BIOL 1134 Hardy Weinberg Pop Beads 3 Student Handout PDF

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lab form for lab. This will help during lba...

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BIOL 1134 – Hardy-Weinberg Pop Beads

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POPULATION GENETICS, SELECTION, AND EVOLUTION INTRODUCT INTRODUCTION ION

It is a common misconception that individuals evolve. While individuals may have favorable and heritable traits that are advantageous for survival and reproduction, the impact of selection is only apparent in the changes in phenotypes and genotypes observed in the population over time. The study of population genetics determines allele and genotype frequency distributions to deduce whether the population is evolving or not and, if it is, to what extent it is evolving. In 1908, two researchers independently derived the Hardy-Weinberg principle, which states that the allele and genotype frequencies in a population will remain constant from generation to generation only if Mendelian segregation and recombination of alleles are at work. If the major conditions of the Hardy-Weinberg principle are not met, then there is a departure from Hardy-Weinberg equilibrium, which indicates that the population is evolving. In this activity, you will apply the Hardy-Weinberg principle and population genetics to understand how allele frequencies in a population are affected by selection and how an allele that causes a disease or other detrimental phenotype can be maintained in a population.

Two researchers, Godfrey Hardy (1877-1947) and Wilhelm Weinberg (1862–1937), independently discovered that if one knows the frequencies of alleles in populations, one can predict the frequencies of different genotypes found in the population provided that certain conditions are met. If genotypes are not within the predicted frequency, a scientist can then investigate whether natural selection or other evolutionary forces are acting on a population. Their discovery, known as the Hardy Hardy--Weinber Weinberg g prin principle, ciple, has become a foundation concept in evolutionary biology. The Hardy-Weinberg model provides a mathematical formula to calculate population allele and genotype frequencies. If a dominant alle A has a frequency represented by p and a recessive allele a has a frequency represented by q, and p + q = 1.0, then we can predict the frequencies of different combinations of A’s and a’s in genotypes by the model: (p + q)2 = p2 + 2pq + q2 where p2 = frequency of AA, 2pq = ˆfrequency of Aa, and q2 = frequency of aa. This relationship among allele and genotype frequencies will exist if five conditions are met for the population: 1. Large population size of sperm and/or egg producing individuals. 2. Random mating, no mate choice. 3. No mutation, there are no new alleles produced by changes in genetic material. 4. No migration out or immigration into the population, everybody stays in their home population. 5. No selection, all genotypes produce phenotypes with equal chance of survival and reproduction.

If these conditions are not met, allele and genotype frequencies will change from generation in a predictable or unpredictable way, depending on which of the conditions is not met. MATERIALS: ●

Container for parent population gene pool

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Container of stock population beads

! ▪

~100 beads of one color

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~100 beads of a different color

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Calculator

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Colored pencils

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Graph paper (optional)

DO NOT JOIN THE BEADS TOGETHER. PROCEDURE, DATA COLLECTION, AND QUESTIONS

1. Simulation 1: Examining the Hardy-Weinberg Principle a. Working in groups of two or three students, use a container that will serve as the “Parent Population” gene pool. b. Designate one color of bead as “Allele A” and the other color as “Allele a.” Write this information below. (Example: A = Red, a = White). The “A” will refer to a dominant allele and the “a” a recessive allele. Allele A: _________ (frequency __________ represented by p) Allele a: _________ (frequency __________ represented by q) c.

In the stock population container, add the appropriate number of each color bead (allele) to establish a gene pool of 100 total beads with the allele frequencies assigned to your group by the instructor. For example, if your group is assigned p = 0.5 and q = 0.5, you will have 50 beads of each color in the container because each bead represents one allele.

d. Using the allele frequencies for your population, use the Hardy-Weinberg equation to calculate the expected frequencies of each genotype for the parent population and record them in the expected column in Table 1.1. Multiply the genotype frequency by the population size (50 in this case) to calculate the expected number of each genotype in 50 offspring. p2 = _______, 2pq = _______, q2 = _______ e. From the Parent Population container, randomly select two beads. The two beads represent a diploid individual produced by joining egg and sperm. If they are the same color, the individual is homozygous (AA, aa) and if they are different, they are heterozygous (Aa). Make a tally mark in the appropriate observed genotype cell to record the genotype of this individual and return the beds to the gene pool. Repeat this process until you have produced 50 offspring. f.

Calculate the observed frequency of each genotype and record it in Table 1.1. How do the expected and observed numbers compare? Are the identical? Similar?

g. Calculate the allele frequencies in the 50 offspring? How do they compare with the initial values in the gene pool? h. The expected and observed results can be compared using a statistical test called chi-square test. It statistically evaluates how observed events meet predictions It is important to remember that for this test, you must use actual values and not frequencies!. This test does not evaluate causation or correlation, only fit of observations and expectations. In the chi-square, Ho (the null hypothesis) is that the observed and expected values are not significantly different, and Ha (the alternative hypothesis) is that the observed and expected values are significantly different i.

To conduct the chi-square test, transfer your values from Table 1.1 to Table 1.2 and complete the calculations.

! Table 1.1. Expected and observed genotypes for allele frequencies of p = __________ and q = _________. Genotype

Expected frequency of genotypes

Expected number of individuals in 50 offspring

Observed number of individuals in 50 offspring

Observed frequency of genotypes

AA

Aa

aa

Table 1.2. Chi-square results from Table 1.1 Observed

Expected

(O)

(E)

(O – E) = D

D2

D2/E

AA

Aa

aa Chi-square (C 2)= S D2/E =

j.

For this test, we have only one degree of freedom (df). Although there are three genotypes, once a single allele frequency is known in the two-allele system, all other values can be determined. If there are more alleles, df increases. To interpret the test, compare the calculated chi-square with a value from a chi-square table for a predetermined level of significance (a). Critical values for comparison are presented in tables for different degrees of freedom (df) and significance levels. We will always use a significance level of a £ 0.05. If your calculated 𝛘 2 > table 𝛘 2 , reject the null hypothesis, meaning the observed and expected are significantly different. If your calculated 𝛘2 < table 𝛘2 , you fail to reject the null hypothesis, meaning observed and expected are not significantly different. For this example, the critical value for comparison is 5.99.

k.

What can you conclude? The observed and expected genotype frequencies should agree. The parent population should be in Hardy-Weinberg equilibrium.

! 2. Simulation 2: Examining the Hardy-Weinberg Principle With Selection a. In the previous simulation there was no selective advantage or disadvantage; so individuals with either allele or any phenotype caused by their genotype survive 100% of the time. We will now investigate selection. b. To study the effects of selection, enter the observed numbers of each genotype from Table 1.1 in Table 2.1. c.

Suppose that the recessive allele causes a detrimental phenotype in the homozygous condition that results in 50% mortality for those individuals. Copy the observed number of AA and Aa individuals in the “after selection” column. Reduce the number of aa individuals by half and record the new number.

d. Using the new total number of surviving individuals, calculate the new allele frequencies. Are they the same or different from the initial allele frequency? e. Using the allele frequencies in Table 2.1 that you calculated after selection, establish a new parent population gene pool. Repeat step 1e above and record results in Table 2.2. f.

Now it’s time to analyze results with a chi-square test in Table 2.3. Before you begin the chi-square test, think about what we are studying in this experiment. Suppose you did not know that selection had acted on the population, a common scenario. What expected values should you use in your chi-square test?

g. Conduct the statistical test and interpret the results. What can you conclude? h. Using Tables 2.4 - 2.6, repeat steps 2c – 2g to impose one more round of selection on this population. Compare your results to other groups. What is similar about your results? What is different?

Table 2.1. First Generation of Offspring, after selection

Genotype

Observed number of individuals in 50 offspring

Number of individuals after selection

Allele

AA

A

Aa

a

aa

Number of alleles after selection

Allele frequency after selection

! Table 2.2. Observed genotypes in offspring following reproduction after one round of selection. Genotype

Observed number of individuals in 50 offspring

Observed frequency of genotypes

AA

Aa

Aa

Table 2.3. Chi-square analysis after selection Observed

Expected

(O)

(E)

D2

(O – E) = D

AA

Aa

aa Chi-square (C 2)= S D2/E =

Table 2.4. Second Generation of Offspring, after selection

Genotype

Observed number of individuals in 50 offspring

Number of individuals after selection

Allele

AA

A

Aa

a

aa

Number of alleles after selection

Allele frequency after selection

D2/E

! Table 2.5. Observed genotypes in offspring following reproduction after two rounds of selection. Genotype

Observed number of individuals in 50 offspring

Observed frequency of genotypes

AA

Aa

Aa

Table 2.6. Chi-square analysis after selection Observed

Expected

(O)

(E)

(O – E) = D

D2

D2/E

AA

Aa

aa Chi-square (C 2)= S D2/E =

3. Simulation 3: Examining the Hardy-Weinberg Principle With Additional Types of Selection a. Simulation 1 had no selection, and Simulation 2 used directional selection against homozygous recessive phenotype. In Simulation 3, you will design an experiment to analyze selection against the dominant phenotype. Following the procedures outlined above, design and conduct an experiment for a scenario when individuals with the dominant phenotype experience 50% mortality. Additional tables are provided below. b. How is this similar or different from selection against the recessive phenotype? Why do you think that is? Explain.

! Table3.1. First Generation of Offspring, after selection

Genotype

Observed number of individuals in 50 offspring

Number of individuals after selection

Allele

AA

A

Aa

a

Number of alleles after selection

Allele frequency after selection

aa

Table 3.2. Observed genotypes in offspring following reproduction after one round of selection. Genotype

Observed number of individuals in 50 offspring

Observed frequency of genotypes

AA

Aa

Aa

Table 3.3. Chi-square analysis after selection Observed

Expected

(O)

(E)

(O – E) = D

D2

AA

Aa

aa Chi-square (C 2)= S D2/E =

Table 3.4. Second Generation of Offspring, after selection

D2/E

! Genotype

Observed number of individuals in 50 offspring

Number of individuals after selection

Allele

AA

A

Aa

a

Number of alleles after selection

Allele frequency after selection

Aa

Table 3.5. Observed genotypes in offspring following reproduction after two rounds of selection. Genotype

Observed number of individuals in 50 offspring

Observed frequency of genotypes

AA

Aa

Aa

Table 3.6. Chi-square analysis after selection Observed

Expected

(O)

(E)

(O – E) = D

D2

AA

Aa

aa Chi-square (C 2)= S D2/E =

D2/E

! QUESTIONS 1. What happened to allele frequencies in each simulation? Did allele frequencies change at the same rate in Simulations 2 and 3? Why or why now? 2. How would you summarize and explain the results of this experiment? Prepare a figure to support your answer. 3. How do you think the results would differ if there were selection against any homozygous genotype? Selection against heterozygous genotypes? Explain. 4. How could you modify this procedure to simulate the effects of small population size and genetic drift?...