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 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

= 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

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

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

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

(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 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

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 = ——————————————————–

(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

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 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

= (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 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. ……………………………………………………………………..

……………………………………………………………………………………………………………………………………………………………………………….

……………………………………………………………………………………………………………………………………………………………………………….

0 1 2 3 4

1.0

0.5

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?

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 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

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 _________ _________ __________ _________

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?

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 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

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

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 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.

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

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 compare to the larger original population?