Download LAB 14 API LAB 2 Hardy

AP Biology
Lab 2, Evolution of Populations
Background (Chapter 23)
Humans contain their genetic information coded as genes found within a set of
46 chromosomes. These chromosomes are arranged into 23 homologous pairs. During
meiosis each pair of homologues separates to form haploid gametes. Each person
inherits one chromosome in each of the 23 pairs from their mother and one from their
father. Each gene allele can be thought of as having two different forms, dominant or
recessive. The gene pool is the sum distribution of these different alleles in a
population.
In 1908, G. H. Hardy and W. Weinberg independently suggested a scheme
whereby evolution could be viewed as changes in the frequency of alleles in a
population of organisms. In this scheme, if A and a are alleles for a particular gene locus
and each diploid individual has two such loci, then p can be designated as the frequency
of the A allele and q as the frequency of the a allele. Thus, in a population of 100
individuals (each with two loci) in which 40% of the alleles are A, p would be 0.40. The
rest of the alleles (60%) would be a, and q would equal 0.6 (i.e., p + q = 1.0). These are
referred to as allele frequencies. The frequency of the possible diploid combinations of
these alleles (AA, Aa, aa) is expressed as p2 + 2 pq + q2 = 1.0. Hardy and Weinberg also
argued that if five conditions are met, the population’s allele and genotype frequencies
will remain constant from generation to generation. These conditions are as follows:
1. The breeding population is large. (The effect of chance on
changes in allele frequencies is thereby greatly reduced.)
2. Mating is random. (Individuals show no mating preference for a
particular phenotype.)
3. There is no mutation of the alleles.
4. No differential migration occurs. (No immigration or emigration.)
5. There is no selection. (All genotypes have an equal chance of
surviving and reproducing.
The Hardy-Weinberg equation describes an existing situation. If the five conditions are
met, then no change will occur in either allele or genotype frequencies in the
population. Of what value is such a rule? It provides a yardstick by which changes in
allele frequency, and therefore evolution, can be measured. One can look at a
population and ask: Is evolution occurring with respect to a particular gene locus? Since
evolution is difficult (if not impossible) to observe in most natural populations, we will
model the evolutionary process using the class as a simulated population. The purpose
of this simulation is to provide an opportunity to test some of the basic tenets of
population genetics and evolutionary biology.
OBJECTIVES
Before doing this laboratory you should understand:
Page 1 of 9
AP Lab 2, Evolution2015
 how natural selection can alter allelic frequencies in a population;
 the Hardy-Weinberg equation and its use in determining the frequency of alleles in a
population; and
 the effects on allelic frequencies of selection against the homozygous recessive or
other genotypes.
After doing this laboratory you should be able to:
 calculate the frequencies of alleles and genotypes in the gene pool of a population
using the Hardy-Weinberg formula, and
 discuss natural selection and other causes of microevolution as deviations from the
conditions required to maintain Hardy-Weinberg equilibrium.
EXERCISE 1: Estimating Allele Frequencies for a Specific Trait within a Sample
Population
Using the class as a sample population, the allele frequency of a gene controlling the
ability to taste the chemical PTC (phenylthiocarbamide) could be estimated. A bittertaste reaction to PTC is evidence of the presence of a dominant allele in either the
homozygous condition (AA) or the heterozygous condition (Aa). The inability to taste the
chemical at all depends on the presence of homozygous recessive alleles (aa). (Instead
of PTC tasting, other traits, such as tongue-rolling, may be used.) To estimate the
frequency of the PTC-tasting allele in the population, one must find p. To find p, one
must first determine q (the frequency of the nontasting PTC allele), because only the
genotype of the homozygous recessive individuals is known for sure (i.e., those that
show the dominant trait could be AA or Aa).
Procedure
1. Using the PTC taste-test papers provided, tear off a short strip and press it to your
tongue tip. PTC tasters will sense a bitter taste. For the purposes of this exercise these
individuals are considered to be tasters.
2. A decimal number representing the frequency of tasters (p2 + 2pq) should be
calculated by dividing the number of tasters in the class by the total number of
students in the class. A decimal number representing the frequency of nontasters (q 2)
can be obtained by dividing the number of nontasters by the total number of
students. You should then record these numbers in Table 2.1.
3. Use the Hardy-Weinberg equation to determine the frequencies (p and q) of the two
alleles. The frequency q can be calculated by taking the square root of q 2. Once q has
been determined, p can be determined because 1 - q = p. Record these values in
Table 2.1 for the class and also calculate and record values of p and q for the North
American population.
Table 2.1: Phenotypic Proportions of Tasters and Nontasters and Frequencies of the
Determining Alleles
Phenotypes
Tasters
(p2+2pq)
Class Population
North American
Population
#
%
0.55
Nontasters
(q2)
#
Allele Frequency Based on the
Hardy WeinbergEquation
p
q
%
0.45
Page 2 of 9
AP Lab 2, Evolution2015
e
1. What is the percentage of heterozygous tasters (2 pq) in your class?
2. What percentage of the North American population is heterozygous for the trait?
EXERCISE 2: Case Studies
CASE A (A Test of an Ideal Hardy-Weinberg Population)
The entire class will represent a breeding population, In order to ensure random mating,
choose another student at random. In this simulation, we will assume that gender and
genotype are irrelevant to mate selection.
The class will simulate a population of randomly mating heterozygous individuals with
an initial gene frequency of 0.5 for the dominant allele A and the recessive allele a and
genotype frequencies of 0.25AA, 0.50Aa, and 0.25aa. Your initial genotype is Aa. Record
this on the data page. Each member of the class will receive four cards. Two cards will
have A and two cards will have a. The four cards represent the products of meiosis. Each
“parent” contributes a haploid set of chromosomes to the next generation.
1. Hold the cards behind your back, shuffle them, and take one card to contribute to the
production of the first offspring. Your partner should do the same. Put the two cards
together. The two cards represent the alleles of the first offspring. Record the genotype
of this offspring in your journal. Each student pair must produce two offspring, so all
four cards must be reshuffled and the process repeated to produce a second offspring.
2. The very short reproductive career of this generation is over. You and your partner
now become the next generation by assuming the genotypes of the two offspring. That
is, student 1 assumes the genotype of the first offspring and student 2 assumes the
genotype of the second offspring.
3. Obtain, if necessary, new cards representing the alleles in his or her respective
gametes after the process of meiosis. For example, student 1 becomes genotype Aa and
obtains cards A, A, a, a; student 2 becomes aa and obtains cards a, a, a, a. Mate
randomly again with a new partner. Record your new genotype in your journal. Repeat
the procreation process for ten generations. At the end of each generation, remember
to record the genotype that you have assumed. Class data will be collected following ten
generations.
Allele Frequency: The allele frequencies, p and q, should be calculated for the
population after ten generations of simulated random mating.
Number of A alleles present at the tenth generation
Number of offspring with genotype AA ______ x 2 = _______A alleles
Number of offspring with genotype Aa ______ x 1 = _______A alleles
Total =_______A alleles
p = TOTAL number of A alleles
= __________
TOTAL number of alleles in the population
Page 3 of 9
AP Lab 2, Evolution2015
In this case, the total number of alleles in the population is equal to the number of
students in the class x 2.
Number of a alleles present at the tenth generation
Number of offspring with genotype aa ________x 2 = _______a alleles
Number of offspring with genotype Aa________x 1 = _______a alleles
Total = ______a alleles
q = TOTAL number of a alleles
= __________
TOTAL number of alleles in the population
1. What does the Hardy-Weinberg equation predict for the new p and q?
2. Do the results you obtained in this simulation agree? If not, why not?
3. What major assumption(s) were not strictly followed in this simulation?
CASE B (Selection- Lethal Allele)
In this Case, you will modify the simulation to make it more realistic. In the natural
environment, not all genotypes have the same rate of survival; that is, the environment
might favor some genotypes while selecting against others. An example is the human
condition, sickle-cell anemia. It is a disease caused by a mutation on one allele, in which
individuals who are homozygous recessive often do not survive to reach reproductive
maturity. For this simulation, you will assume that the homozygous recessive individuals
never survive (100 percent selection against), and that heterozygous and homozygous
dominant individuals survive 100 percent of the time.
The procedure is similar to that for Case A. Start again with your initial genotype, and
produce your “offspring” as in Case A. This time, however, there is one important
difference. Every time your “offspring” is aa, it does not reproduce. Since we want to
maintain a constant population size, the same two parents must try again until they
produce two surviving offspring. You may need to get new “allele” cards from the pool.
Proceed through ten generations, selecting against the homozygous recessive
offspring 100 percent of the time. Then add up the genotype frequencies that exist in
the population and calculate the new p and q frequencies in the same way as it was
done in Case A.
1. How do the new frequencies of p and q compare to the initial frequencies in Case A?
2. How has the allelic frequency of the population changed?
3. Predict what would happen to the frequencies of p and q if you simulated another
ten generations.
Page 4 of 9
AP Lab 2, Evolution2015
4. In a large population, would it be possible to completely eliminate a deleterious
recessive allele? Explain.
CASE C (Heterozygote Advantage)
From Case B, it is easy to see that the lethal recessive allele rapidly decreases in the
population. However, data from many human populations show an unexpectedly high
frequency of the sickle-cell allele in some populations. In other words, our simulation
does not accurately reflect the real situation; this is because individuals who are
heterozygous are slightly more resistant to a deadly form of malaria than homozygous
dominant individuals. In other words, there is a slight selection against homozygous
dominant individuals as compared to heterozygotes. This fact is easily incorporated into
our simulation. In this round, keep everything the same as in Case B, except that if your
offspring is AA, flip a coin. If heads, the individual does not survive, and if tails the
individual does survive.
Simulate ten generations, starting again with the initial genotype from Case A. The
genotype aa never survives, and homozygous dominant individuals only survive if the
coin toss comes up tails. Total the class genotypes and calculate the p and q frequencies.
1. Explain how the changes in p and q frequencies in Case II compare with Case A and
Case C.
2. Do you think the recessive allele will be completely eliminated in either Case B or
Case C?
3. What is the importance of heterozygotes (the heterozygote advantage) in
maintaining genetic variation in populations?
CASE D (Genetic Drift)
It is possible to use our simulation to look at the phenomenon of genetic drift in
detail. Divide the lab into several smaller “populations” (for example, a class of 30 could
be divided into 3 populations of 10 each) so that individuals from one isolated
“population” do not interact with individuals from another population. Now go through
ten generations as in Case I. Record the new genotypic frequencies, and calculate the
new frequencies of p and q for each population. If the class is small to begin with
genetic drift may already be a factor.
1. Explain how the initial genotypic frequencies of the populations compare.
2. What do your results indicate about the importance of population size as an
evolutionary force?
Page 5 of 9
AP Lab 2, Evolution2015
EXERCISE 3: Computer Population Models
Case Study: Evolution of a gene that fights HIV infections
CCR5 is a protein on the surface of white blood cells that is involved in the immune
system as it acts as a receptor for chemokines. This is the process by which T cells are
attracted to specific tissue and organ targets. Many forms of HIV, the virus that
causes AIDS, initially use CCR5 to enter and infect host cells. Certain individuals carry
a mutation known as CCR5-Δ32 in the CCR5 gene, protecting them against these strains
of HIV.
In humans, the CCR5 gene that encodes the CCR5 protein is located on the short arm
at position 21 on chromosome 3. Certain populations have inherited the Delta
32 mutation resulting in the genetic deletion of a portion of the CCR5 gene.
Homozygous carriers of this mutation are resistant to HIV-1 infection even after multiple
exposures. Individuals heterozygous for the gene have partial immunity and typically
once infected do not show the severity symptoms associated with individuals not
carrying the CCR5-Δ32 mutation (homozygous for the wild type CCR5 gene).
To model how the CCR5-Δ32 mutation can effect a population and how the HardyWeinberg model has application to the modern study of population dynamics you will
use a computer model called AlleleA1. The program need not be installed, only resident,
on the computer you are using in order to run. Exercises 3A – 3D are designed to
familiarize you with the use of the program; you will then use the program to explore
the population dynamics of the CCR5-Δ32 gene mutation.
Exercise 3-A (CASE A - Test of an Ideal Hardy-Weinberg Population)
This mirrors the first class exercise 2-Case A.
Open the program AlleleA1. Accept the defaults and select Run at the lower left side
of the window. The simulator will graph 500 generations of data for a unrestricted
population (infinite) with a starting gene frequency of A1 = 0.5 and A2 = 0.5. There is no
selection, no immigration, emigration. All criteria of the Hardy Weinberg equilibrium are
met. Unsurprisingly the final gene frequencies are the same as the initial frequencies.
Change the A1 frequency to 0.25 while leaving the other parameters the same.
Predict what the final A1 frequency will be. Record your prediction in your journal.
Select Run to see if your prediction is accurate. Include a printed screen shot of the
graph in your journal. Try an A1 frequency of 0.75 and predict the outcome before
running the model. If you have a good understanding of the Hardy Weinberg population
model your predictions and the actual results should agree.
Exercise 3-B (CASE B - Selection - Lethal Allele)
Reset the Allele Model to reflect the selection pressure represented in Case B of the
whole class exercise. Accept all default settings, then change the fitness settings so that
Page 6 of 9
AP Lab 2, Evolution2015
genotype A1A1 has a fitness of 1.0; A1A2 has a fitness of 1.0; and genotype A2A2 has a
fitness of 0.0. The fitness settings represent what % of offspring in each genotype
survive to produce offspring. Setting the fitness value of the A2A2 allele reflects the fact
that the allele is lethal in the homozygous state. Predict the outcome in your journal.
Run the model and then explain the results in your journal. Include a printed screen shot
of the graph in your journal.
Exercise 3-C (CASE C - Heterozygote Advantage)
Reset the Allele Model to reflect the selection pressure represented in Case C of the
whole class exercise. Accept all default settings, then change the fitness settings so that
genotype A1A1 survives to reproduce 50% of the time, genotype A1A2 survive at a rate
of 100%, and genotype A2A2 is lethal with a survivability of 0%. Predict the outcome in
your journal. Run the model and then explain the results in your journal. Include a
printed screen shot of the graph in your journal.
Exercise 3-D (CASE D – Genetic Drift)
Reset the Allele Model to reflect the small population size represented in Case D of
the whole class exercise. Accept all default settings, then change the Population size
setting to 100 individuals. You will run the model eight times. In order to retain each run
set the graph lines button option to multiple. Predict the outcome in your journal. Run
the model eight times. Each time you run the model select a different color for the
graph line. Explain the results in your journal. Include a printed screen shot of the graph
in your journal.
Case Study: Evolution of a gene that fights HIV infections
Now go back and reread the introduction to this section concerning the CCR5-Δ32
mutation. Some additional information for using the model is;
 Individuals homozygous for the CCR5-Δ32 mutation are effectively immune
from HIV infection.
 Individuals heterozygous for the wild type/mutant gene show a 50%
reduction in the CCR5 cell receptor on cell surfaces.
 Individuals homozygous for the wild type gene are 100% susceptible to HIV
infection.
 The CCR5-Δ32mutation can be tentatively traced back to a single mutation
event (one individual) occurring between 700 and 1500 years ago
 The CCR5-Δ32 gene currently has a frequency of approximately 10%.
 HIV arose in the human population somewhere around 1900 (approximately
5 generations ago)
Using the above information use the Allele program to model the selective pressure
required in order for the CCR5-Δ32 gene to have a 10% frequency in the current human
population. In truth you will have difficulty doing this since 5 generations is far too short
Page 7 of 9
AP Lab 2, Evolution2015
a time for any novel gene to attain a 10% frequency. Failing successful modelling of the
gene in five generations use the model to determine how many generations would be
required for it to establish a 10% frequency given the selective pressures present by the
HIV virus. Keep track of your research and findings in your journal. Develop and record
your own theory as to how the CCR5-Δ32 gene reached the current distribution in the
human population. Class, as well as the scientific community’s, theories will be
discussed in class.
Hardy-Weinberg Problems
Answer these in your journal
1. In Drosophila, the allele for normal length wings is dominant over the allele for
vestigial wings (vestigial wings are stubby little curls that cannot be used for flight). In
a population of 1,000 individuals, 360 show the recessive phenotype. How many
individuals would you expect to be homozygous dominant and heterozygous for this
trait?
2. The allele for the ability to roll one’s tongue is dominant over the allele for the lack of
this ability. In a population of 500 individuals, 25 percent show the recessive
phenotype. How many individuals would you expect to be homozygous dominant and
heterozygous for this trait?
3. The allele for the hair pattern called “widow’s peak” is dominant over the allele for
no “widow’s peak.” In a population of 1,000 individuals, 510 show the dominant
phenotype. How many individuals would you expect of each of the possible three
genotypes for this trait?
4. In the United States, about 16 percent of the population is Rh negative. The allele for
Rh negative is recessive to the allele for Rh positive. If the student population of a
high school in the U.S. is 2,000, how many students would you expect for each of the
three possible genotypes?
5. In certain African countries, 4 percent of the newborn babies have sickle-cell anemia,
which is a recessive trait. Out of a random population of 1,000 newborn babies, how
many would you expect for each of the three possible genotypes?
6. In a certain population, the dominant phenotype of a certain trait occurs 91 percent
of the time. What is the frequency of the dominant allele?
Page 8 of 9
AP Lab 2, Evolution2015
Data Sheet
CASE A(Hardy-Weinberg Equilibrium)
CASE C (Heterozygote Advantage)
Initial Class Frequencies:
Aa 100%
p = 0.5
q = 0.5
My Initial Genotype: Aa
Initial Class Frequencies:
Aa 100%
p = 0.5
q = 0.5
My Initial Genotype: Aa
F10 Genotype _____
Final Class Frequencies:
AA____Aa aa____
p _____
q _____
F10 Genotype _____
Final Class Frequencies:
AA
Aa
aa____
p _____
q _____
CASE B (Selection)
Initial Class Frequencies:
Aa 100%
p = 0.5
q = 0.5
My Initial Genotype: Aa
F10 Genotype _____
Final Class Frequencies:
AA
Aa
aa___
p _____
q _____
CASE D (Genetic Drift)
Initial Class Frequencies:
Aa 100%
p = 0.5
q = 0.5
My Initial Genotype: Aa
F10 Genotype _____
Final Class Frequencies:
AA____Aa aa____
p _____
q _____
Page 9 of 9
AP Lab 2, Evolution2015