Pop Gen Worksheet

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University of Illinois, Chicago *

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310

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Feb 20, 2024

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BIOS 310 Population Genetics Worksheet Copyright © Jer Pin Chong 1 Student Name: _________________________ TA name: ____________________________ Lab Objectives • Introduce the Hardy-Weinberg Principle. • Reiterate the term homozygous, heterozygous, allele, genotype, and phenotype. • Estimate allele frequency and genotype frequency. • Test for Hardy-Weinberg equilibrium. Population Genetics Lab I • Examine the impact of predation on the allele and genotype frequencies in a population. • Students form groups of 4. Each student will complete individual worksheet. • Each group will select a habitat (colored cloth) located in the room. • Assign one student as monitor/data recorder, one student as timer, two students as hunters. Background Information : A new bird species has recently been discovered on an island. They have three types of body colors: red, blue, and yellow. Their feathers have huge economic value, and that attracts poachers to the island to hunt the birds. These birds reside in six different habitats on the island. As a conservation geneticist, you would like to know if the hunting activity has applied significant selective pressure on the six bird populations living on different habitats. Lab Procedures 1. There are 3 bags of colored dots at each station. Each colored dot represents an individual of the bird species with that specific body color. The cloth is the habitat that this bird population lives in. 2. Transfer 26 yellow dots, 35 blue dots, and 14 red dots from the bags to the transparent cup. The initial bird population size = 26 + 35 + 14 = 75 individuals. 3. Hunters carry the blue cups and face away from the habitat. Monitor and timer mix the colored dots in the transparent cup and scatter them randomly on the habitat. 4. When the timer gives the signal, hunters will turn to the habitat and hunt for 20 seconds. Each hunter collects one individual (one colored dot) at a time . Hunters have to place the individual into the cage (cup) before they can hunt another individual. 5. Upon the end of the hunt, each group will count the captured individuals for each body color. Record those numbers in Table 1 below. Leave the remaining colored dots on the habitat. Note: hunters should help count the dots and complete the calculation in Table 1. Tryphosa tha then Alex

BIOS 310 Population Genetics Worksheet Copyright © Jer Pin Chong 2 6. After the hunt, the remaining individuals in the population reproduce and double the population size. Based on this information, complete Table 1. 7. Add the number of color ed dots listed on the “Remaining Population” column in Table 1 into the transparent cup. E.g. If 15 blue birds survive the hunt and remain in the population, add additional 15 blue dots into the habitat to indicate that these individuals reproduce and double the population size. Do that for each body color. 8. Monitor and timer mix the new individuals and distribute them onto the habitat while the hunters are facing away. 9. The second hunt begins when the timer gives the signal. The initial population size of the second hunt is equal to the “After Reproduction” population size in Table 1. Repeat step 4-8. Complete Table 2. 10. Double the number of remaining individuals in the habitat after the second hunt. Initiate the third hunt by repeating step 4-6. Complete Table 3. 11. Each group submits your “Initial Population Size” and “# of Individuals Captured” data of all three hunts to your TA. TA will compile the data collected from all groups for class discussion later. 12. Carefully remove the colored dots from the habitat. Separate them by colors and put them back into the plastic bags. Please check your bench to make sure all the colored dots have been returned to their bags. 13. Complete the rest of the worksheet. Results Table 1. Data collection for the first hunt . Body Color Initial Population Size # of Individuals Captured Remaining Population After Reproduction Yellow 26 Blue 35 Red 14 Table 2. Data collection for the second hunt . Body Color Initial Population Size # of Individuals Captured Remaining Population After Reproduction Yellow Blue Red 4 9 58

BIOS 310 Population Genetics Worksheet Copyright © Jer Pin Chong 3 Table 3. Data collection for the third hunt . Body Color Initial Population Size # of Individuals Captured Remaining Population After Reproduction Yellow Blue Red Data Analysis Genetic analysis has revealed that the body color of this bird species is controlled by two alleles (B and b) from the same locus. Genotype Phenotype (Body Color) BB Yellow Bb Blue bb Red 1. What are the observed genotype frequencies of the initial bird populations for each body color before the first hunt? Show your work. Observed genotype frequency of BB = Observed genotype frequency of Bb = Observed genotype frequency of bb = 2. What are the allele frequencies of the initial bird populations? Let p = frequency of allele B, q = frequency of allele b. p = q = 3. What are the expected genotype frequencies of this bird population before the first hunt? Expected genotype frequency of BB = Expected genotype frequency of Bb = Expected genotype frequency of bb = 4. What are the expected counts for each body color if this bird population is under Hardy-Weinberg equilibrium (HWE)? Expected counts for yellow = Expected counts for blue = Expected counts for red = É 13 3 78 2 1 35 0 58 100 15812 14 35 0 42 100 1421J 0 58 0 58 0 3364 100 33 6 0 0 2 0 58 0 42 0.4872 100 48.7f 0 42 X 0 42 0 1 7 64 X 100 17 6 D 3364 75 25 2 0 4872 75 36 5 0 1764 75 13 2

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BIOS 310 Population Genetics Worksheet Copyright © Jer Pin Chong 4 5. Was the initial bird population under Hardy-Weinberg equilibrium? Conduct a chi- square test to support your answer. Note: The chi-square distribution table is located on the last page of this worksheet. Phenotype Observed (O) Expected (E) O − E (O − E) 2 (O − E) 2 /E Yellow Blue Red Total X 2 = You reject / fail to reject the null hypothesis of the chi-square test, with p -value greater / less than 0.05. (circle the answers) The initial bird population is under HWE / deviated from HWE (circle one answer). 6. Using the “After Reproduction” population size in Table 3, calculate the observed genotype frequencies, allele frequencies, expected genotype frequencies, and expected counts of each body color in the bird population after three hunts. Observed genotype frequencies Observed genotype frequency of BB = Observed genotype frequency of Bb = Observed genotype frequency of bb = Allele frequencies p = q = Expected genotype frequencies Expected genotype frequency of BB = Expected genotype frequency of Bb = Expected genotype frequency of bb = Expected counts Expected counts for yellow = Expected counts for blue = Expected counts for red = 74 158 0 468 100 46.84 66 158 0 418 100 41.84 18 158 0 114 100 11.47 74 66 0.677 100 67.7 to 185 1 0 323 100 32.3 0.677 0 677 0.458 100 45.8 Y 2 0.677 0.323 0 437 100 43.7 of 0.3233 0.3233 0 104 100 10.4 Ye 0.458 158 72.36 0.437 158 69.05 0.104 158 16.43

BIOS 310 Population Genetics Worksheet Copyright © Jer Pin Chong 5 7. Is the bird population under Hardy-Weinberg equilibrium after three hunting incidents? Conduct a chi-square test to support your answer. Phenotype Observed (O) Expected (E) O − E (O − E) 2 (O − E) 2 /E Yellow Blue Red Total X 2 = You reject / fail to reject the null hypothesis of the chi-square test, with p -value greater / less than 0.05. (circle the answers) The bird population is under HWE / deviated from HWE (circle one answer). 8. Why do individuals with certain body color survive better in your habitat? 9. Why do some bird populations deviate from HWE after the hunting incidents? 10. Why do some bird populations remain under HWE despite the hunting pressure? 11. If the bird population is deviated from HWE because the hunters constantly removing the body color that is more common in a population, what type of natural selection this is? Hint: This is a common type of evolutionary process that we did not cover in the lecture. Use your cell phone or laptop, search online about the type of natural selection that affects the allele/genotype frequencies in a population based on the frequency of the phenotype. a. Directional Selection b. Disruptive Selection c. Stabilizing Selection d. Frequency Dependent Selection Combining the molecular data and statistical inferences, we now have a better understanding of how populations evolve. _________________________________________________________________________________________________________ 74 72 36 1.64 98 69.05 3.595 3 3 8,8 fE 16.46 e e some bird populations deviate fromthe awe because the population probably went through selectivepressure This causes the deviation be HWE assumes that selective pressures are not affecting the population some bird populations remain under theawe because hunting in this activity was timed and the dots were randomly collected based on how far away they are from the hunters so they randomly ended up under the HUE