Phylogenetic Trees and Cladograms

Works Cited

Samanthi. "Home." Difference Between. N.p., 05 Apr. 2017. Web. 21 May 2017.

"Phylogenetic Tree of Life." Wikipedia. Wikipedia, Sept. 2006. Web. 21 May 2017.

Reece, Jane B., Lisa A. Urry, Michael L. Cain, Steven Alexander Wasserman, Peter V. Minorsky, Robert B. Jackson, and Neil A. Campbell. "Phylogeny and the Tree of Life." Campbell Biology. 10th ed. Boston: Pearson, 2014. N. page. Print.

Genetics of Fruit Flies

Hypothesis: If fruit flies with different phenotypes are mated, then their offspring would express the dominant phenotypes.

Materials:

• Vials of purebred parental flies
• Vial of experimental mated cross
• 4 vials containing the media for the cross
• 1 bottle of BugOut solution
• Camel hair paintbrush to manipulate flies
• Filter Paper
• Foam Lids
• Pasteur Pipets
• Petri Plate
• Drosophila Culture Tubes
• Drosophila Growth Media
• Dissecting Microscope
• Microscope
• Vegetable or Mineral Oil for morgue
• Flask with fitted cork (morgue)
• NaCl solution
• Slide and Cover
• Acetocarmine Stain
• Glass Slide

Procedures:

1. Obtain a vial of F1 flies from your teacher
1. Note the vial number and parental cross marked on the vial in your notebook.
2. Using standard fly handling techniques, collect the F1 flies and collect the F1 flies and observe their phenotypes
3. Record the results.
2. Place 5-6 male and female F1 flies into the fresh vial with media
3. After 10 days, remove F1 parents and discard into the fly morgue
4. The F2 generation flies will begin to emerge within several days
1. Remove the F2 generation flies as they begin to emerge to an empty vial without media and anesthetize
2. Observe the flies under the dissecting microscope. Record the F2 results over a 3-4 day period. The more data you accumulate the more significant the results.
5. Analyze the data using the chi-squared statistic. Obtain the class results for the other crosses in this experiment and analyze the results using a chi-square as well.

Crosses

Monohybrid Cross

Results

F1 Phenotype	My Data		Class Data
	Female	Male	Female	Male
Red Eyes	586	601	9	64
Sepia Eyes	0	0	0	0
F2 Phenotype	My Data		Class Data
	Female	Male	Female	Male
Red Eyes	446	461	2	4
Sepia Eyes	158	156	0	0

Justification:  The data shows that the majority of the flies inherited red eyes instead of sepia eyes in both generations. There also tends to be more male flies than female flies. The class data may not match up with my data because there may have been an error when inputting the data into the class spreadsheet.

Parentals: Sepia (rr), Red Eyes (RR), RR x rr

F1 Generation: Red Eyes (Rr)

	R	R
r	Rr	Rr
r	Rr	Rr

Chi-Square

Phenotype	Observed	Expected	(E-O)2/E
Red Eyes	1187	1187	0
Sepia Eyes	0	0	0
	1187	Total:	0
		Degrees Freedom:	1

Justification: Since the chi-square statistic was lower that the P-value, 0.455, we keep the null hypothesis.

F2 Generation: Red Eyes (RR)(Rr), Sepia (rr), Rr x Rr

	R	r
R	RR	Rr
r	Rr	rr

Chi-square

Phenotype	Observed	Expected	(E-O)2/E
Red Eyes	907	916	0.0884
Sepia Eyes	314	305	0.2656
	1221	Total:	0.3540
		Degrees Freedom:	1

Justification: Since the chi-square statistics, 0.3540, is smaller than the P-value, 0.455, we keep the null hypothesis.

Sex-Linked Cross

F1 Phenotype	My Data		Class Data
	Female	Male	Female	Male
Red eyes	616	609	4	72
White Eyes	0	0	8	5
F2 Phenotype	My Data		Class Data
	Female	Male	Female	Male
Red Eyes	623	313	2	36
White Eyes	0	313	1	5

Justification: The table shows that there are more red-eyed flies in both generations than there are white-eyed flies. This could be because red eyes are a dominant trait. Errors while inputting the class data could have affected the results on this table.

Parentals: Female Red Eyes(RR), Male White Eyes(rr), RR x rr

F1 Generation:

	R	R
r	Rr	Rr
r	Rr	Rr

Chi-Square:

Phenotype	Observed	Expected	(E-O)2/E
Female Red Eyes	616	612	0.03
Male Red Eyes	609	613	0.03
	1225	Total:	0.06
		Degrees Freedom:	1

Justification: Since the chi-square statistic, 0.06, is smaller than the P-value, 0.455, we keep the null hypothesis.

F2 Generation:

	R	r
R	RR	Rr
r	Rr	rr

Chi-Square:

Phenotype	Observed	Expected	(E-O)2/E
Female Red Eyes	623	468	51.33
Male Red Eyes	313	468	51.33
Female White Eyes	0	156	156
Male White Eyes	313	156	158.01
	1249	Total:	416.67
		Degrees Freedom:	3

Justification: Since the Chi-Square statistic is larger than the P-value, 2.366, with a degrees of freedom of 3, we reject the null hypothesis.

Dihybrid Cross

F1 Phenotype	My Data		Class Data
	Males	Females	Males	Females
Red Eyes/Normal Wings	617	585	46	4
Red Eyes/Vestigial Wings	0	0	97	29
Sepia Eyes/Normal Wings	0	0	10	2
Sepia Eyes/ Vestigial Wings	0	0	37	6
F2 Phenotype	My Data		Class Data
	Males	Females	Males	Females
Red Eyes/Normal Wings	342	324	11	5
Red Eyes/Vestigial Wings	121	129	50	4
Sepia Eyes/Normal Wings	105	128	35	3
Sepia Eyes/ Vestigial Wings	40	36	25	0

Justification: The table shows that most flies are born with red eyes and normal wings. It is less likely for a fly to be born with recessive phenotypes such as sepia eyes and vestigial wings. The class data may not match my data because of an error.

Chi-square

Phenotype	Observed	Expected	(E-O)2/E
Red Eyes/Normal Wings	666	689	0.77
Red Eyes/Vestigial Wings	250	230	1.74
Sepia Eyes/Normal Wings	233	230	0.04
Sepia Eyes/ Vestigial Wings	76	76	0
		Total:	2.55
		Degrees Freedom	3

Justification: Since the chi-square statistic, 2.55, is higher than the P-value, 2.366, we reject the null hypothesis.

Study Questions

If the genes analyzed by the dihybrid cross were linked on the same chromosome, how would that affect your result?
If the genes analyzed were linked on the same chromosome, then the results would be affected because the genes on the same chromosome would most likely be present together in the offspring. This means that instead of the genes being scattered evenly with other genes, they stay together which could lead to the lack of diversity.

Why is it important that the parental females be virgins?
It is important that the parental females be virgin because if they weren’t virgin, they would probably not mate with the male flies when we wanted them to which could have affected the results.

Why are the adult flies removed?
The adult flies are removed because it makes it easier to identify the phenotypic differences of their offspring. If they weren’t removed, it would be difficult to identify which are the parentals and which are from the first or second generation.  

Why is the drosophila favorite experimental model for geneticists?
The drosophila are favorite experimental models for geneticists because they have a short life cycle and are easier to handle than other organisms are. 

Why is it necessary to analyze a large number of offspring before making conclusions about genotypic and phenotypic ratios?
It is necessary to analyze a large number of offspring before making conclusions about genotypic and phenotypic ratios because analyzing a large population, or large sample size of offspring, would result in more accurate results. The more flies that are observed, the more information one will get.

Why did you collect data for both males and females?
We collect data for both males and females because we can identify which genes or more commonly found in males or females. In other words, it helps us find out if the genes are sex-linked.

If you were a molecular biologist and had obtained two gene clones for eye color one isolated from purebred wild-type red eyed flies, the other from the mutant sepia-eyed flies, how would you analyze these genes to identify the type of gene mutation?
To identify the type of gene mutation found in the flies, I would probably breed the flies and observe their offspring's phenotypes. If the mutation were dominant, then the majority of the flies would inherit it. If it isn’t dominant, then only the homozygous recessive flies would have the mutation.

What possible genotypes and phenotypes would you observe if the F2 flies from the dihybrid cross were allowed to randomly mate?
If the F2 flies were allowed to randomly mate, then some possible genotypes that would be observed would be RRvv, Rrvv, rrvv, RRVv, RrVv, rrVv, rrVV, and RrVV where R is the dominant allele for red eyes, r is the recessive allele for sepia eyes, V is the dominant allele for normal wings, and v is the recessive allele for vestigial wings.  The phenotypes observed would be red eyes with vestigial wings, sepia eyes with vestigial wings, red eyes with normal wings, and sepia eyes with normal wings.

Assume that during a hypothetical monohybrid cross, the double recessive gene was lethal and expressed itself early in the fly development. Would that skew the results in a large population? Would the recessive eventually disappear from the population?

The results in a large population would be skewed if the double recessive gene were lethal because the flies who inherited the homozygous recessive genotype would die early. However, this does not mean that the recessive allele would disappear because heterozygous flies would carry the recessive allele without being harmed. 

Based on the example in the background section, set up a Punnett Square to predict the genotypic and phenotypic ratios obtained from a Dihybrid cross in the F1 generation and F2 generation?

F1

	Rv	Rv	Rv	Rv
rV	RrVv	RrVv	RrVv	RrVv
rV	RrVv	RrVv	RrVv	RrVv
rV	RrVv	RrVv	RrVv	RrVv
rV	RrVv	RrVv	RrVv	RrVv

RrVv - Red Eyes and Normal Wings

F2

	RV	Rv	rV	rv
RV	RRVV	RRVv	RrVV	RrVv
Rv	RRVv	RRvv	RrVv	Rrvv
rV	RrVV	RrVv	rrVV	rrVv
rv	RrVv	Rrvv	rrVv	rrvv

RRVV - Red Eyes and Normal Wings

RRVv - Red Eyes and Normal Wings

RrVV - Red Eyes and Normal Wings

RrVv - Red Eyes and Normal Wings

RRvv - Red Eyes and Vestigial Wings

Rrvv - Red Eyes and Vestigial Wings

rrVV - Sepia Eyes and Normal Wings

rrVv - Sepia Eyes and Normal Wings

rrvv - Sepia Eyes and Vestigial Wings

Use the χ2 statistic to determine the values for the monohybrid, dihybrid, and Sex-Linked crosses for your individual data and for the class data. Are the hypotheses valid?

The chi-square statistic for the monohybrid was 0.3450, the chi-square statistic for the dihybrid was 2.55, and the chi-square statistic for the sex-linked crosses was 416. 67. The hypothesis for the monohybrid cross was valid since the chi-square statistic was less than the P-value; however, the hypothesis for the dihybrid cross and the sex-linked traits were invalid because their chi-square statistics were higher than the P-value.

Conclusion:

In conclusion, this experiment showed that the alleles for red eyes and normal wings are dominant to the alleles for sepia eyes and vestigial wings. Since we were able to identify these phenotypes in the flies, the hypothesis, “If fruit flies with different phenotypes are mated, then their offspring would express the dominant phenotypes.” was valid. There could have been many errors in this experiment, such as the flies escaping from the vials which resulted in their death, also we could have wrongly identified their phenotype which could have affected the data.