Lab 4 Genetic Drift (Online) PDF

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Foundations of Biology: Ecology & Evolution LAB Biology 206

LAB 4

LABORATORY 4: Genetic Drift (Bottlenecked Ferrets)

Introduction The black-footed ferret is the cutest vicious killer in the world. Also known as the American polecat (and

as

Mustela nigripes), this member of the weasel family is a specialist predator of prairie dogs (Russell et al. 1994). Black-footed ferrets were once distributed throughout the American Great Plains (Wisely et al. 2003). However, due to habitat loss and extirpation of its prey, the black-footed ferret was nearly driven to extinction (Dobson and Lyles 2000). Indeed, it was thought to be extinct at the end of the 1970s. In 1981, a lone surviving population was found near Meeteetse, Wyoming. Photo by Trisha M Shears.

In 1985, the Meeteetse population numbered about 40 individuals. Then the population was hit by both canine distemper and sylvatic plague (Wisely et al. 2002). Eighteen individuals were taken into captivity for a managed breeding program. In 1986, no individuals were known to remain in the wild.

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Foundations of Biology: Ecology & Evolution LAB Biology 206

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The captive breeding program has been sufficiently

successful

that

wildlife

managers have been reintroducing blackfooted ferrets into the wild for two decades (Grenier 2007). Self-sustaining populations have been established in South Dakota, Arizona, and Wyoming (Jachowski et al. 2011). Efforts continue to establish more. Not surprisingly, ferrets do better where there are lots of prairie Photo from Bureau of Land Management

dogs to eat. However, numbers and food are not the

only challenges the black-footed ferret face. Genetic diversity is also a concern (Wisely et al. 2002, 2003, 2008). All extant members of the species are descended from just seven individuals. In this lab, you

will

investigate why this population bottleneck in the black-footed ferret’s recent past may continue

to

threaten its survival. At the end, you will have a chance to conduct experiments to determine the

best

way to allocate limited conservation resources to best preserve what remains of the ferret’s genetic heritage.

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Foundations of Biology: Ecology & Evolution LAB Biology 206

LAB 4

Exercise 1: Luck of the Draw [1]

If you haven’t already, start SimUText® by double-clicking the program icon on your computer or by selecting it from the Start menu. When the program opens, enter your Log In information and select the Genetic Drift and Bottlenecked Ferretslab from your My Assignments window.

[2]

In the top half of the main window you should see a large population of black-footed ferrets. To give a visual indication of genetic diversity, we have given some of the ferrets lighter coats and others darker coats. Coat color is determined by a single fictitious gene with 2 alleles: allele S, for “standard,” and allele C , for “charred.” To see an individual ferret’s genotype, double-click on it. An Information Window appears listing the ferret’s genotype and gender. Individuals with genotype SS or SC have standard coats. Individuals with genotype CC have charred —that is, dark—coats. Dismiss the window by clicking the CLOSE button.

In truth, although much is known about the genetics of coat color in other mammals, little is known about the genetics of coat color in black-footed ferrets. However, by studying the hypothetical coat color gene we have created for this lab, you will learn general principles that apply to all genes for all traits— including invisible but crucially important traits like resistance to disease. One thing you must keep in mind during this lab is that our simulated ferret population’s coat color and underlying genotype have no effect whatsoever on a ferret’s ability to survive and reproduce. (We know this because we built the model!) Alleles S and C are neutral. Coat color is not subject to natural selection. [3]

The Controls at the bottom left of the screen allow you to run and stop the simulation. Start the model by clicking the GO button. You should see ferrets running around as they search for food, seek mates, produce kittens, and ultimately die. The clipboard above the Controls shows the size of the field population and the frequency of allele S in the population.

A frequency of, say, 0.45 means that 45 out of every 100 copies of the coat color gene in the population are copies of allele S. Because there are only two alleles in our model, the other 55 of every 100 copies are copies of allele C. [4]

Keep an eye on the frequency of allele S while the simulation runs for a bit. [ 1.1 ]

How much does the frequency jump around over time? What do you think makes it do this? (Remember: Coat color has no effect on survival and reproduction.)

Ans. The initial frequency is 0.51. Over the time, it decreases and go below 0.20. Genetic drift might be the reason for this as coat color has no effect on survival and reproduction.

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Foundations of Biology: Ecology & Evolution LAB Biology 206

[5]

LAB 4

Pause the model by clicking the STOP button in the Control Panel.

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Foundations of Biology: Ecology & Evolution LAB Biology 206

[6]

LAB 4

To begin exploring the genetic consequences of small population size, capture a few ferrets and move them to Breeding Pen 1. To do this, look in the Tools panel (bottom of the screen, in the middle) and make sure the Arrow Tool is selected. Then move your cursor up into the field and hold the mouse button down while you drag the cursor over a group of ferrets. When you release the cursor, your selected ferrets should be highlighted. Now click-and-drag the highlighted ferrets into the breeding pen. Move approximately 10 ferrets into the pen. Breeding pens have a maximum capacity of 15 individuals. [ 1.2 ]

Is the frequency of allele S in the field population the same as the frequency of allele S among ferrets in Breeding Pen 1?

Ans. No, the frequency differ. Total population frequency is 0.11 and pen frequency is 0.011.

[ 1.3 ]

If not, how did they come to be different?

Ans. It is different because unbalance representation of the population. The representation of population in breeding pen is very smaller than overall population.

[7]

Stock Breeding Pens 2 through 5 with randomly-chosen ferrets from the field population. Move roughly 10 ferrets into each pen. [ 1.4 ]

Record the frequency of allele S in the field and the five breeding pens.

FIELD

PEN 1

PEN 2

PEN 3

PEN 4

PEN 5

0.11

0.050

0.050

0.15

0.15

0.20

It is likely that the frequency of allele S is different in each of your 6 populations. The reason is that when you moved samples of ferrets from the field into the pens you just happened to pick collections

of

individuals who, as a group, carried alleles S and C at somewhat different frequencies than the alleles occur at in the larger field population. The chance occurrence of a difference between the frequency of an allele, gene, or trait in a large population versus its frequency in a smaller sample of the population is called sampling error. Sampling error in the establishment of a new population of organisms is called the founder effect. Your experience with the founder effect demonstrates that sometimes differences among populations can arise not by natural selection but instead by sampling error. [8]

Now make some predictions about what will happen to the frequencies of allele S in each of your breeding pens when you run the simulation. Record your predictions below, and briefly explain your reasoning.

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Foundations of Biology: Ecology & Evolution LAB Biology 206

[ 1.5 ]

LAB 4

Will the allele frequencies in the pens tend to move toward the frequency in the larger field population?

Ans. No, it will not move toward the frequency in the larger field population. The frequency which is lower than field will further decrease and the frequency which is higher than field will further increase as it will not balance out due to the presence of both the alleles.

[ 1.6 ]

Will the frequencies in the pens tend to move toward 0.5? 0.25? 0.75?

Ans. It seems like some frequencies will decreases and some will increase over the time.

[ 1.7 ]

Will the frequencies all do the same thing, or will something different happen in each one?

Ans. There will be something different happen in all the pen.

[9]

Click the GO button to run the simulation. Let it run for at least 100 time steps. Our model ferrets live for a maximum of eight time steps, so this will represent at least a dozen generations. Then pause the simulation with the STOP button. [ 1.8 ]

Record the frequency of allele S in the field and the five breeding pens.

FIELD

PEN 1

PEN 2

PEN 3

PEN 4

PEN 5

0.058

0.17

0.0

0.0

1.0

0.0

[ 1.9 ]

Were your predictions in Questions 1.5 – 1.7 correct? If not, can you explain what happened?

Ans. Yes, prediction was correct as we can see some frequencies decreased and some increased. But, the surprising thing is that I wasn’t expecting that some frequencies will completely decrease to 0 and some to 1.0.

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Foundations of Biology: Ecology & Evolution LAB Biology 206

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[ 10 ]

You may repeat this exercise if you wish by clicking the RESET button in the Control Panel.

[ 11 ]

Click the TEST YOUR UNDERSTANDING button in the bottom right corner of the screen and answer the question in the window that pops up.

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Foundations of Biology: Ecology & Evolution LAB Biology 206

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Exercise 2: Random Mating As you may suspect by now, running the simulation in the previous exercise offered additional opportunities for sampling error beyond the error that occurred during the founding of new populations in breeding pens. These additional opportunities occurred during the production of offspring within each population. When the ferrets in our model are ready to produce offspring, they choose their mates at random. We can model random mating to produce a new generation as follows. Imagine taking all the egg cells produced by the breeding females in the population and all the sperm cells produced by the breeding males, dumping them together in a giant womb, and stirring. The collection of gene copies carried in these stirred-up gametes is known as the gene pool. We now let the sperm swim about at random in the womb and bump into eggs. When an egg and sperm collide, they unite to form a zygote. The zygotes will then develop into a new generation of ferret kittens. [1]

Use the SELECT AN EXERCISE button the exercise Random Mating.

[2]

You should see just such a womb for a ferret population on the left side of the main window. The frequency of allele S in this gene pool is set at 0.5 by default.

[3]

Make a prediction. [ 2.1 ]

in the upper left-hand corner of the screen to select

How will the frequency of allele S among the zygotes compare to the allele’s frequency among the eggs and sperm in the gene pool? Explain your reasoning.

Ans. The allelic frequency S will depend on the genotype of the parents. For example, if mother has SS genotype than frequency of S will be higher compare to the other genotypes.

[4]

Click the STEP button in the Control Panel to run the simulation 1 time step at a time until you see a green dot appear in the graph on the right side of the window, which indicates that eggs and sperm have combined to make zygotes in the womb..

[5]

The graph shows the frequency of allele S among the zygotes as a function of the number of zygotes made. Click the green line on the graph to see exact values. [ 2.2 ]

How does the frequency of S among zygotes (shown by the green line) compare to the frequency of S in the gene pool (shown by the gray line)?

Ans. The frequency of S among zygotes is increasing, while the frequency of S in the gene pool is constant.

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Foundations of Biology: Ecology & Evolution LAB Biology 206

[6]

LAB 4

Click the STEP button a few more times, watching the allele frequency graph as you do so.

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Foundations of Biology: Ecology & Evolution LAB Biology 206

[2.3 ]

LAB 4

What seems to be happening to the frequency of S among the zygotes relative to the frequency in the gene pool?

Ans. The frequency of S among the zygotes was increasing over the time and at one point it reaches to the gene pool frequency at one point. [7]

Now click the GO button to run the simulation. [ 2.4 ]

What happens to the allele frequency over time?

Ans. The allele frequency remains constant over time 0.50. [8]

RESET the simulation and RUN it again at least three times, letting it run for at least 150 time steps each time. (NOTE: Move the Speed Slider to the right if you want the simulation to run faster.) [ 2.5 ]

Briefly describe what happened during each run.

Ans. During the first run and third run, in the beginning it was declining and then start increasing and reach to the gene pool frequency by random mating. During the second run, it start above the 0.50 frequency and start declining over the time and reach to the gene pool frequency as number of zygotes increases.

[ 2.6 ] You should begin to see a general pattern. Describe what happens to the frequency of S among the zygotes, as it compares the frequency in the gene pool, as the number of zygotes made increases. Ans. In the beginning the frequency of the S among zygotes was different. As number of zygotes start increasing over the time and reaches to the gene pool frequency.

[9]

Use the Initial Frequency of S Allele Slider above the allele frequency graph to set the frequency of S in the gene pool to a value different from 0.5. [ 2.7 ] Predict what will happen to the frequency of S among zygotes when you run the simulation. (Put a check mark in the blank next to your choice.) The frequency of S among the zygotes will move ever closer to 0.5 as more and more zygotes form. The frequency of S among the zygotes will move ever closer to the frequency of S in the gene pool as more zygotes form. Other. Explain

[ 10 ]

RUN the simulation.

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Foundations of Biology: Ecology & Evolution LAB Biology 206

LAB 4

[ 2.8 ] Was your prediction in Question 9.1 correct? Ans. Yes.

[ 11 ]

Try one or two more values for the frequency of S in the gene pool, and RUN the simulation. [ 2.9 ] Summarize your observations on the relationship between the frequency of an allele in the gene pool, the frequency of the same allele among the zygotes, and the number of zygotes made. Ans. According to my observation, by the time number of zygotes increases and move closer to the frequency of S in the gene pool as zygotes form.

Your observations illustrate a general principle. The larger the random sample we take from a population, the closer the expected match between the frequency of an allele/gene/trait in our sample and the frequency of the allele/gene/trait in the population. [ 12 ]

Think about how many zygotes you have to make to be confident of a reasonably close match between the frequency of S in the gene pool and the frequency of S among the zygotes. As an example, recall that there were around 15 ferrets in each breeding pen and 500 in the field population in the Luck of the Draw exercise. These are the average number of successful zygotes made each generation. [ 2.10 ] How might these numbers, combined with your observations here (in the Random Mating exercise), explain why allele frequencies jumped around so much more in your Luck of the Draw breeding pens than in the field? Ans. It is because of the sampling error. When we have small sample size the allelic frequency differ relatively from the large group of population.

[ 13 ] Click the TEST YOUR UNDERSTANDING and answer the pop-up question.

A change in allele frequencies across generations due to sampling error is known as random genetic drift, or simply genetic drift. Because evolution is defined as change in allele frequencies across generations, genetic drift is a mechanism of evolution. Your observations have established that there is another mechanism of evolution besides natural selection. There is a crucial difference between natural selection and genetic drift. In natural selection, alleles rise (or fall) in frequency because they endow individuals that carry them with superior (or inferior) ability

to

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Foundations of Biology: Ecology & Evolution LAB Biology 206

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survive and reproduce. In genetic drift, alleles rise (or fall) in frequency because the individuals that carry them happened to be lucky (or not). Just by chance, some eggs and sperm find each other, while others don’t.

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Foundations of Biology: Ecology & Evolution LAB Biology 206

LAB 4

Exercise 3: Size Matters [1]

So far you have learned the basics about how genetic drift works, according to the idea that populations evolve as a result of sampling error. Now consider this prediction: Allele frequencies change by genetic drift equally quickly in large populations and small populations. [ 3.1 ]

Do you agree with this prediction?

Ans. Yes, I agree with this prediction.

[ 3.2 ]

Describe a study that would test the prediction. Include a description of the results we will see if the prediction is correct versus incorrect. Ans. The study to test the prediction should be conducted with the different population size. The population size must be known in order to take out the comparable extent of the population. We will observe genetic diversity of the population, whether it would be equal or greater loss.

Select Size Matters from the SELECT AN EXERCISE button the screen.

[2]

in the upper left-hand corner of

In this exercise, you’ll have the opportunity to study the relationship between population size and the rate of evolution by drift. On the left side of the screen are four fields stocked with black-footed ferrets. By default each field contains 500 ferrets, but you can change this with...