Foundations of Biological Sciences I Evolutionary Agents - 1 A quick recap…. There are several terms that need to be clarified so that you can more easily follow the exercise. A gene is a piece of DNA that directs the expression of a particular characteristic (trait). Genes are located on chromosomes, and the location where a particular gene is found is referred to as the locus (plural: loci) of that gene. An allele is a gene for which there is an alternative expression, which can lead to the alterative form of a trait. For example, a diploid organism carries the allele “A” on one homologous chromosome, and the allele “A” on the other. The genotype of this organism is then AA and it is said to be homozygous. An organism may also carry two different alleles. For example on one chromosome it could carry the allele “A” and on the other it could carry the allele “a”. The genotype of such an organisms is then Aa, and it is described as heterozygous for this chromosomal locus. The genotype of an organism is the listing of the two alleles for each trait that it possesses. The phenotype of an organism is a description of the way a trait is displayed in the structure, behavior, or physiology of the organism. Some alleles are dominant to others and mask the presence of other alleles. The dominant condition is indicated by uppercase letters (e.g., “A”). The alleles that are masked are called recessive alleles. The recessive condition is indicated by lowercase letters (e.g., “a”). When both dominants are present in the genotype (AA), the organism is said to be homozygous dominant for the trait, and the organisms will show the dominant phenotype (trait expression A). When both recessives are present in the genotype (aa), the organism is said to be homozygous recessive for the trait, and the organisms will show the recessive phenotype (trait expression a). In the case of complete dominance, the dominant allele completely masks the recessive allele, and an organism with a heterozygous genotype (Aa) will show the dominant phenotype (trait expression A). Evolutionary Agents Evolution is a process resulting in changes in gene frequencies (= the genetic make-up) of a population over time. The mechanisms of evolution include selection (which can cause change over time & adaptation), and forces that provide variation and cause change over time (but not adaptation). Factors that change gene frequencies over time are referred to as evolutionary agents. A powerful way to detect the presence of evolutionary agents is the use of the Hardy–Weinberg model. This model can be applied to traits that are influenced by several loci; the simplest case is for a trait that is regulated by one locus with two alleles. With the Hardy–Weinberg model, the frequency of genotypes in the population can be predicted from the probability of encounters between gametes bearing the different alleles. With alleles R .

1. Foundations of Biological Sciences I Evolutionary Agents - 1
A quick recap….
There are several terms that need to be clarified so that you can
more easily follow the exercise. A gene is a
piece of DNA that directs the expression of a particular
characteristic (trait). Genes are located on
chromosomes, and the location where a particular gene is found
is referred to as the locus (plural: loci) of that
gene. An allele is a gene for which there is an alternative
expression, which can lead to the alterative form of a
trait. For example, a diploid organism carries the allele “A” on
one homologous chromosome, and the allele “A”
on the other. The genotype of this organism is then AA and it is
said to be homozygous. An organism may also
carry two different alleles. For example on one chromosome it
could carry the allele “A” and on the other it
could carry the allele “a”. The genotype of such an organisms is
then Aa, and it is described as heterozygous for
this chromosomal locus.

2. The genotype of an organism is the listing of the two alleles for
each trait that it possesses. The phenotype of an
organism is a description of the way a trait is displayed in the
structure, behavior, or physiology of the organism.
Some alleles are dominant to others and mask the presence of
other alleles. The dominant condition is indicated
by uppercase letters (e.g., “A”). The alleles that are masked are
called recessive alleles. The recessive condition
is indicated by lowercase letters (e.g., “a”). When both
dominants are present in the genotype (AA), the organism
is said to be homozygous dominant for the trait, and the
organisms will show the dominant phenotype (trait
expression A). When both recessives are present in the genotype
(aa), the organism is said to be homozygous
recessive for the trait, and the organisms will show the
recessive phenotype (trait expression a). In the case of
complete dominance, the dominant allele completely masks the
recessive allele, and an organism with a
heterozygous genotype (Aa) will show the dominant phenotype
(trait expression A).
Evolutionary Agents
Evolution is a process resulting in changes in gene frequencies

3. (= the genetic make-up) of a population over
time. The mechanisms of evolution include selection (which can
cause change over time & adaptation), and
forces that provide variation and cause change over time (but
not adaptation). Factors that change gene
frequencies over time are referred to as evolutionary agents.
A powerful way to detect the presence of evolutionary agents is
the use of the Hardy–Weinberg model. This
model can be applied to traits that are influenced by several
loci; the simplest case is for a trait that is regulated
by one locus with two alleles.
With the Hardy–Weinberg model, the frequency of genotypes in
the population can be predicted from the
probability of encounters between gametes bearing the different
alleles. With alleles R and B occurring at
frequencies p and q, respectively, the frequency of genotypes in
the population is described by the formula:
p
2
+ 2pq + q
2

4. = 1
Hardy-Weinberg
equilibrium
If p is the frequency of one allele, and q
is the frequency of the other allele, then:
p + q = 1
Foundations of Biological Sciences I Evolutionary Agents - 2
If certain conditions are met, the proportions of genotypes that
make
up a population remain constant from generation to generation,
and
can be predicted from the Hardy-Weinberg equilibrium.
For example, if flower color is controlled by two alleles (R &
B),
and the allele for red color is present in the population 80% of
the

5. time, than the other allele for blue color must be present 20% of
the
time. Consequently, the allele frequencies in the population are
p =
0.8 and q = 0.2. (0.8 + 0.2 = 1).
From this we can calculate the expected genotype frequencies in
the
population. Since p = 0.8, we would expect 64% of the flowers
in
the populations to be homozygous for red flower color
(expected
genotype frequency for p
2
= 0.8 x 0.8 =0.64). 32% of the
populations would be heterozygous for flower color. They
would
have one R allele (p = 0.8) and one B allele (q = 0.2), and if
neither
allele were dominant they would appear purple. The expected
genotype frequency of these purple individuals is 2pq = 2 x 0.8
x 0.2
= 0.32. Finally, 4% of the population would be homozygous for
the

6. blue flower color (q
2
= 0.2 x 0.2 = 0.04).
The Hardy–Weinberg model applies
when the following conditions are met:
1) No genetic drift
2) No selection
3) No mutation
4) No migration
By contrast, there will be change in gene
frequencies in a population when at least
one of these conditions occur:
1) Genetic drift
2) Selection
3) Mutation
4) Migration

7. In today’s lab, you will do a series of exercises that illustrate
the effect of the different evolutionary agents on the
genetic structure of a model population. You will work with
populations composed of individuals that are
represented by colored beads. White beads represent individuals
that are homozygous for the white allele (WW);
red beads are individuals that are homozygous for the red allele
(RR), and pink beads are heterozygous (WR).
These beads live in a habitat – a plastic dishpan filled with
smaller beads. The larger beads of our population will
be retained by the mesh, while the smaller beads pass through
the mesh.
When the individuals are recovered with the help of the mesh,
the frequencies of the color alleles are determined
using the Hardy-Weinberg model. The alleles in our populations
are codominant – each white individual
possesses two white alleles, each red individual two red alleles,
and the pink individuals have one red and one
white allele. Consequently, the total number of color alleles in a
population of 40 individuals is 80. If such a
population contains 10 white individuals, 20 pink individuals,
and 10 red individuals, the frequency of white
alleles (p) is

8. (2 x number white beads) + number pink beads
p = ----------------------------------------------------------------
(2 x number of beads total)
(2 x 10) + 20
p = ----------------------- = 0.5
80
Because p + q = 1, the frequency of the red allele (q) must also
be 0.5.
1. NAT URAL S E L E CT I O N
Natural selection disturbs the Hardy-Weinberg equilibrium by
discriminating between individuals with respect to
their ability to survive and reproduce. Individuals that are better
at surviving to produce young will contribute
more genes to the next generation; they are said to have greater
fitness than those individuals that leave no or
fewer offspring.
In this experiment you will test the hypothesis that individuals

9. are more likely to survive and reproduce when
their coloration makes it easier to hide from predators in the
environment.
Foundations of Biological Sciences I Evolutionary Agents - 3
1. Work in groups of four. Each group member assumes one of
the following roles
Predator: Search for prey (large beads)
Data Recorder / Timer: record numerical results and time the
predation sessions
Calculator: use a calculator to calculate the allele frequencies
Caretaker: look after and manipulate the experimental setup
2. Create a white habitat by filling the dishpan with small white
beads. Establish an initial population by
adding 10 large white beads, 20 large pink beads and 10 large
red beads into the habitat. “Hide” the
individuals in the habitat by mixing the large and small beads.
The predator will prey on the large beads,
removing as many individuals as possible in a set amount of
time. The survivors will reproduce a new

10. generation, upon which the predator will prey again. This cycle
will be repeated several times. Make a
prediction as to how the frequency of red alleles in the
populations will change over time.
Prediction:
3. The predator hunts for prey (large beads) in the habitat, and
uses the pair of forceps to catch as many prey
items as possible in 30 seconds.
4. After the predation (selection) episode, strain the habitat with
the sieve and count the remaining red, pink
and red individuals. Record the numbers in the second row in
Table 1. Calculate the frequencies of the white
(p) and red (q) alleles remaining in the population, and record
them in Table 2 (under First generation). For
example, if 6 white, 8 pink and 8 red individuals remain, the
frequency of the white alleles is
To calculate p, use the observed numbers of each color within
the formula:
(2 x number white beads) + number pink beads
p = --------------------------------------------------------

11. (2 x number of beads total)
(2 x 6) + 8
p = ----------------------- = 0.45
44
Table 1: Large- Bead counts before and after four rounds of
Natural Selection (Predation)
Population
White Beads
Pink Beads
Red Beads
Total Beads
Initial
Before 10 20 10 40
After

12. Second Generation
Before
After
Third Generation
Before
After
Fourth Generation
Before
After
Foundations of Biological Sciences I Evolutionary Agents - 4
Table 2: Allele and genotype frequencies due to Natural
Selection (Predation)
Population p q p
2
2pq q

13. 2
Initial 0.5 0.5 0.25 0.5 0.25
First Generation
Second Generation
Third Generation
Fourth Generation
5. Based on the new values (after selection) for allele
frequencies, calculate the genotype frequencies for the
homozygous white (p
2
) and red (q
2
) individuals, and for the heterozygous pink individuals (2pq).
Record the
new allele frequencies in Table 2. For example, if p now equals
0.43, the frequency of the homozygous
white individuals is
p
2

14. = (0.48)
2
= 0.23
6. Assuming that 40 individuals comprise the next and all
succeeding generations, calculate the number of
white, red and pink individuals to create the next generation,
and record the numbers in the Before row
under Second generation in Table 1. For this, and all future
calculations, round up or down to the nearest
whole number. For example, if p
2
=0.23, the number of white individuals for the next generation
is
p
2
x 40 = 0.23 x 40 = 9.2 or 9 white individuals
7. Calculate the numbers of white, red and pink individuals you
need to construct the new generation, and
introduce them into the habitat for a new round of selection.
8. Repeat the selection and reproduction steps for three more
rounds, filling in the remaining rows in Tables 1
and 2. When you are done, use the frequencies of the red allele

15. from Table 2 to construct a histogram in the
appropriate space in Figure 1 below. Remember to label your
axes and complete the figure caption.
Figure 1: Changes in frequency of the red allele (q) due to
selection.
................................................................................

16. ...............................................................................................
...............................................................................................
.........
...............................................................................................
...............................................................................................
.........
0 1 2 3 4
1.0
0.5

17. 0.0
Foundations of Biological Sciences I Evolutionary Agents - 5
What is your conclusion as to the prediction you made in point
2?
There are 3 different patterns of selection. Directional selection
favors one extreme phenotype over the other and
causes allele frequencies to change in a predictable direction.
Stabilizing selection favors an intermediate
phenotype, rather than one at the extremes. Disruptive selection
disfavors intermediate phenotypes, and favors
the extreme ones. Which kind of selection is illustrated by
predation of white, pink and red individuals in a white
habitat?
If two identical populations inhabited different environments
(e.g. white and red habitats), how would the
frequency of the color genes in each habitat compare after a
large number of generations?

18. When two populations become genetically different through
time (divergence), individuals can lose the ability
to interbreed, and two new species are formed. This process is
called speciation.
2. EFFECT OF GENE FLOW ON NATURAL SELECTION
New members may join populations (immigrations) or leave the
population (emigration). As they do, the
frequencies of alleles in the population change. This gene flow
due to migration can be a powerful force in
evolution.
1. Establish a new population as described in the previous
section.
2. Begin the selection process as before, but this time 5 red
individuals will immigrate into the population
before the new allele frequencies are determined. Write down a
prediction of the hypothesis that gene flow
resulting from migration of individuals into a population
undergoing predation affects the change in allele
frequencies expected from selection alone. Focus your

19. prediction on the change in the frequency of red
alleles in the population.
3. Conduct 4 cycles of predation with migration. For each
generation, write down the number of surviving
individuals in Table 3, and the allele frequencies in Table 4.
When you are done, use the frequencies of the
red allele from Table 4 to construct a histogram as your
homework.
Homework: Write a hypothesis and prediction for this
evolutionary model based on your understanding of
gene flow. Create a histogram that displays the change through
four generations of natural selection with
migration. Remember to include a figure caption and axis labels
(10 pts). *Hint: see Figure 1
Foundations of Biological Sciences I Evolutionary Agents - 6
Table 3:
Large- Bead counts before and after four rounds of simulated
Natural Selection and Gene Flow
Population

20. White Beads
Pink Beads
Red Beads
Total Beads
Initial
Before 10 20 10 40
After (First Gen) (survivors + 5)
Second Generation
Before
After (survivors + 5)
Third Generation
Before _________ _________ __________
_________

21. After _________ _________ (survivors + 5)
Fourth Generation
Before _________ _________ __________
_________
After _________ _________ (survivors + 5)
Table 4: Allele and Genotype frequencies due to Natural
Selection and Gene Flow
Population p q p
2
2pq q
2
Initial
First Generation
Second Generation
Third Generation
Fourth Generation
How did migration influence the effectiveness of selection in
this example?

22. If white individuals would have immigrated into the population
instead of the red ones – how would this have
influenced the change in gene frequencies?
Through immigration, new genetic information is introduced
into the population. Gene flow thus maintains
genetic variation in a population. Barriers to gene flow can
decrease genetic variation within populations, and
also accelerate divergence between populations.
Foundations of Biological Sciences I Evolutionary Agents - 7
3. MUTATION
New genetic information can also be introduced into a
population through mutation.
1. Establish a new population by placing 10 large white beads,
10 large red beads and 20 large pink beads in
the bowl. Do not add the small beads this time.
2. Designate one group member to pick 20 large beads from the

23. bowl (without looking!). Use these 20 beads to
establish a new generation. Then replace one white bead with a
silver bead. This represents a mutation in the
gamete that one parent contributes to this generation.
3. Calculate the allele frequencies of the new generation,
including the frequency of the new color allele (r),
and write them down in Table 5.
Table 5: Change in Allele Frequencies due to Mutation
Population p
q
r
Initial
New Generation
After the mutation, three alleles are present in the population (p
+ q + r = 1). Consequently, the Hardy-Weinberg
equation must be expanded to

24. p
2
+ 2pq + q
2
+ 2pr + 2qr + r
2
= 1.0.
In addition to white, pink and red phenotypes, there are now
silver, silver-red, and in subsequent generation
potentially black phenotypes. If the next generation contains 50
individuals, how many offspring of each
phenotype would be found in the population? Use Table 6 to
calculate the genotype and phenotype frequencies.
Table 6: Phenotypes two generations after a mutation
Phenotype Genotype Frequency
x 50
# Individuals
White p
2

25. Pink 2pq
Red q
2
Silver 2pr
Silver-Red 2qr
Black r
2
Imagine a population made up of individuals of the color
phenotypes in these proportions. What effect will
natural selection have on the phenotypes in a white habitat?
Under which conditions would a rare black allele be favored?
Foundations of Biological Sciences I Evolutionary Agents - 8
4. GENETIC DRIFT
Gene frequencies can change over generations as a result of

26. chance (Genetic Drift). Genetic drift is often a
problem for small populations, because it can result in a loss of
genetic variability. In very small populations,
chance can even eliminate an allele from a population.
1. Establish a new population by placing 10 large white beads,
10 large red beads and 20 large pink beads in
the bowl. Do not add the small beads this time.
2. If all 40 members of this population have an equal chance of
getting to reproduce, the allele frequencies for
the colors in the population are p = 0.5 and q = 0.5 (see first
column of Table 7).
3. Now let’s see what happens when only a subset of the
population gets a chance to reproduce. Choose,
without looking, 10 beads from the bowl. They will make up a
small group of individuals that reproduce.
Record the allele frequencies in this cluster in the second
column of Table 7.
4. Replace the 10 beads to the population and mix well. Then
pick 30 new beads. They represent a larger group
of individuals that get to reproduce. Calculate the allele
frequencies in this group, and add them to the third
column in Table 7.

27. Table 7: Allele frequencies resulting from Genetic Drift
Observed Frequency in
Expected Frequency Small Group Large Group
n
40
p
0.5
q
0.5
Compare the allele frequencies of the three groups of
reproducing individuals. How does group size affect the
makeup of the next generation?
When members of an old population emigrate to establish a new
population, the allele frequencies in the new

28. population can be heavily influenced by chance.
5. Reestablish the old 10/20/10 beads population you have
worked with before. Then pick (without looking) 6
individuals which will represent the 6 founding members of a
new population.
6. Move these individuals to a new habitat. Calculate the allele
frequencies and record them in Table 8.
Table 8: Allele Frequencies in a Founder Population
Allele Frequency
Initial population Founder Population
p
0.5
q
0.5
How do the allele frequencies of the small founder population

29. compare to the larger original population?