BIOLOGY Assignment

The following questions are designed to help you become familiar with the operation of Fly Lab by studying the inheritance of traits in frut flies. The purpose of this laboratory is to simulate basic principles of genetic inheritance based on Mendelian genetics, to understand the relationship between phenotype and genotype, and how to construct punnet squares to determine characteristic phenotypic ratios. Follow the instructions in the lab manual and answer the questions below as you work through the FlyLab using the lab manual. Remember to show numerical data in tables or figures using the guidelines provided (“Data Presentation Basics” Powerpoint presentation found in the START HERE FIRST folder under the Lesson’s tab on the Angel website),, to explain the data in simple, clear, concise sentences, and to then answer the questions or draw conclusions using the data. Data always appears in the text in the form of a table or a figure not both as soon after it is mentioned as possible. References are cited in your responses not at the end of the lab report! Insert your responses in the green text boxes below. They will expand as you enter text as needed. Copy and paste figures from the lab simulations as needed into the green response boxes. Use the “Export Feature” of the lab, the select the text or figure using the click, drag, select features of your mouse, type ctrl C to copy to the clipboard, place cursor in destination document and type ctrl V to copy from the clipboard. If the “Export” command in the lab simulations doesn’t work for you turn off “ALL” of your popup blockers!

Gene Symbols (Creation and Use)
1. A gene symbol shall consist of a base of one to three letters. Previously published gene symbols will have priority. Additional information can be appended as described below. 
2. For cases in which one allele is dominant, the first letter of the base symbol shall be capitalized to designate the dominant allele while all lower case letters will indicate the recessive allele. For example big “A” for the dominant version of the gene and little “a” for the recessive allele. 
3. For diploid individuals AA, Aa, aa would be the correct form for the genotype of a homozygous dominant, heterozygous dominant, and homozygous recessive individuals, respectively. Use different letters for different characters.
Related Resources
Drosophila Virtual Library – comprehensive list of web resources on Drosophila research. 
http://www2.edc.org/weblabs/WebLabDirectory1.html The genetics web lab directory. There are several great exercises here for your enjoyment. I highly recommend the Punnet Square exercise
I can’t provide the link for this but I highly recommend Thinking as a Scientist: How Is the Chi-Square Test Used in Genetic Analysis? (9.23) found on the C&C website under chapter 9. 
Berkeley Drosophila Genome Project – consortium to determine the complete DNA sequence of the euchromatic genome of the fruit fly, and to develop experimental and computational tools to probe its biological significance. 
Cooley Lab – Yale School of Medicine – studying the regulatory pathways that control the cytoskeletal reorganization during Drosophila egg chamber development. 
http://www.biology.arizona.edu/mendelian_genetics/mendelian_genetics.html Mendelian Genetics exercises at the Biology Project.
Assignment #1

1. To begin a cross in FlyLab, you must first select the phenotypes of the flies that you want to mate. Follow the directions in each question to create a monohybrid cross between a wild- type female fly and a male fly with sepia eyes.

To design a wild-type female fly, click on the Design button below the gray image of the female fly. Click on the button for the Body Color trait (or any trait) on the left side of the Design view. The small button next to the words “Wild Type” should already be selected (bolded). To choose this phenotype, click the Select button below the image of the fly at the bottom of the design screen. Remember that this fly represents a true-breeding parent that is homozygous for wild type alleles. The selected female fly now appears on the screen with a “+” symbol indicating the wild-type phenotype.

To design a male fly with sepia eyes, click on the Design button below the gray image of the male fly. Click on the button for the Eye Color trait on the left side of the Design view. Click on the small button next to the word “Sepia.” Note how eye color in this fly compares with the wild-type eye color. Choose this fly by clicking on the Select button below the image of the fly at the bottom of the Design screen. The male fly now appears on the screen with the abbreviation “SE” indicating the sepia eye mutation. This fly is homozygous for the sepia eye allele. These two flies represent the parental generation (P generation) for your cross.

Based on what you know about the principles of Mendelian genetics, predict the phenotypic ratio and phenotype that you would expect to see for the F1 offspring of this cross. (2pt)

Respond to question 1 here 

2. To select the number of offspring to create by this mating, click on the popup menu on the left side of the screen and select 10,000 flies. To mate the two flies, click on the Mate button between the two flies. Note the fly images that appear in the box at the bottom of the screen. Scroll up to see the parent flies and down to see the wild type offspring. These offspring are the F1 generation. Note: The actual number of F1 offspring created by FlyLab does not exactly equal the 10,000 offspring that you selected. This difference represents the experimental error introduced by FlyLab. 

Examine the results of this cross and save the results to your lab notes. Tabulate your data and present it. Provide a punnet square, tabulate data. What is the observed phenotypic ratio? Are the phenotypes and the phenotypic ratio of the F1 offspring what you would have predicted for this cross? Why or why not? (2pts)

Respond to question 2 here 

3. To set up a cross between two F1 offspring to produce an F2 generation, be sure that you are looking at the two wild-type offspring flies in the box at the bottom of the screen. If not, scroll to the bottom of this box until the word “Offspring” appears in the center of the box. Click the Select button below the female wild-type fly image, then click the Select button below the male wild-type fly image. Note that the two F1 offspring that you just selected appear at the top of the screen as the flies chosen for your new mating. Click on the Mate button between the two flies. The F2 generation of flies now appears in the box at the bottom of the screen. Use the scroll buttons to view the phenotypes of the F2 offspring. 

Examine the results of this cross and save the results to your lab notes. . Tabulate your data and present it. Provide a punnet square, tabulate data.. What is the phenotypic ratio of the F2 offspring? What are the phenotypes of the F2 offspring? (2pts)

Respond to question 3 here 

4. To validate or reject a hypothesis, perform a Chi-square analysis as follows. Click on the Chi-Square Test button on the lower left side of the screen. To ignore the effects of sex on this cross, click on the Ignore Sex button. Enter a predicted ratio for a hypothesis that you want to test. For example, if you want to test a 4:1 ratio, enter a 4 in the first box under the Hypothesis column and enter a 1 in the second box. To evaluate the effects of sex on this cross, simply type a 4 in each of the first two boxes, and type a 1 in each of the last two boxes. Click the Test Hypothesis button at the bottom of the panel. A new panel will appear with the results of the chi-square analysis. Note the level of significance displayed with a recommendation to either reject or not reject your hypothesis. 

What was the recommendation from the chi-square test with a 4:1 ratio? Was your ratio accepted or rejected. . Tabulate your data and present it. (2pts)

Respond to question 4 here 

5. Repeat the Chi-square analysis with a new ratio until you discover a ratio that will not be rejected. 

5a. What did you discover to be the correct phenotypic ratio for this experiment? . Tabulate your data and present it. Was this what you expected? Why or why not? (2pts)

5b.What do the results of this experiment tell you about the dominance or recessiveness of the sepia allele for eye color? (2pts)

Respond to question 5a here 

Respond to question 5b here 

6. Click on the New Mate button in the lower left corner of the screen to clear your previous cross. 

6a. Examine the results of this cross and save the results to your lab notes. . Tabulate your data and present it. Provide a punnet square, tabulate data. Following the procedure described above, perform monohybrid crosses for at least three other characters. For each cross, develop a hypothesis to predict the results of the phenotypes in the F1 and F2 generations and perform chi-square analysis to compare your observed ratios with your predicted ratios. Tabulate your data and present it. (6pts)

6b. Examine the results of this cross and save the results to your lab notes. Tabulate your data and present it. For each individual cross, try varying the number of offspring produced. What effect, if any, does this have on the results produced and your ability to perform chi-square analysis on these data? Tabulate your data and present it. (Hint: what happens to the size of the sums of squres and the estimate of Chi-square as the number of progeny are increased?)(6pts)

6c. If any of your crosses do not follow an expected pattern of inheritance, provide possible reasons to account for your results. Some of the characteristics available in this simulation are inherited via simple mendelian genetics (one copy of the dominant allele masks the expression of the recessive allele and some are sex-linked. The expected phenotypic ratios will be different (CC p176) (3pts)

Respond to question 6a character #1 here 

Respond to question 6a character #2 here 

Respond to question 6a character #3 here 

Respond to question 6b here 

Respond to question 6c here 

7. Once you are comfortable with using FlyLab to perform a monohybrid cross, design a dihybrid cross by selecting and crossing an ebony body female fly with a male fly that has the vestigial mutation for wing size. 

7a. Develop a hypothesis to predict the phenotypic ratio in the F1 and F2 progeny of this cross and describe each phenotype that you would expect to see in both the F1 and F2 generations of this cross. For example a phenotypic ratio could be 3:1 or 1:1:1:1 or 9:3, it isn’t just words. (2pt)

7b. Examine the results of this cross and save the results to your lab notes. . Tabulate your data and present it. Provide a punnet square, tabulate data.. Describe the phenotypes that you observed in both the F1 and F2 generations of this cross. How does the observed phenotypic ratio for the F2 generation compare with your predicted phenotypic ratio? Explain your answer. (5pts)

Respond to question 7a here 

Respond to question 7b here 

8. Use FlyLab to perform a trihybrid cross by designing and crossing a wild-type female fly and a male fly with dumpy wing shape, ebony body color, and shaven bristles. 

8a. Develop a hypothesis to predict the phenotypic ratio in the F1 and F2 progeny of this cross and describe each phenotype that you would expect to see in both the F1 and F2 generations of this cross. (2pt)

8b. Examine the results of this cross and save the results to your lab notes. Tabulate your data and present it. Perform your cross and evaluate your hypothesis by Chi-square analysis. What was the trihybrid phenotypic ratio produced for the F2 generation? . Tabulate your data and present it. Provide a punnet square, tabulate data. (5pts)

Respond to question 8a here 

Respond to question 8b here 
Assignment #2

A testcross is a valuable way to use a genetic cross to determine the genotype of an organism that shows a dominant phenotype but unknown genotype. For instance, using Mendel’s peas, a pea plant with purple flowers as the dominant phenotype could have either a homozygous or a heterozygous genotype. With a testcross, the organism with an unknown genotype for a dominant phenotype is crossed with an organism that is homozygous recessive for the same trait. In the animal- and plant-breeding industries, testcrosses are one way in which the unknown genotype of an organism with a dominant trait can be determined. Perform the following experiment to help you understand how a testcross can be used to determine the genotype of an organism.

9. Design a female fly with brown eye (BW) color (keep all other traits as wild-type), and design a male fly with ebony body color (E; keep all other traits as wild-type). Mate the two flies. Examine the F1 offspring from this cross and save your data to your lab notes. Add to your data any comments that you would like. To determine the genotype of an F1 wild-type female fly, design a male fly with brown eye color and ebony body color, then cross this fly with an F1 wild-type female fly. 

Examine the results of this cross and save the results to your lab notes. Tabulate your data and present it. What was the phenotypic ratio for the offspring resulting from this testcross? Show work! Tabulate your data and present it. (5pts)

Respond to question 9 here 

10a. Based on the phenotypic ratio, determine whether the F1 wild-type female was double homozygous or double heterozygous for the eye color and body color alleles. Show work ! (5pts)

10b. Explain your answer. If your answer was double homozygous, describe an expected phenotypic ratio for the offspring produced from a testcross with a double heterozygous fly. If your answer was double heterozygous, describe an expected phenotypic ratio for the offspring produced from a testcross with a homozygous fly. Show work! This requires a punnet square (5pts)

Respond to question 10a here 

Respond to question 10b here 