Copy of Lab 2 - HWEQ Modeling a Population

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Modeling a Population How do factors such as gene flow , natural selection and genetic drift affect a population of organisms? You’re going to be answering these questions by working on a model set of organisms: gem beetles. The gem beetles are represented here by different colored plastic beads. These particular gem beetles can exist in one of three color phenotypes: red, pink, or white. The red gem beetles (AA) are homozygous for the ‘A’ allele, the white beetles (aa) are homozygous for the ‘a’ allele, and the pink gem beetles (Aa) are heterozygous for the two alleles. Color in gem beetles is an example of incomplete dominance, since the heterozygous phenotype is different from either of the homozygotes. Gem beetles normally live in environments found on islands (replicated around the room, at different tables). On each island, the environment varies according to the geographical location. N side: RED BANDANA S side: GREEN E side: BLACK AND WHITE W side: PINK AND WHITE DOTS. I. CREATING THE EQUILIBRIUM POPULATION – Gene Pool of the Original Population Let’s study the starting gene pool of the gem beetle population on your island. You will be working primarily at one of the four environments, on one island. Table 2 indicates the number of gem beetles of each color that you should add to your assigned environment at your island. Add a total of 100 gem beetles to your environment, indicated in table 2. Be sure to spread them around and mix them up within that environment. Table 2. Original gene pools of the gem beetle populations at each geographic location on an island. Location # Red (AA) # Pink (Aa) # White (aa) Total # (N) Total ALLELES North (Red Bandana) 25 50 25 100 200 South (Green) 49 42 9 100 200 East (Black and White) 4 32 64 100 200 West (Pink and White dots) 25 50 25 100 200 Note the differing initial number of the red, pink, and white gem beetles varies at the different locations on the island. Since the color of the gem beetles is an example of incomplete dominance, the genotype and phenotype frequencies are the same. 1. Based on the # of individuals of each genotype, and the total # of individuals, calculate:

a) the frequencies for each genotype: AA, Aa, and aa (write in Table 3 below) b) the population-level allele frequencies ( p and q ). (also write in Table 3 below) If we leave these gem beetles alone they will (hopefully) survive, and reproduce. You should recognize that each environment’s gene pool is currently a closed population, and the probability of two gem beetles mating is only related to their frequency in the population. Right now, there is no immigration/emigration, or natural selection. 2. Calculate the expected genotype frequencies of the offspring (next) generation of your population (table 3). How do you do this? You use your parental allele frequencies to construct a population-level Punnett Square in the space provided, which gives you expected genotype frequencies in the next generation. Record these expected genotype frequencies in Table 3. Table 3 . Genotype/phenotype and allele frequencies for your initial gem beetle population, in your environment. Genotype/Phenotype FREQUENCIES Allele FREQUENCIES Red (AA) Pink (Aa) White (aa) ‘A’ allele ( p ) ‘a’ allele ( q ) Parental (initial) frequencies 0.25 0.50 0.25 0.5 0.5 Offspring (next) frequencies P^2 0.25 2pq 0.5 Q^2 0.25 YOUR STUDY SITE (Geographic location): North 3. Is your population in Hardy-Weinberg equilibrium? Explain your answer. Our population is in Hard-Weinberg equilibrium because nothing has changed. II. EFFECTS OF GENE FLOW Spring has come to your island, and the reproductively mature gem beetles are anxious to find a mate. The gem beetles at the four geographic locations on your island tend to behave somewhat differently during mating season. The gem beetles on the north and south sides of the islands are homebodies. They find a neighborhood male or

female they are compatible with and mate. However, the gem beetles living on the east and west sides of the island are more restless. Some of these gem beetles leave their native population to find a mate. Due to the presence of mountain ranges on the island, gem beetles from the EAST shore can only migrate to the SOUTH, and gem beetles from the WEST shore can only migrate to the NORTH shore. This annual mating migration results in gene flow among the populations in each island. Gem beetles are emigrating away from the eastern and western sides and immigrating to the southern and northern sites, respectively. We are now violating one of the basic assumptions of the Hardy-Weinberg principle. Now try to determine the impact of this gene flow on your original population’s genetics. Make a prediction – Look at the population on your environment, and also at the population on the other environment that is either immigrating or emigrating with yours. What do you expect to happen to your population’s genotypes, after migration has occurred? Increase (+), decrease (-), or stay the same (0). Genotype Frequency Predicted Result after Gene Flow AA: 0 Aa: + aa: - If your study population is either on the EAST or WEST side, some of your gem beetles will now migrate (east to south, west to north). RANDOMLY remove (mix your beetles, close your eyes and grab) 15 gem beetles from your environment. Give these emigrants to one of the researchers at the destination environment on your island. At this point, each location should have either lost or gained some gem beetles through emigration or immigration. Complete table 4 and calculate the new numbers of each genotype/phenotype in the population. Table 4 . NUMBER of gem beetles of each color before and after gene flow. Red (#AA) Pink (#Aa) White (#aa) Total # (N) Total Alleles Starting population, before gene flow (from table 2) 25 50 25 100 Number added or removed 5 5 5 15 New population, after gene flow 30 55 30 115 230 Complete table 5 to show the effect of gene flow on your population. The Initial population values and allele frequencies for row 1 of this table come from table 3. In the second row of Table 5, calculate the genotype/phenotype frequencies in your new population after gene flow, and then the new allele frequencies. Table 5 . FREQUENCIES of genotype/phenotype and allele for your gem beetle population before and after gene flow. Genotype/Phenotype FREQUENCIES Allele FREQUENCIES Red (AA) Pink (Aa) White (aa) ‘A’ allele ( p ) ‘a’ allele ( q ) Starting population, before gene flow (from table 3, row 1) 0.25 0.50 0.25 0.5 0.5

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New population, after gene flow 0.26 0.478 0.26 0.5 0.5 Next generation , after reproduction P^2 0.25 2pq 0.50 Q^2 0.25 Use the allele frequencies (above) to calculate the Next generation’s genotype frequencies (at left) Difference between Starting population and Next generation (absolute value) 0 0 0 Sum of differences: 0 Recall that your initial population was in Hardy-Weinberg equilibrium. Is your population still in Hardy-Weinberg equilibrium? To answer this question, compare the starting population to the next generation’s genotype/phenotype frequencies in table 5. If they are IDENTICAL (or nearly so), the population is still in Hardy-Weinberg equilibrium. If they are not, the population is no longer in Hardy-Weinberg equilibrium . It is evolving! QUESTIONS: a) Drawing a conclusion – How did your predictions of what would happen to your population after gene flow compare to the actual results you found? - My prediction was a change happening to my population after gene flow being false compared to the actual results I found which were no differences happening due to the same population numbers of WEST and NORTH. b) Which populations on your island (if any) are still in Hardy-Weinberg equilibrium? Is there a difference between the populations that emigrated (lost beetles), and the ones that had immigrants (gained beetles)? - Both islands are in Hardy-Weinberg equilibrium. They both started with the same population therefore there is no difference after migration. c) While gene flow can cause evolution in populations, in what circumstances does gene flow NOT cause evolution in a population? - Gene flow does not cause evolution to a population when everything stays the same. III. EFFECTS OF NATURAL SELECTION In the absence of unusual environmental changes, the major factor affecting the survival of gem beetles is predation. The major predator of the gem beetles is the ravenous finch (you). You look for gem beetles in their environment and pick them up, one at a time, with a pair of forceps (meant to simulate your beak pecking at them, which would happen one at a time). The ability of the ravenous finch to successfully prey upon the gem beetles depends on both the color of the gem beetles and its environment.

In evolutionary terms, some colors of gem beetles may have a higher fitness and be more likely to escape predation than other colors. These gem beetles are more likely to survive to reproductive age and contribute to the gene pool of the next generation. The relative fitness associated with a particular phenotype varies with the environment. Over time, we would expect the frequency of the gem beetles with the greatest fitness to increase if the environment remains constant. In this part of the exercise, you will study the change in the gene pool that occurs due to the predatory activities of the ravenous finch. Make a prediction – Look at the current population on your environment. What do you expect to happen to your population’s genotypes after finch predation? Increase (+), decrease (-), or stay the same (0). Genotype Frequency Predicted Result after Natural Selection AA: Aa: aa: Thoroughly scramble your gem beetles randomly across your entire environment. Choose a person to be the ravenous finch predator. The ravenous finch predator has to use a pair of forceps to grab the FIRST GEM BEETLE it sees in the environment. It must process the beetle, one at a time (looking away from the environment briefly), and then go back for its next gem beetle prey, again, grabbing the first one it sees. The gem beetles that were eaten by the ravenous finch should be permanently removed from the population you are studying. They’re dead! (and are being digested…) Keep eating until the finch has eaten 20 beetles. After the finch has eaten its 20 beetles, count the number of each type of gem beetle removed and complete table 6. Entries for the top row of table 6 come from the bottom row of table 4. Table 6 . The NUMBER of gem beetles of each color before and after natural selection. Red (#AA) Pink (#Aa) White (#aa) Total # (N) Total Alleles Starting population before natural selection (from table 4, row 3) Number removed by predation New population after natural selection To determine any effects of predation (natural selection) on your population, calculate the new genotype and allele frequencies and enter this data into the appropriate row of table 7. Table 7 . FREQUENCIES of genotypes and alleles before and after natural selection, and expected genotype frequencies for the next generation. Genotype /Phenotype FREQUENCIES Allele FREQUENCIES Red (AA) Pink (Aa) White (aa) ‘A’ allele ( p ) ‘a’ allele ( q ) Starting population before natural selection (from table 5, row 2)

New population after natural selection Expected frequency (in the next generation) P^2 2pq Q^2 Use these allele frequencies to calculate the next generation’s genotype frequencies Difference between Starting population and Next generation (absolute value) Sum of differences: QUESTIONS: a) Drawing a conclusion – How did your predictions of what would happen to your population after natural selection compare to the actual results you found? b) Is your new population after natural selection still in Hardy Weinberg equilibrium? Explain your answer. c) Your population may have only changed a couple of percent—what if you compound that change over 100 generations? Over 1000? Do you expect the population to be different at the end of multiple rounds of selection? d) What do you predict would happen to your three genotype frequencies if predation continued to impact the population as it did in your environment (assuming all the survivors randomly reproduced)? IV. GENETIC DRIFT Gem beetles have now become quite popular amongst beetle collectors. They are now so valuable, in fact, that beetle collectors come to your island and have randomly collected all but SIX individuals of your gem beetle population. Of the SIX individuals left, the collectors managed to leave an equal number of males and females. All six of these remaining gem beetles manage to survive and reproduce. Let’s simulate the effect of this “bottleneck” event, and see if it results in genetic drift in your population.

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Make a prediction – Look at the current population on your environment. What do you expect to happen to your population’s genotypes after this “bottleneck” event? Increase (+), decrease (-), or stay the same (0). Genotype Frequency Predicted Result after Genetic Drift AA: Aa: aa: Closing your eyes, RANDOMLY grab SIX gem beetles. These are the survivors that will remain on your island, the rest have been stolen and placed into beetle collections! Set these six aside. (go to next page!) Fill in the first and second rows of table 8. Complete the first row by transferring numbers from the last row of table six. The second row of table 8 is the post-bottleneck population (of 6 beetles) you just selected. Wait to fill in the 3 rd and 4 th rows until later. Table 8 . The NUMBER of gem beetles of each color before and after the bottleneck event. Red (#AA) Pink (#Aa) White (#aa) Total # (N) Total Alleles Number in initial population, before genetic drift (table 6, row 3) 30 55 30 115 Number in surviving population after bottleneck (1 st generation) 2 2 2 6 12 Number in surviving population (2 nd generation) 3 2 1 6 12 Number in surviving population (3 rd generation) 3 3 0 6 12 Now go to table 9, the FREQUENCY table for the bottleneck population. Calculate the allele and genotype frequencies for the new, post-bottleneck population. Fill in the first and second rows of table 9 (below). The first row of table 9 contains the genotype frequencies from the second row of table 7. Entries for the second row of table 9 are calculated from the observed number of beetles (for each genotype) in the post-bottleneck population (second row in table 8). Now, in the 3 rd row of table 9, calculate the expected genotype frequencies of this new population reproducing, using the observed population’s allele frequencies (2 nd row) in a Punnett square. Table 9 . FREQUENCIES of genotypes and alleles of your gem beetle population before and after bottleneck

Genotype/Phenotype FREQUENCIES Allele FREQUENCIES Red (AA) Pink (Aa) White (aa) ‘A’ allele ( p ) ‘a’ allele ( q ) Starting Population before bottleneck (table 7, row 2) Observed Frequencies of your Surviving Population (1 st generation) Expected Frequencies of the 2 nd generation (given p and q in row 2) P^2 2pq Q^2 Observed Frequencies of the 2 nd generation (mate your beetles!) Expected Frequencies of the 3 rd generation (given p and q in row 4) P^2 2pq Q^2 Observed Frequencies of the 3 rd generation (mate them again!) Difference between Starting population and Observed 3rd generation (absolute value) Sum of differences: Assume Hardy-Weinberg conditions exist on your island now with this smaller population. Calculate the genotype frequencies in this new population after one generation of random mating. Using p and q allele frequencies you just calculated (in table 9), predict the expected genotype frequencies for the next (2 nd ) generation, and complete the third row of table 9. These expected genotype frequencies would be established after one generation of random mating IF the assumptions of Hardy Weinberg are met.

We will now observe the effects of further genetic drift on this population through two or more generations. To produce the Observed numbers and frequencies of the next (2 nd ) generation, only two pairs will randomly mate (the other pair doesn’t ever find each other). 1. Randomly create 2 mating pairs from the 6 surviving adults. 2. What will the genotypes of their offspring be? To determine this, complete an INDIVIDUAL Punnett square for the first of the two “couples,” showing the possible genotypes of their offspring. Once you’ve completed the individual Punnett square for this couple, grab the 4 beetles of the appropriate. These are the possible kids from the first couple. 3. Cup these 4 possible beetles from your 1 st couple’s Punnett cross in your hand and shake them up a bit. Have your lab partner close their eyes, pick one, and record that offspring’s genotype. Replace (replace!) that gem beetle back in your hand. Repeat the process twice more, for a total of three times to produce 3 surviving offspring. Record the number of each offspring type. The first couple has now had their 3 kids, and they die! (They’re not in the population anymore.) 4. Now mate that second couple. Again follow steps 2 and 3 above: complete another Punnett square for this pairing, obtain the four possible gem beetle offspring, select (& replace, then select again) three offspring total. When done, combine the two couple’s kids (6 in all) and record the numbers of each offspring type in row four of table 8. 5. Now, using your newly-entered actual #’s of offspring from row 3 of table 8, calculate that new population’s observed genotype and allele frequencies in row 4 of table 9. Compare observed with expected (row 3 above). Are they different? 6. Calculate the allele frequencies of this population, and use those allele frequencies to predict the genotype frequencies of the next generation (make a population Punnett square). 5. Now, do the actual mating and see how it compares, by repeating steps 1-5 with the 6 survivor kids. That is, follow the protocol you just followed (2 couples mating, each have 3 kids). Complete the fourth row of table 8, and then the sixth row of table 9. QUESTIONS a) Compare the observed genotype and allele frequencies recorded in the last row of table 9 with the 1 st and 2 nd rows. Has the bottleneck effect and genetic drift resulted in evolution in your population?

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b) When you were picking possible offspring from the mating pairs (randomly grabbing one of the four beetles from your hand), why did you have to replace (put back in your hand) the offspring after you selected it? c) Note that mating of the new generation on the island involves inbreeding. Often the individuals mating are full siblings (brother and sister). What effect does inbreeding have on the gene pool of the post-bottleneck gem beetles? d) Suppose that the collectors had left 50 beetles, instead of 6. What effect would that have had on your results? V. SUMMARY Table 10. Summary of genotype/phenotype and allele FREQUENCIES for your gem beetle population before and after GENE FLOW, NATURAL SELECTION, and GENETIC DRIFT. ENVIRONMENT: Genotype/Phenotype FREQUENCIES Red (AA) Pink (Aa) White (aa) Your Initial Population (from table 3) Sum of differences you calculated After Gene Flow (table 5, row 3) (sum from table 5, row 4) After Natural Selection (table 7, row 3) (sum from table 7, row 4) After Genetic Drift (table 9, row 6) (sum from table 9, row 7) a) Which of the factors above appears to have affected the genetic makeup of your population the most?

b) Do you think that factor always has the most impact on all populations? Explain.

Copy of Lab 2 - HWEQ Modeling a Population

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