rate of 1.6X10-7 mutations per site
per generation. Ten mutations were
insertion/deletions and 16 substitutions.
Mutation rates

Applying mutation rates to entire
genome gives estimate of
approximately 15
mutations/individual/generation.
Where do new genes
come from?

Mutation can produce new alleles, but
new genes are also produced and
gene duplication appears to be most
important source of new genes.
Gene duplication


Duplication results from unequal
crossing over when chromosomes
align incorrectly during meiosis.
Result is a chromosome with an extra
section of DNA that contains
duplicated genes
4.7
Gene duplication


Extra sections of DNA are duplicates and
can accumulate mutations without being
selected against because the other copies of
the gene produce normal proteins.
Gene may completely change over time so
gene duplication creates new possibilities for
gene function.
Globin genes


Human globin genes are examples of
products of gene duplication.
Globin gene family contains two major
gene clusters (alpha and beta) that
code for the protein subunits of
hemoglobin.
Globin genes

Hemoglobin (the oxygen-carrying
molecule in red corpuscles) consists of
an iron-binding heme group and four
surrounding protein chains (two coded
for by genes in the Alpha cluster and
two in the Beta cluster).
Globin genes


Ancestral globin gene duplicated and
diverged into alpha and beta ancestral
genes about 450-500 mya.
Later transposed to different
chromosomes and followed by further
subsequent duplications and
mutations.
From Campbell and Reese Biology 7th ed.
Globin genes

Lengths and positions of exons and
introns in the globin genes are very
similar. Very unlikely such similarities
could be due to chance.
Exons (blue), introns (white), number in box is number of nucleotides.
4.9
Globin genes


Different genes in alpha and beta families
are expressed at different times in
development.
For example, in very young human fetus,
zeta (from alpha cluster) and epsilon (from
beta cluster) chains are present initially then
replaced. Similarly G-gamma and A-gamma
chains present in older fetuses are replaced
by beta chains after birth.
4.8
Gestation (weeks)
Post-birth(weeks)
Fetal hemoglobin has a higher affinity for oxygen than adult hemoglobin.
Enhances oxygen transfer from mother to offspring.
Chromosomal alterations

Two major forms important in
evolution: inversions and polyploidy.
Inversions


A chromosome inversion occurs when
a section of chromosome is broken at
both ends, detaches, and flips.
Inversion alters the ordering of genes
along the chromosome.
4.10
Inversions



Inversion affects linkage (linkage is the likelihood
that genes on a chromosome are inherited together
i.e., not split up during meiosis).
Inverted sections cannot align properly with
another chromosome during meiosis and crossingover within inversion produces non-functional
gametes.
Genes contained within inversion are inherited as a
set of genes also called a “supergene”
Inversions



Inversions are common in Drosophila (fruit
flies)
Frequency of inversions shows clinal pattern
and increases with latitude.
Inversions are believed to contain
combinations of genes that work well in
particular climatic conditions.
Inversions

Drosophila introduced to Washington
and Chile from Old World. Spread
along both coasts and within a few
years had developed similar clines in
number of inversions to those found in
native range.
4.11
Polyploidy



Polyploidy is the duplication of entire
sets of chromosomes.
A polyploid organism has more than
two sets of chromosomes.
E.g. A diploid (2n chromosomes)
organism can become tetraploid (4n),
[where n refers to one set of
chromosomes].
Polyploidy


Polyploidy is common in plants, rare in
animals.
Half of all angiosperms (flowering
plants) and almost all ferns are
polyploid.
Polyploidy

Polyploid animal taxa include
earthworms and flatworms, which can
self-fertilize, and some other groups
including insects that can reproduce
asexually (parthenogenesis).
Polyploidy


Polyploidy can occur if an individual
produces diploid gametes and selffertilizes generating tetraploid
offspring.
If an offspring later self fertilizes or
crosses with its parent, a population of
tetraploids may develop.
FIG 4.12
Polyploidy

If a sterile plant undergoes polyploidy
and self-fertilization a new species can
develop essentially immediately.
Polyploidy


Cross-fertilization of different species,
followed by polyploidy, was responsible for
the development of many crop plants e.g.
wheat.
Initial cross-fertilization produces sterile
offspring, because chromosomes cannot
pair up during meiosis.
Polyploidy


Triticum monococcum (AA) X wild Triticum (BB)
cross produced sterile hybrid with 14
chromosmomes (AB; 1-7A and 1-7B). {capitalized
letters symbolize species source of chromosomes,
number denotes individual chromosome e.g. 1A,
3B}
Polyploidy of first sterile hybrid produced Emmer
Wheat T. turgidum (AABB) which has 28
chromosomes. Emmer Wheat isn’t sterile. It has
two copies of each chromosome (e.g. two 1A
chromosomes, two 3B chromosomes, etc.).
Polyploidy


Further cross between Emmer Wheat and T.
tauschii which has a total of 14
chromosomes (DD) produced a sterile
hybrid with 21 chromosomes (ABD).
Further polyploid error in meiosis produced
T. aestivum Bread Wheat with 42
chromosomes (AABBDD). Those
chromosomes are derived from 3 ancestral
species.
Example of inter-species cross-fertilization and meiotic errors leading to
production of a fertile hybrid
Polyploidy


Genes in polyploid chromosome sets
are free to develop new functions
through natural selection and
evolution.
Polyploidy is a key source of genetic
variation.
What is mutation rate to
polyploidy in plants?



Flowering plants produce diploid gametes at
frequency of 0.00465 per generation
Thus tetraploid offspring produced at rate of
approx 0.00465 X 0.00465 or 2.16 X 10-5 per
generation (approx. 2 in every 100,000
offspring per generation are tetraploid).
This is comparable to rate of point
mutations in individual genes.
Measuring genetic
variation in populations


Classical view: little genetic variation
expected because one allele at a locus
expected to be superior, favored by
natural selection and thus fixed in the
population.
Now recognized that there is
substantial genetic variation in natural
populations.
Identifying genotypes



Gel electrophoresis used to determine
genotypes of individuals.
DNA isolated, amplified and cut using
restriction enzymes. Different patterns on
gel can be distinguished.
Also direct sequencing can be used to
identify different alleles.
Calculating allele
frequencies


Recall Δ32 (delta32) variant of CCR5
gene (CCR5 used as coreceptor by HIV
to enter white blood cells).
Δ32 allele offers protection against
HIV. How can its frequency in a
population be estimated?
Calculating allele
frequencies

Simplest way is to count frequencies,
but can also be estimated from the
frequencies of heterozygotes and
homozygotes as we will see when we
study Hardy-Weinberg equilibrium
shortly.
How much genetic
diversity exists in a
typical population?


Electrophoretic studies have shown
that most populations have substantial
genetic variation.
In general, 33-50% of enzyme loci are
polymorphic and average individual is
heterozygous at 4-15% of loci.
Frequency distribution of enzyme heterozygosity in plants. Heterozygosity is the
mean percentage of loci hetoerozygous per individual or the mean percentage of
individuals heterozygous per locus.
4.16
Why are populations
genetically diverse?



Two major hypotheses.
Selectionist: Diversity maintained by
selection. Selection favors rare individuals,
heterozygotes or different alleles at different
times and places.
Neutral: Most alleles at polymorphic loci
functionally and selectively equivalent.
Neutralist vs Selectionist
controversy


Both neutralist and selectionist schools
recognize the importance of selection.
I.e. that many alleles are fixed as a
result of selection.
The disagreement is about the
proportion of molecular variation that
is due to the effects of selection.
Neutralist vs Selectionist
controversy


Neutralist argument is that most of the
diversity seen in DNA at the molecular level
is functionally neutral (i.e. does not have an
effect on fitness).
In most cases, neutralists argue that a
change in a codon leads to an amino acid
change that has no effect on the functioning
of the protein produced.
Neutralist vs Selectionist
controversy


Through the process of genetic drift
(chance) different alleles may become
fixed in different populations.
Selectionist would argue that most
variation is subject to selection.
Neutralist vs Selectionist
controversy



One way to evaluate the situation in nature is to
look at synonymous and non-synonymous changes
in nucleotides.
Synonymous changes are ones where the codon is
changed but the amino acid produced is not [i.e. a
silent mutation] . This will be invisible to selection
and so must be .
In non-synonymous changes, the amino acid is
changed and this change may result in a
phenotypic change and thus be selected for or
against.
McDonald-Kreitman test



You would expect that if selection acts on most nucleotides
that the ratio Dn/Pn of fixed to polymorphic nucleotides for
non-synonymous codons would be much higher than the
same ratio Ds/Ps for synonymous codons (not subject to
selection).
This is because fixation implies a particular nucleotide is
better than the alternatives at that site.
Fixed means that only one nucleotide occurs at a site in a
species, but there are differences between species.
Polymorphic means multiple nucleotides occur at a site in a
species.
Neutralist vs Selectionist
controversy


Using an extension of the McDonaldKreitman test it is possible to estimate the
proportion of nucleotide substitutions fixed
by natural selection.
It is estimated that 45% of the amino acid
differences between two species of
Drosophila (D. simulans and D. yakuba)
have been fixed by selection and 35% of AA
differences in primates have been fixed by
selection (Barton et al. Evolution 2007).