Basic genetics terminology
DNA is the genetic material. The
instructions for making and “operating”
an organism are written in DNA.
DNA is divided into sections called
genes.
What a gene does
Each gene codes for a single protein. The
gene specifies the sequence of amino acids
that should be joined together to make a
protein.
Together the genes determine the
characteristics of an organism.
Alleles and genes
Alleles are different versions of a
gene.
If a single gene codes for flower color,
white and blue flowers would be coded for
by 2 different alleles.
Number of copies of genes
You possess two copies of each gene in
your body*.
One copy is inherited from each parent.
For a given gene you may have two
different alleles or two copies of the same allele.
(* excluding genes on sex chromosomes
in males).
Homozygous vs heterozygous
A homozygous individual has two copies of
a particular allele. (AA)
A heterozygous individual has two different
alleles. (Aa)
Genotype and phenotype
An organism’s genes (its genotype) play a
large role in determining its physical
appearance (its phenotype).
But remember an organism’s phenotype is
also affected by the environment.
The relationship between genes and
evolution
We express evolutionary ideas in terms of
genes because genes are the only thing that
are passed from one generation to the next.
Process of Natural Selection
In the process of natural selection, genes
that help organisms to survive and
reproduce become more common.
Genes that help less or are harmful
gradually are eliminated from the
population.
Process of Natural Selection
Individuals that are the best adapted to their
environments (the best camouflaged, best at
finding food, etc.) will generally be more
successful at breeding than less well adapted
individuals.
As a result, their genes (which make them well
adapted) will be commoner in the next generation
than the genes of less well adapted individuals.
Chapter 23. The Evolution of
Populations
Remember individual organisms do not
evolve. Individuals are selected, but it is
populations that evolve.
Because evolution occurs when gene pools
change from one generation to the next,
understanding evolution require us to
understand population genetics.
Some terminology
Population: All the members of one species
living in single area.
Gene pool: the collection of genes in a
population. It includes all the alleles of all
genes in the population.
Some terminology
If all individuals in a population all have the same
allele for a particular gene that allele is said to be
fixed in the population.
If there are 2 or more alleles for a given gene in
the population then individuals may be either
homozygous or heterozygous (i.e. have two
copies of one allele or have two different alleles)
Detecting evolution in nature
Evolution is defined as changes in the structure of
gene pools from one generation to the next.
How can we tell if the gene pool changes from one
generation to the next?
We can make use of a simple calculation called
the Hardy-Weinberg Equilibrium
Hardy-Weinberg Equilibrium
Before discussing Hardy-Weinberg need to review some
basic facts about Mendelian Inheritance.
In Mendelian Inheritance alleles are shuffled each
generation into new bodies in a way similar to which cards
are shuffled into hands in different rounds of a card game.
The process of Mendelian Inheritance preserves genetic
diversity from one generation to the next. A recessive
allele may not be visible because it is hidden by the
presence of a dominant allele, but it is still present.
Hardy-Weinberg Equilibrium
The shuffling process occurs because an
individual has two copies of any given gene
(one inherited from father and one from
mother), but can put only one or the other
copy into a particular sperm or egg. E.g. for
an individual who is heterozygous Aa 50%
of sperm will contain A and 50% will
contain a.
Hardy-Weinberg Equilibrium
Individuals alleles thus go through a process
where they are sorted into gametes (sperm
or egg) which combine to form a zygote
which will one day again sort alleles into
gametes.
See Chapter 14 to review Mendelian
Inheritance
Hardy-Weinberg Equilibrium
Consider a population of 100 individuals.
This population will contain 200 copies of
any given gene because each individual has
two copies.
Gene we are interested in has two alleles A
and a.
Hardy-Weinberg Equilibrium
If 80% of the alleles in the gene pool are A and
20% are a, we can predict the genotypes in the
next generation.
Basic probability: To determine the probability of
two independent events both occurring, you
should multiply the probabilities of the individual
events together.
Hardy-Weinberg Equilibrium
Probability of an AA individual is 0.8*0.8 =
0.64
Probability of an aa individual is 0.2*0.2 =
0.04
Probability of an Aa individuals is 0.2*0.8 =
0.16, but there are two ways to produce an
Aa individual so 0.16*2= 0.32.
Note these probabilities sum to 1.
Hardy-Weinberg Equilibrium
General formula for Hardy-Weinberg is
p2 + 2pq + q2 = 1, where p is frequency of
allele 1 and q is frequency of allele 2.
p + q = 1.
Hardy-Weinberg Equilibrium
Hardy-Weinberg equilibrium can be used to
estimate allele frequencies from information
about phenotypes and genotypes.
Hardy-Weinberg Equilibrium
E.g. approx 1 in 10,000 babies are born with
phenylketonuria (PKU) (causes retardation
if diet is not kept free of amino acid
phenylalanine).
Disease due to individual being
homozygous for a recessive allele k. i.e., the
babies’ genotype is kk.
Hardy-Weinberg Equilibrium
What is frequency of k allele in population?
q2 = frequency of PKU in population = 0.0001.
q = square root of q2 or 0.01. Frequency of allele k
Therefore p the frequency of the K allele = 1 0.01 = 0.99
Frequency of carriers (heterozygotes) in
population is 2pq =
2*0.99*0.01 = 0.0198 or almost 2% of population.
Much greater than frequency of PKU.
Working with the H-W equation
You need to be able to work with the HardyWeinberg equation.
For example, if 9 of 100 individuals in a
population suffer from a homozygous recessive
disorder can you calculate the frequency of the
disease-causing allele? Can you calculate how
many heterozygotes are in the population?
Working with the H-W equation
p2 + 2pq + q2 = 1. The terms in the equation represent the
frequencies of individual genotypes. [A genotype is
possessed by an individual organism so there are two
alleles present in each case.]
P and q are allele frequencies. Allele frequencies are
estimates of how common alleles are in the whole
population.
It is vital that you understand the difference between allele
and genotye frequencies.
Working with the H-W equation
9 of 100 (frequency = 0.09) of individuals
are homozygous for the recessive allele.
What term in the H-W equation is that equal
to?
Working with the H-W equation
It’s q2.
If q2 = 0.09, what’s q? Get square root of q2,
which is 0.3, which is the frequency of the allele a.
If q=0.3 then p=0.7. Now plug p and q into
equation to calculate frequencies of other
genotypes.
Working with the H-W equation
p2 = (0.7)(0.7) = 0.49 -- frequency of AA
2pq = 2 (0.3)(0.7) = 0.42 – frequency of Aa.
To calculate the actual number of heterozygotes
simply multiply 0.42 by the population size =
(0.42)(100) = 42.
Other examples of working with HW
equilibrium: is a population in HW
equilibrium?
In a population there are 100 birds with the
following genotypes:
44 AA
32 Aa
24 aa
How would you demonstrate that this
population is not in Hardy Weinberg
equilibrium
Three steps
Step 1: Calculate the allele frequencies.
Step 2: Calculate expected numbers of each
genotype (i.e. figure out how many
homozygotes and heterozygotes you would
expect.)
Step 3: Compare your expected and
observed data.
Step 1 allele frequencies
Step 1. How many “A” alleles are there in
total?
44 AA individuals = 88 “A” alleles
(because each individual has two copies of
the “A” allele)
32 Aa individuals = 32 “A” alleles (each
individual one A allele)
Total “A” alleles is 88+32 =120.
Step 1 allele frequencies
Total number of “a” alleles is similarly
calculated as 2*24 + 32 = 80
What are allele frequencies?
Total number of alleles in population is
120 + 80 = 200 (or you could calculate it by
multiplying the number of individuals in the
population by two 100*2 =200)
Step 1 allele frequencies
Allele frequencies are:
A = 120/200= 0.6. Let p = 0.6
a = 80/200 = 0.4. Let q = 0.4
Step 2 Calculate expected
number of each genotype
Use the Hardy_Weinberg equation
p2 + 2pq + q2 = 1 to calculate what expected genotypes we
should have given these observed frequencies of “A” and
“a”
Expected frequency of AA = p2 = 0.6 * 0.6 = 0.36
Expected frequency of aa = q2 = 0.4*0 .4 =0.16
Expected frequency of Aa = 2pq = 2*.6*.4 = 0.48
Step 2 Calculate expected
number of each genotype
Convert genotype frequencies to actual
numbers by multiplying by population size
of 100
AA = 0.36*100 = 36
aa = 0.16*100 = 16
Aa = 0.48*100 = 48
Step 3 Compare Observed and
Expected values
Observed population is:
44 AA 32 Aa 24 aa
Expected population is:
36AA 48Aa 16aa
These numbers are not the same so the population is
not in Hardy-Weinberg equilibrium. An
assumption of the Hardy Weinberg equilibrium is
being violated. What are those assumptions?
Hardy-Weinberg Equilibrium
Remember that the Hardy-Weinberg
equation tells us what we would expect to
find if alleles are simply randomly assorted
into gametes and gametes come together
randomly to produce new genotypes.
If a population is found to depart
significantly from H-W equilibrium this is
strong evidence that evolution is taking
place, i.e., the gene pool of the population is
changing.
Hardy-Weinberg Equilibrium
Five Conditions under which HardyWeinberg equilibrium holds:
No gene flow – no migration.
Random mating – no inbreeding.
No mutations.
Large population size – reduces effects of
chance events
No natural selection.
Gene flow
Movement of individuals between
populations can alter gene frequencies in
both populations.
Frequent migration may cause populations’
gene pools to become more similar to each
other.
Non-random mating
Mating preferentially with others that are
phenotypically similar to you [in extreme
cases inbreeding (mating with relatives)]
can prevent random mixing of genes
Homozygotes are common in inbred
populations.
Inbreeding in California Sea
Otters
Because inbreeding produces an excess of
homozygotes in a population, deviations
from Hardy-Weinberg expectations can be
used to detect such inbreeding in wild
populations.
Inbreeding in California Sea
Otters
Sea otters, once abundant along the west
coast of the U.S., were almost wiped out by
fur hunters in the 18th and 19th centuries.
photo: www.turtletrack.org
Inbreeding in California Sea
Otters
• California population reached a low of 50
individuals (now over 1,500). As a result of
this bottleneck, the population has less
genetic diversity than it once had.
Inbreeding in California Sea
Otters
Population is still at a low density and
Lidicker and McCollum (1997) investigated
whether this resulted in inbreeding.
They determined genotypes of 33 otters for
PAP locus, which has two alleles S (slow)
and F (fast)
Inbreeding in California Sea
Otters
The genotypes of the 33 otters were:
SS 16
SF 7
FF 10
This gives approximate allele frequencies of
S= 0.6 and F = 0.4
Inbreeding in California Sea
Otters
If otter population in H-W equilibrium,
genotype frequencies should be
SS = 0.6* 0.6 = 0.36
SF =2*0.6*0.4 = 0.48
FF = 0.4*0.4 = 0.16
However actual frequencies were:
SS= 0.485, SF= 0.212, FF =0.303
Inbreeding in California Sea
Otters
There are more homozygotes and fewer
heterozygotes than expected for a random mating
population.
Having considered alternative explanations for
deficit of heterozygotes, Lidicker and McCollum
(1997) concluded that sea otter populations show
evidence of inbreedng.
Mutation
Mutation adds new genes, but generally so
slowly that H-W equilibrium not affected.
However, mutation and sexual
recombination ultimately responsible for the
variation that natural selection depends on.
Mutations
Mutations are randomly occurring changes in the
DNA.
Only mutations that occur in cell lines that
produce gametes [i.e. the sex cells – sperm and
egg] can be passed on.
Simplest mutation is a point mutation in which
one base is changed or a base is inserted or
deleted.
Mutations
Changing a base may have no effect if the base
change does not change the amino acid coded for
or if the change occurs in a non-coding section of
the gene.
However, some changes alter the amino acid
coded for and hence the protein produced (e.g. as
occurs in sickle cell anemia), which can have
severe effects.
Insertion/deletion mutations
In insertion/deletion mutations a base is
added or deleted, which because bases are
read in groups of three shifts the “reading
frame” so that all sequences after the
mutation are misread, being off by one base.
This almost always produces a nonfunctional protein
Mutations that alter gene number or
sequence
Gene duplication is an important source of
variation.
In gene duplication a section of DNA may be
copied and inserted elsewhere in the genome.
Often these cause major problems, but sometimes
they do not and the overall number of genes is
increased. And the new genes can take on novel
functions through mutation and selection
Mutations that alter gene number or
sequence
Humans have about 1,000 olfactory
receptor genes and mice about 1,300. These
appear all to have been derived from a
single ancestral gene.
In humans about 60% of these are turned
off, but in mice only about 20% are turned
off.
Sexual Recombination
In the process of meiosis alleles are
reshuffled as parental chromosomes
exchange portions.
This process produces new combinations of
alleles in the sex cells produced in meiosis.
In addition, the combining of sperm and
egg also produces new combinations of
alleles.
How populations’ gene pools are
altered
Natural Selection: as discussed previously
selection for or against allele can cause its
frequency to change quickly from one
generation to the next.
However, natural selection is not the only
way allele frequencies can change. Chance
often plays a role.
Genetic drift
Fluctuations in allele frequencies that result
from chance are referred to as genetic drift.
Chance effects are strongest when
populations are small. In a small
population it is easy for alleles to be lost or
become fixed as a result of chance events.
Large population size
If populations are small, chance events can
have a large effect on allele frequencies.
These chance events can cause the genetic
structure to randomly change from one
generation to the next. This random change
is called Genetic Drift.
Genetic Drift: events that reduce
population size
Genetic drift is most likely to affect
populations after events that greatly reduce
population size.
Two of the most common are Bottleneck
Events and Founder Events
Bottleneck Effect
A bottleneck effect occurs when some disaster
causes a dramatic reduction in population size.
As a result, by chance certain alleles may be
overrepresented in the survivors, while others are
underrepresented or eliminated. Genetic drift
while the population is small may lead to further
loss or fixation of alleles.
Bottleneck Effect
Humans have been responsible for many
bottlenecks by driving species close to extinction.
For example, the Northern Elephant seal
population was reduced to about 20 individuals in
the 1890’s. Population now >30,000, but an
examination of 24 genes found no variation, i.e. in
each case there was only one allele. Southern
Elephant Seals in contrast show lots of genetic
variation.
23.8
Founder Effect
When populations are founded by only a
few individuals (as island communities
often are) the gene pool is unlikely to be as
diverse as the source pool from which it
was derived.
Founder Effect
Founder effect coupled with inbreeding explains
the high incidence of certain recessive diseases
among humans in many isolated communities.
For example, polydactylism (having extra fingers)
is quite common among the Amish and retinitis
pigmentosa a progressive form of blindness is
common among the residents of Tristan da Cunha.
Natural Selection
Natural selection is generally the main
reason populations will deviate from H-W
equilibrium.
With natural selection certain alleles are
selected against or for and so are are rarer or
more common than would otherwise be
expected in the next generation.
Natural Selection the primary
mechanism of adaptive evolution
Terms such as “survival of the fittest” and
“struggle for existence” do not necessarily mean
there is actual fighting for resources.
Competition is generally more subtle and success
in producing offspring and thus contributing genes
to the next generation (i.e. fitness) may depend on
differences in ability to gather food, hide from
predators, or tolerate extreme temperatures, which
all may enhance survival and ultimately
reproduction
Natural Selection the primary
mechanism of adaptive evolution
Three major forms of natural selection:
Directional
Disruptive
Stabilizing
Directional Selection
Favors one extreme in the population
Average value in population moves in that
direction
E.g. Selection for darker fur color in an area
where the background rocks are dark
Disruptive selection
Intermediate forms are selected against.
Extremes are favored
E.g. Pipilo dardanus butterflies. Different
forms of the species mimic the coloration of
different distasteful butterflies.
Crosses between forms are poor mimics and
so are selected against by being eaten by
birds.
Stabilizing Selection
Commonest form
Extreme forms are selected against
Birth weights in human babies. Highest
survival is at intermediate birth weights.
Babies that are too large cannot fit through
the birth canal, babies that are born too
small are not well developed enough to
survive
Natural selection acts on individuals, but
its effects accumulate in populations
Individuals live or die during a the selection
event.
But change occurs in the characteristics of the
population, not in individuals.
Natural selection acts on individuals,
its effects accumulate in populations
During a drought on the Galapagos
individual ground finch’s beaks did not
change, but the populations’ average beak
dimensions changed because more smallbeaked birds died than large-beaked birds.
Natural selection does not plan
ahead.
Each generation is result of selection by
environmental conditions of the previous
generation.
Evolution always one generation behind
environmental changes.
New traits evolve even though
selection acts on existing traits.
This occurs because:
1. mutation produces new alleles.
2. In sexually reproducing organisms meiosis
and fertilization recombine existing alleles to
produce new genotypes.
New traits evolve even though
selection acts on existing traits.
Artificial selection for oil content in corn.
After 60 generations oil levels were well
above starting values.
Fig 3.12
Important points about evolution
and natural selection
The fundamental unit of natural selection is
the gene.
Only genes are passed on from one
generation to the next.
Important points about evolution
and natural selection
Nothing in nature happens for “the good of
the species.”
Alleles that sacrifice themselves would
disappear from the gene pool.
Important points about evolution
and natural selection
Organs must be useful at all stages of their
evolutionary history
Structures cannot pass through intermediate
stages where they make an organism less
well adapted.
Important points about evolution
and natural selection
Natural selection cannot fashion perfect
organisms for several reasons
1. Evolution is limited by historical
constraints. Birds cannot run around on
four legs because their forelimbs have
evolved into wings.
Important points about evolution
and natural selection
Natural selection cannot fashion perfect organisms
for several reasons
2. Adaptations are often compromises.
Auks (a group of seabirds that includes puffins)
can fly and use their wings to swim underwater,
but the shape and size of the wing is a compromise
between the demands of flight and swimming.
Little Auk
Razorbill
polar.alaskapacific.edu/aharding/images/Littl...
http://media-2.web.britannica.com/eb-media/16/26016-004-13D8FA4C.jpg
Important points about evolution
and natural selection
Natural selection cannot fashion perfect
organisms for several reasons
3. Selection can only make use of the
material that is available. New alleles do
not arise on demand.