The exercises described below will help you to understand the principles that are introduced in the various lectures about Mendelian genetics. The exercises described below are matched to the course Lecture in which the principles that they demonstrate are described. Links are also provided to permit you to jump to the lecture notes, and to return to the exercises from the lecture notes. Be sure to read the course web page containing Virtual FlyLab Information for Beginners before attempting to do these exercises.

Menu of Available Exercises You may click on the menu that follows to jump directly to the exercises for a particular lecture, or you may scroll down. All of the exercises are on this extended web page.

Lecture 21, Equal Segregation
Lecture 22, Independent Segregation
Lecture 24, Chi-Square Analysis
Lecture 25, Dominant Lethal Alleles
Lecture 26, Gene Interactions
Lecture 28, Sex-Linked Genes
Lecture 30, Linkage, Map Distance
Lecture 31, Three-Point Crosses, Gene Order

Lecture 21, Equal Segregation

This set of exercises illustrates the principle of random segregation through the use of monohybrid crosses of wild-type flies with strains that are homozygous for autosomal (not sex linked) dominant or recessive mutations. In this set of exercises, you will employ four different mutant strains, brown eyes, ebony body, shaven bristles, and lobed eyes. For each of the strains, perform the following set of experiments (parts of this exercise have been incorporated into problem set #6).

1. Mate a mutant female fly with a wild type male fly. Examine the F1 hybrids to determine whether the marker was dominant or recessive.

2. Perform a test cross to verify your conclusions from experiment 1. For recessive mutations, mate the F1 hybrid with the mutant parent and examine the phenotypic distribution of the progeny. For dominant mutations, mate the F1 hybrid with a wild type fly (wild type is recessive to a dominant mutation) and examine the phenotypic distribution of the progeny. In both cases, verify that the distributions are those expected from test crosses. Also, be sure that you understand why you expect that distribution from a test cross.

3. Mate a male F1 hybrid with a female F1 hybrid to generate an F2 population. Examine the phenotypic ratio and verify that it is what is expected for F2 progeny. Also be certain that you understand the genetic mechanisms that give rise to that phenotypic ratio.

4. Repeat steps 1 and 3 starting with a mutant male and a wild type female to verify that these markers are autosomal. Because there is only one X chromosome in males, sex-linked markers behave differently in the two sexes, as we shall see when we get to lecture 28.

Lecture 22, Independent Assortment

This set of exercises illustrates the principle of independent assortment through the use of crosses involving two or three unlinked autosomal mutations.

1. Place ebony body and shaven bristles in the same parent (either sex) and mate with a wild-type fly. Do a test cross of the F1 progeny with the doubly-recessive parent and examine the phenotypic distribution of the progeny. Verify that the results are consistent with the expectations for such a test cross and be sure that you understand why the expectations are what they are.

2. Use the F1 progeny from step 1 to generate F2 progeny. Verify that the phenotypic distribution is consistent with the expectation for an F2 dihybrid cross and be certain that you understand the basis for that expectation.

3. Place the two markers in a trans configuration in the parental generation. Determine whether there is any affect on the F2 generation. Also be sure you understand why you cannot do a test cross with the markers in a trans configuration.

4. You know from the Lecture 21 exercises that lobed eyes is dominant, and that ebony body and shaven bristle mutations are recessive. Construct a cross that will allow to do a test cross of the F1 triple heterozygote for these three mutations. Remember that all of the recessive alleles must be in the same parent to be able to do a test cross. Perform the test cross and examine the phenotypic ratios. Be sure you understand why these ratios come out the way they do.

5. Mate the F1 hybrids from part 4 to obtain an F2 generation. Be certain that you understand the theoretical basis for the phenotypic ratios that are obtained.

Lecture 24, Chi-Square Analysis

The exercises that follow provide you with some opportunities to see chi-square analysis in action without having to do the actual numerical calculations. Please note that some of the crosses have been deliberately selected to yield unexpoected results that you will not be required to understand fully until the principles that are involved are covered in future lectures. The point at this time is that a chi-square analysis will not support predictions based solely on the elementary aspects of genetics that have already been covered in this course. Thus, we will need to look for more complex explanations before the semester is completed.

Whenever you obtain the results of a cross with the Virtual FlyLab, one of the options that is offered to you is to propose a hypothesis to explain the results, which you can then analyze for goodness of fit using the chi-square formula. Scroll down the results screen to "Possible Actions" and click on the bar labeled "Propose and Test Hypotheses" (note that the formula for chi-square is also on the bar).

The screen that comes up will allow you either to work with the results including the sex of the progeny flies or by scrolling down further, results excluding sex. To keep things simple, this set of exercises excludes the sex of the progeny, which will not become important until we begin to work with sex-linked loci.

In either case, you are asked to propose a theory to explain the results and to insert your hypothetical ratios into a set of windows that follow the observed ratios. For example, if you are looking at the F2 of a monohybrid cross, the most likely theory to test would be a 3:1 ratio of dominant phenotype to recessive. Click on each window and insert a number that corresponds to your expectations. You must place numbers in all of the windows for the data set you are working with. Then click on the bar to perform the analysis.

The results that are shown will include the expected number (E) for each observation, based on your hypothesis and the total number of flies examined, the value (O-E)²/E for each observation, the X² value, the number of degrees of freedom, and the probability that the amount of deviation from your hypothesis could have occured by random chance. There is also a recommendation either to reject the hypothesis or not to reject the hypothesis, based on the chi-square value and the number of degrees of freedom. .

1. Mate a male fly with brown eyes and ebony body to a wild-type female. Mate the F1 progeny to generate an F2 generation. Test the hypothesis that the results fit the expected 9:3:3:1 distribution for the F2 generation of an unlinked dihybrid cross. If the Virtual FlyLab has the right amount of randomness programmed into it, there should be a 1:20 chance that the results of your first trial will fall outside the 0.05 confidence limit, such that you will recive a recommendation to reject the hypothesis. If this happens to you, start over with another set of crosses. The probability should be very low (1/400) that you will have two independent crosses that both fall outside the limits.

2. Scroll to the bottom of the page that gave you the results of your analysis of the data and click on the bar for proposing another hypothesis for the same data. This time alter the expected ratio slightly (for example, 10:3:3:1) and run another analysis to see the effect on the chi-square value.

3. Mate a female fly with curly wings to a wild type male. The progeny of both sexes will be half curly and half wild-type, which tells you that curly is dominant and that the original curly-winged female fly and the curly-wnged progeny are heterozygous. Mate the curly-winged F1 progeny and examine the phenotypic distribution of the F2, which will come out about 2 curly:1 wild type. Test the hypothesis that this is really a random deviation from 3:1. Also test the hypothesis that the ratio actually is 2:1. The reason for this unusual ratio is that the curly wings allele is lethal when it is homozygous. This phenomenon will be discussed in lecture 25.

4. Mate a male fly with brown eyes and dumpy wings with a wild type female. Do a test cross of an F1 female double heterozygote with the parental double recessive male. Analyze the results using the hypthesis of a 1:1:1:1 ratio of the four possible genotypes in the test cross progeny. These two genetic loci are on the same chromosome, but so far apart that there is enough crossover so they exhibit only a slight tendancy to stay linked together. Try other ratios, such as 3:2:2:3 or 29:21:21:29 to see if you can find one that will not be rejected by the chi-square analysis. We will begin studying linkage in Lecture 30.

Lecture 25, Dominant Lethal Alleles

Lecture 25 covers several distantly related topics, including partial dominance, codominance, and dominant lethal alleles. The only part of this lectue that can be illustrated with examples from the Virtual FlyLab is the effect of dominant lethal alleles, which have already been introduced in exercise 3 from Lecture 24.

1. Produce F2 offspring of parental mutant strains crossed with wild type to determine which of the following dominant mutations are lethal when homozygous: Lobed eyes, Curly wings, Stubble Bristles, and Star eyes. Remember that dominant lethal parents must be alive, and are therefore heterozygous.

2. Cross a curly winged male with a stubble bristled female. Explain the phenotypic distribution of the offspring. (These two genetic loci are not linked and undergo independent assortment. You may find it convenient to construct a Punnett Square to explain the results of the cross)

3. Cross a male double mutant from the F1 generation in part 2 with a female double mutant. Construct a Punnett Square for the cross and use it to predict the F2 phenotypic ratios. (Remember that being homozygous for either of the lethal genes will be lethal). Do a Chi-square analysis to test the validity of your predicted phenotypic ratios.

4. Cross a curly winged fly with an ebony body fly. (Remember that the dominant lethal Curly-winged parent will be heterozygous, whereas the unlinked recessive ebony body parent will be homozygous. Mate the male and female curly winged progeny of this cross, which will also be heterozygous for ebony body. Use a forked line approach to predict the phenotypes of the F2 progeny. Then do a chi-square analysis to test the validity of your prediction. Be able to explain why this cross yields a 6:3:2:1 ratio. If you have trouble with the forked line, first do a Punnett square, and then convert your results to a forked line diagram.

Lecture 26, Interaction Among Genes

The Virtual FlyLab can produce epistasis in two ways. The recessive apterous and vestigial wing mutations will mask any mutations involving wing shape, wing angle, or wing veins. The recessive eyeless mutation will mask any of the eye color mutations. The exercises that follow have been designed to avoid complications due to sex linkage or loci carried on the same chromosome.

If you wish, you may substitute vestigial wings in place of apterous wings. However, most of the other combinations that can be examined using the Virtual FlyLab will yield more complex results due to linkage of genes on the same chromosome or sex linkage. We are unable to examine interactions among eye color mutations because the system only allows us to work with one eye color mutation at a time.

1. Mate a fly that has apterous wings with a fly that has radius incompletus wings. Mate the F1 progeny to produce an F2 generation. Examine the phenotypic distribution of the F2 progeny. Propose a theoretical explanation for the distribution and use a Chi-square test to examine goodness of fit (see the exercises for lecture 24 if you have forgotten how to do Chi-square using the Virtual FlyLab). If you are having trouble generating a hypothesis, construct a Punnett square for the F2 generation.

2. Mate an eyeless fly with one that has brown eyes. Mate the F1 progeny to produce an F2 generation. Propose a theoretical explanation for the phenotypic distribution of the F2 progeny. Test the goodness of fit of your prediction with a Chi-square test.

3. Mate a fly that has apterous wings with a fly that has dichaete wings (the last panel at the bottom of the selection menu). Observe the phenotypic ratio of the offspring. (The Dichaete wings mutation is lethal when homozygous, making this an extra interesting exercise). Mate the male and female progeny that have dichaete wings. Examine the phenotypic distribution of their progeny and propose an explanation for that phenotypic ratio. Text the goodness of fit of your explanation with a Chi-square analysis. You will probably need to construct a Punnett square or a forked line diagram to develop your proposed explanation.

Go to Notes for Lecture 26
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Lecture 28, Sex Linked Genes

1. This exercise attempts to recreate some of the early experiments done with sex linkage in Drosophila. You have found a male fly with white eyes in your laboratory cultures.
   a. Mate the white eyed male with a wild type female and observe the progeny. What can you conclude about the mutation based on this experiment alone.

   b. Mate two F1 flies and observe the F2 progeny. What conclusions can you reach from the phenotypic distributions?

   c. Cross a heterozygous female with a white-eyed male. Interpret the phenotypic distributions that are observed in male and female progeny in terms of possible chromosomal mechanisms.

   d. Mate a white-eyed female with a wild-type male. Interpret the phenotypic distribution observed in the progeny.

   e. Summarize the steps that must be completed to generate a true breeding stock of white-eyed flies, starting with the original white-eyed male and a wild-type female.

2. Repeat as many of the above exercises as you can starting with a Bar eyed male. At each step, be sure that you understand the differences in the pattern of inheritance exhibited by the bar eyed and white eyed mutations. .

3. Compare the patterns of inheritance of bar eyes and lobed eyes.

   a. What features do their inheritance patterns share in common?

   b. How do their inheritance patterns differ?

   c. Compare the F2 phenotypic distributions for a bar eyed male mated to a wild type female and a lobed eyed male mated to a wild type female.

4. Compare the patterns of inheritance for sable body and ebony body.
   a. What features do their inheritance patterns share in common?

   b. How do their inheritance patterns differ?

   c. Compare the F2 phenotypic distributions for a ebony body male mated to a wild type female and a sable body male mated to a wild type female.

5. Based on the results you obtained in the two previous quesitons, devise a simple procedure for distinguishing between each of the following pairs. Perform the appropriate matings to verify that you procedure will achieve the desired results.
   a. Sex-linked dominant vs. sex-linked recessive.

   b. Sex-linked dominant vs. autosomal dominant

   c. Autosomal dominant vs. autosomal recessive

   d. Autosomal recessive vs. sex-linked recessive.

6. Determine which of the following loci are sex-linked and whether the sex linked mutations are dominant or recessive. :
   a. Tan Body

   b. Black body

   c. Bar eyes

   d. Forked bristles

   e. Singed bristles

   f. Spineless bristles

   g. Crossveinless wings

   h. Dumpy wings

7. Mate a male that has purple eyes and a sable body with a wild type female and generate F2 progeny. Explain the phenotypic distribution in the F2 generation in terms of chromosomal locations of the two loci.

Go to Notes for Lecture 28
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Lecture 30, Linkage, Map Distance

1. Miniature wings and white eyes are both sex linked.
   a. Mate a male that has miniature wings and white eyes to a wild-type female. Test cross the F1 female with the parental male.

   b. Mate a wild-type F1 male with a heterozygous F1 female.

   c. Determine the phenotypic ratios of the male progeny.

   d. Use the data from the male progeny to calculate the distance between these two loci in centimorgans.

   e. Mate a heterozygous F1 female with the hemizygous parental male and repeat steps c and d examining only the male progeny of the cross.

   f. Determine the phenotyopic ratios of the female progeny of the cross in part e and calculate map distance based on those data.

   g. Compare the three map distances that you have obtained. How much do they differ. To what do you attribute the differences that you may have observed?

2. All of the genetic loci in this example are sex-linked.
   a. Determine the distance in centimorgans from yellow body to each of the following loci. white eyes, crossveinless wings, forked bristles, miniature wings and singed bristles.

   b. Construct a crude map of the X-chromosome, based on the assumption that yellow body is at 0.0 map units.

   c. Determine the map distances between all nearest neighbors on the map by doing appropriate crosses.

   d. Compare the apparent map distance from yellow to the most distant locus on your map based on direct measurement with that obtained by adding together all of the intermediate distances.

   e. Determine the map distance from white eyes to sable body and to tan body (note that direct measurements cannot be made between body color mutations using the Virtual Fly Lab, and that they might have problems in real life because of interactions of the body color genes).

   f. Use the data from part e to add sable body and tan body to the map you have constructed.

   g. Determine the distances from sable body and tan body to their nearest neighbors.

   h. Perform the necessary crosses to add Bar eues to your map, keeping in mind that it is dominant.

Go to Notes for Lecture 30
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Lecture 31, Three-Point Crosses, Gene Order

1. Three sex-linked mutations, white eyes, yellow body, and miniature wings were used in the earliest mapping experiments by Sturtevant and Morgan. Mate a male fly that carries all three mutations with a wild type female and then do a test cross on the F1 female.
   a. Identify the paired recombinational events based on relative frequencies of progeny. (If you work directly from the results page, you must first combine males and females for each phenotype -- alternatively, you can go to the Chi-square page where males and females are already added together.)

   b. Determine the fraction of progeny that fall into each recombinational class by dividing by the total number of flies counted.

   c. Verify the identity of the parental pair (which you already know from the original cross).

   d. Identify the double recombinant pair.

   e. Identify the middle genetic locus.

   f. Identify the two single crossover pairs

   g. Determine the corrected map distances between each of the possible pairings of these three loci, adding in double crossover frequencies where appropriate.

   h. Reexamine your data, looking only at those classes of progeny in which the two outside loci have recombined. This is equivalent to examining a two point cross. How much does the apparent distance between these two loci differ from the corrected distance, which is based on a three point cross.

2. Set up another experiment in which you can mate a female that is heterozygous at all three of the loci in question 1 with a wild type male. Repeat all of the exercises in question 1, looking only at male progeny of the new cross. How closely do the results of the two experiments correlate?

3. The loci for sable body, bar eyes, and crossveinless wings are also sex linked. Determine whether each of these mutations is dominant or recessive, and then perform appropriate three point crosses to determine their map positions relative to loci whose locations you already know from problem 1 or earlier parts of this problem. (Remember that wild-type is recessive to a dominant mutation. Also, be aware that you can only use one mutation at a time from each category in the Virtual FlyLab and plan your crosses accordingly.).

4. Sepia eyes, radius incompletus wings, and ebony body are linked.
   a. Determine the nature of each of the mutations.

   b. Do two point crosses for each combination and construct a rough map of the linkage group.

   c. Do a three point cross and use the data to refine the two point map.
   d. Calculate the interference to crossing over that was observed in your two point cross.

   e. Aristapedia antennae is very closely linked to one of these three markers. Determine the nature of the AR mutation and see if you can place it on your map relative to the other three mutations. (Remember that the test parent must be all recessive, and that the fly that you select for recombinational studies must be heterozygous for all of the markers you are examining.)

5. All of the makers in this exercise are recessive and carried on chromosome II. Perform the following steps to obtain a partial map of chromosome II and to examine the underestimation of map distance that occurs in direct measurements between distant markers. Note that VFL can only work with one eye color mutation at a time. Also, vestigial wings and apterous wings cannot be used in the same cross. In addition, these two mutations are epistatic to wing shape mutations.

   a. Measure the distance from purple eyes to apterous wings in a two point cross.

   b. Use a three point cross to identify the middle locus and measure apparent map distance among black body, apterous wings and purple eyes.

   c. Use a three point cross to identify the middle locus and measure apparent map distances among dumpy wings, black body, and purple eyes.

   d. Use a three point cross to identify the middle locus and measure apparent map distances among apterous wings, black body, and brown eyes. (If you wish to shorten this exercise, you may skip to part g at this time. However, doing so will reduce the accuracy of your final result by reducing the number of intermediate measurements available.)

   e. Use a three point cross to identify the middle locus and measure apparent map distances among brown eyes, curved wings, and black body.

   f. Use a three point cross to identify the middle locus and measure apparent map distance among curved wings, purple eyes, and black body.

   g. Construct a map of chromosome II, using the intermediate distances obtained in all of the exercises above. Use the map to determine the distance between brown eyes and dumpy wings as accurately as you can.

   h. Measure the distance from brown eyes to dumpy wings in a two point cross. How do you reconcile the difference between this measurement and the map distance obtained in part g?

   i. If you wish to expand your map to include more markers, you can find map locations for four additional chromosome II markers, vestigial wings (recessive), Lobed Eyes (dominant, non lethal), Curly wings (Dominant lethal), and Star eyes (Dominant lethal). If you do so, you may wish to calculate total map distance from Star eyes to brown eyes and to compare that distance to the value obtained in a two point cross involving those two markers.

Go to Notes for Lecture 31
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