Download Lab 7-POPULATION GENETICS

 7-­‐1 Biology 1001
Lab 7: POPULATION GENETICS
PREPARTION
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Read this exercise before you come to the laboratory.
Review the lecture notes from October 15 (Hardy-Weinberg Equilibrium)
OBECTIVES
At the end of this lab you should be able to:
1. Explain and define the terms population genetics, genetics, diploid, gene,
genotype, phenotype, allele, homozygote, and heterozygote.
2. Explain the difference between dominant and recessive alleles and how these
affect the phenotype (or survival) of an organism.
3. Apply the Hardy-Weinberg principle to populations and properly use the HardyWeinberg equation.
MATERIALS (per laboratory team)
Calculator
1 500-ml beaker
100 light-colored beads
100 dark-colored beads
10 toothpicks
INTRODUCTION
Population genetics is the study of allele frequency distribution and change
under the influence of four main evolutionary processes: 1) natural selection; 2) genetic
drift; 3) mutation and 4) gene flow. In other words, population genetics focuses on the
genetic composition of a population and how it changes with time.
Genetics is the science of genes, heredity and variation in living organisms.
Inheritance in organisms occurs by means of discrete traits called genes. In a diploid
organism (an organism with paired chromosomes) two homologous chromosomes
(i.e. two chromosomes with genes for the same characteristic at the same location or loci)
are inherited from the parents. One chromosome is from the mother and one from the
father. This allows for the possibility of two alleles (alternate versions of a gene or two
different forms of the DNA sequence) of each gene in an organism. Different DNA
sequences (alleles) can result in different traits, such as blue, brown or hazel eye color.
An organism’s genotype is its set of alleles (i.e. its genetic makeup). Observable
traits in an organism are its phenotype. If an organism receives two copies of the same
allele then this organism is homozygous at this gene locus. If an organism receives two
different alleles of a given gene then it is heterozygous at this gene locus. When
organisms are heterozygous at a gene locus, often one allele is called dominant as its
qualities dominate the phenotype of the organism, while the other allele is called
7-­‐2 recessive as its qualities recede and are not observed. For example, in humans the allele
for brown eyes (indicated by B) is dominant over the blue allele (indicated by b).
Therefore, BB homozygotes and Bb heterozygotes express a brown-eyed phenotype while
bb homozygotes express a blue-eyed phenotype. Co-dominance also occurs where the
contributions of both alleles (in heterozygous individuals) are visible in the phenotype of
an organism.
The Hardy-Weinberg principle states that both allele and genotype frequencies
in a population remain constant from generation to generation assuming certain
conditions are met.
Requirements for Hardy-Weinberg Equilibrium:
1. Very large population size
2. No gene flow (no movement of genetic material between populations)
3. No mutations
4. Random mating
5. No natural selection
The Hardy-Weinberg equation can be found below.
RESEARCH QUESTION
How do population size and natural selection influence gene frequencies?
EXERCISE 1: Modeling Genetic Drift
1.
Select 10 toothpicks to represent a population of 10 animals.
2.
Place 50 dark-colored beads and 50 light-colored beads into a beaker. These
represent genes in a gamete pool with allelic frequencies 0.5 A (p) and 0.5 a (q). Stir up
the beads to ensure random genetic recombination.
3.
Calculate expected frequencies of AA, Aa, and aa individuals, based on HardyWeinberg expectations. Multiply these expected frequencies by 10 and round off to the
nearest whole numbers to calculate how many AA, Aa and aa individuals to expect in
your population. Record these numbers in DATA TABLE 1 (pg 7-5)
p+q=1
p2+2pq+q2 =1
Where p=the frequency of allele A
q=the frequency of allele a
Therefore, the frequency of AA individuals is p2, the frequency of aa individuals is q2 and
the frequency of Aa individuals is 2pq.
4.
Without looking at the beaker, draw out two beads and slip them onto a
toothpick. If you draw two dark beads, this animal has genotype AA. Two light beads
means aa. One of each means Aa. Repeat this process, placing two beads on each of the
7-­‐3 10 toothpicks. How do your actual genotypic frequencies compare to the expected
frequencies calculated in step 3? Can you explain the reason for any discrepancies?
5.
Calculate gene frequencies in your population by counting “genes” in your
population of 10 animals: p = f(A) = (# dark beads)/20, and q = f(a) = (# light beads)/20.
Record your results for p and q in DATA TABLE 2 (pg 7-5).
6.
Take all of the beads off your 10 toothpicks, and generate a new gamete pool by
changing the ratio of light and dark beads in the beaker to match the p and q values you
calculate in step 5. Keep the size of the gamete pool constant at 100 beads, but take out
or put in beads to create the correct proportions. For example, if your population has
values p = 0.55 and q – 0.45, you would fill the beaker with 55 dark-colored beads and 45
light-colored beads. Since you started with 50 of each, return all beads to the beaker,
then take out five light-colored beads and replace them with five dark-colored ones to
make a new p = 55/100 and q = 45/100.
7.
Repeat steps 4 through 6 a total of 10 times to simulate 10 generations of genetic
drift. Record p and q values on the calculation page each time you recalculate them.
Since departures from original gene frequencies are random, you cannot predict which
way genetic drift will take your small population. If p becomes 1.00, we say that the A
gene has gone to fixation and the a gene to extinction. Fixation of the a gene could also
happen.
ASSIGNMENT: Based on this exercise answer questions 1 and 2 on page 7-7.
EXERCISE 2: Modeling Selection
In this simulation, we will assume that a is a recessive lethal gene. It causes no harm in
heterozygotes (Aa), but is fatal to aa individuals. Rather than a random change in gene
frequency, here we will see how natural selection against one allele can make a directional
change in gene frequencies.
1.
Select 10 toothpicks to represent a population of 10 animals as you did in the first
simulation.
2.
Begin the simulation, as you did in Exercise 1, with 50 dark-colored beads and 50
light-colored beads in the beaker. These represent genes in a gamete pool with allelic
frequencies 0.5 A and 0.5 a. Stir up the beads to ensure random genetic recombination.
3.
Draw two beads to place on each toothpick as you did before. Look at the
resulting genotypes. In this simulation, assume that aa genotypes produce a fatal genetic
illness. Since A is dominant, Aa individuals do not have this disease. Record frequencies
for all three genotypes in DATA TABLE 3 (pg 7-6), then remove the aa toothpicks to
represent selection against the aa genotype.
4.
Calculate p and q for the surviving population, record the p and q values in
DATA TABLE 4 (pg 7-6). This time,
7-­‐4 p = f(A) = (# dark beads)/(all beads in surviving animals), and
q = f(a) = (# light beads)/(all beads in surviving animals).
5.
Remove beads from toothpicks and refill the beaker with dark and light beads to
generate a gamete pool of 100 total beads, in the proportion of p and q that you just
calculated. Mix the beads thoroughly.
6.
Repeat steps 3 through 5 for 10 generations, record the p and q values each time.
ASSIGNMENT: Based on this exercise answer questions 3-5 on page 7-8.
7-­‐5 DATA TABLE 1: Exercise 1- Expected and observed genotypic frequencies
Generation Frequency of AA
Expected
Observed
Frequency of Aa
Expected Observed
1 (initial
generation)
2
3
4
5
6
7
8
9
10
DATA TABLE 2: Exercise 1- Gene frequencies
Generation
1 (initial
generation)
2
3
4
5
6
7
8
9
10
(f)A =p
0.5
(f)a =q
0.5
Frequency of aa
Expected Observed
7-­‐6 DATA TABLE 3: Exercise 2- Genotypic frequencies
Generation
1 (initial
generation)
2
3
4
5
6
7
8
9
10
Frequency of AA
Frequency of Aa
Frequency of aa
DATA TABLE 4: Exercise 2- Gene frequencies
Generation
1 (initial generation)
2
3
4
5
6
7
8
9
10
Frequency of A (p)
0.5
Frequency of a (q)
0.5
7-­‐7 ASSIGNMENT QUESTIONS (Handed in for marking)
1.
In horses, the genes for white coat color and red coat color are codominant.
Heterozygotes have a light red coloration, called roan. If you located a population of
wild mustangs in a valley that had 476 red horses (AA), 323 roan horses (Aa), and 51
white horses (aa), could you say the population is in Hardy-Weinberg equilibrium? First
calculate p and q, then use the Hardy-Weinberg formula to calculate expected genotypic
frequencies. Show all your calculations!
2.
Based on this exercise, you can explain why zoos go to so much trouble to
exchange rare animals such as tigers or gorillas rather than maintaining small separate
breeding populations?
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7-­‐8 3.
Most serious genetic diseases are caused by recessive alleles rather than dominant
alleles. Based on this exercise, can you explain why a recessive lethal gene could persist in
the population, while a dominant lethal gene could not?
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4.
Suppose your model of selection represents the change in frequency of plain white
coquina clams because predatory birds see and remove them more quickly from a beach
with dark-colored sand. If larval offspring from this population drift to a different beach
made of light-colored sand, could selection go the other way? What does this say about
fitness of a particular gene?
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5.
In this simulation, you sampled the gene pool without replacing beads in the
beaker after you drew each one. Thus, f(A) and f(a) in the gene pool changed slightly
after each bead was drawn. For example, if you begin with 50 light and 50 dark beads,
the probability of drawing a dark bead the first time is 50/100 = 0.500. The beaker
would then contain 49 dark beads and 50 light beads, so the probability of drawing a
second dark bead becomes 49/99 = 0.495. Does this make your simulation slightly less
realistic? In small natural populations, does one mating change the gene pool available
for the next mating, or not? What biological factors must be considered in answering this
question?
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