Franklin Xie February 11, 2013

Assignment 1 1. Flylab Lab Notes for Franklin Xie -------------------------------------------------------------------------Results of Cross #1 Parents (Female: +) x (Male: SE) Offspring Phenotype Number Proportion Ratio Female: + 4978 0.5024 1.010 Male: + 4930 0.4976 1.000 Total 9908 These are the results of the F1 generation for my first monohybrid cross. -------------------------------------------------------------------------Chi Square Hypothesis Using Cross #1 Phenotype Female: + Male: + Total Observed Hypothesis 4978 1.0000 4930 1.0000 9908 2.0000 Expected 4954.0000 4954.0000 9908.0000 Chi-Square Term 0.1163 0.1163 0.2325

Chi-Squared Test Statistic = 0.2325 Degrees of Freedom = 1 Level of Significance = 0.6296 Recommendation: Do not reject your hypothesis This is the analysis of hypothesis of phenotype ratios from the F1 generation. -------------------------------------------------------------------------Results of Cross #2 Parents (Female: +) x (Male: +) Offspring Phenotype Number Proportion Ratio Female: + 3720 0.3675 2.993 Male: + 3858 0.3811 3.104 Female: SE 1301 0.1285 1.047 Male: SE 1243 0.1228 1.000 Total 10122 Observed phenotypic ratios of the F2 offspring of my first monohybrid cross. -------------------------------------------------------------------------Chi Square Hypothesis Using Cross #2 Phenotype Female: + Male: + Female: SE Male: SE Total Observed Hypothesis 3720 3.0000 3858 3.0000 1301 1.0000 1243 1.0000 10122 8.0000 Expected 3795.7500 3795.7500 1265.2500 1265.2500 10122.0000 Chi-Square Term 1.5117 1.0209 1.0101 0.3913 3.9340

Franklin Xie February 11, 2013

Chi-Squared Test Statistic = 3.9340 Degrees of Freedom = 3 Level of Significance = 0.2687 Recommendation: Do not reject your hypothesis This is the analysis of hypothesis of phenotype ratios from the F2 generation. -------------------------------------------------------------------------The correct phenotypic ratio for this experiment is 1:1 (wild type eyes to sepia eyes) in the F1 generation and 3:1 (wild type eyes to sepia eyes) in the F2 generation. This was what I expected because I assumed that incomplete dominance and codiminance were not factors that affected the trait for the flies' eye color. This meant that the flies that express the recessive trait must be homozygous recessive. I also assumed that the flies that express the dominant trait are true-bred and homozygous for the dominant alleles for eye type. The cross between the two true-bred fly types should, based on basic principles of dominance, produce only the dominant trait and heterozygous individuals. The parent cross, in this case, can be looked at as a test cross. Because my hypothesis for the F1 generation was analyzed and I was recommended to not reject it, I knew that I was most likely correct in assuming that all of the offspring were heterozygous. A cross between heterozygous individuals that express the dominant trait would produce offspring in a 3:1 ratio (dominant trait to trait recessive). Because the F1 generation's population was completely heterozygous and only expressed one trait, I concluded that that trait is expressed by the dominant allele. In this case, the wild type eyes are expressed by the dominant trait. Further evidence is gathered from the F2 generation. My assumption that the F1 generation was completely heterozygous was proven as the F2 generation expressed traits in a 3:1 ratio (dominant to recessive). There is a 25% chance, in a monohybrid cross between heterozygous individuals, that an offspring with the recessive trait will be born. As about 75% of the population of flies expressed the dominant trait (wild type eyes) and 25% of the population expressed the recessive trait (sepia eyes), I arrived at the conclusion that the dominant allele codes for wild type eyes. I also conclude that the alleles for eye type in this species of flies do not function on the basis of codominance or incomplete dominance because the heterozygous flies of the F1 generation did not display both traits/a mix of both traits.

2. a.
Flylab Lab Notes for Franklin Xie -------------------------------------------------------------------------Results of Cross #1 Parents (Female: +) x (Male: BL) Offspring Phenotype Female: + Male: + Total Number 4934 5020 9954 Proportion 0.4957 0.5043 Ratio 1.000 1.017

Franklin Xie February 11, 2013

-------------------------------------------------------------------------Chi Square Hypothesis Using Cross #1 Phenotype Female: + Male: + Total Observed Hypothesis 4934 1.0000 5020 1.0000 9954 2.0000 Expected 4977.0000 4977.0000 9954.0000 Chi-Square Term 0.3715 0.3715 0.7430

Chi-Squared Test Statistic = 0.7430 Degrees of Freedom = 1 Level of Significance = 0.3887 Recommendation: Do not reject your hypothesis -------------------------------------------------------------------------Results of Cross #2 Parents (Female: +) x (Male: +) Offspring Phenotype Female: + Male: + Female: BL Male: BL Total Number 371 361 115 125 972 Proportion 0.3817 0.3714 0.1183 0.1286 Ratio 3.226 3.139 1.000 1.087

-------------------------------------------------------------------------Chi Square Hypothesis Using Cross #2 Phenotype Female: + Male: + Female: BL Male: BL Total Observed Hypothesis 371 3.0000 361 3.0000 115 1.0000 125 1.0000 972 8.0000 Expected 364.5000 364.5000 121.5000 121.5000 972.0000 Chi-Square Term 0.1159 0.0336 0.3477 0.1008 0.5981

Chi-Squared Test Statistic = 0.5981 Degrees of Freedom = 3 Level of Significance = 0.8969 Recommendation: Do not reject your hypothesis -------------------------------------------------------------------------Changing the number of offspring produced does not affect the results of the chi-square analysis on the data. The data is predictable for the crosses. Using the techniques described in my answer for question number 1, I conclude that the allele for wild type body color in this species of flies is dominant to the allele for black body color.

b.
Flylab Lab Notes for Franklin Xie -------------------------------------------------------------------------Results of Cross #1

Franklin Xie February 11, 2013

Parents (Female: +) x (Male: SN) Offspring Phenotype Female: + Male: + Total Number 528 496 1024 Proportion 0.5156 0.4844 Ratio 1.065 1.000

-------------------------------------------------------------------------Chi Square Hypothesis Using Cross #1 Phenotype Female: + Male: + Total Observed Hypothesis 528 1.0000 496 1.0000 1024 2.0000 Expected 512.0000 512.0000 1024.0000 Chi-Square Term 0.5000 0.5000 1.0000

Chi-Squared Test Statistic = 1.0000 Degrees of Freedom = 1 Level of Significance = 0.3173 Recommendation: Do not reject your hypothesis -------------------------------------------------------------------------Results of Cross #2 Parents (Female: +) x (Male: +) Offspring Phenotype Female: + Male: + Male: SN Total Number 56 37 23 116 Proportion 0.4828 0.3190 0.1983 Ratio 2.435 1.609 1.000

-------------------------------------------------------------------------Chi Square Hypothesis Using Cross #2 Phenotype Female: + Male: + Male: SN Total Observed 56 37 23 116 Hypothesis 3.0000 3.0000 1.0000 7.0000 Expected 49.7143 49.7143 16.5714 116.0000 Chi-Square Term 0.7947 3.2516 2.4938 6.5402

Chi-Squared Test Statistic = 6.5402 Degrees of Freedom = 2 Level of Significance = 0.0380 Recommendation: Reject your hypothesis

Franklin Xie February 11, 2013

-------------------------------------------------------------------------By restricting the number of offspring in a cross, the results become more unpredictable. The wild type bristles should be dominant over singed bristles on a 3 to 1 basis, assuming the parents are homozygous. The F2 generation should exhibit the dominant trait to recessive trait on a 3:1 ratio. However, because I restricted the F2 generation to approximately 100 offspring, the ratio became more unpredictable. This is because of the Law of Independent Assortment and the Law of Segregation. These laws account for the randomness of genetic crosses. Based on probability, the ratio of dominant to recessive traits should be 3:1, but because the outcome of genetic crosses is random in many cases, there will be a degree of unpredictability in the outcome of the crosses. This is more apparent when there are less offspring than more offspring because a large number of crosses, due to principles of probability, will cause the results to even out towards the expected outcome. c. Flylab Lab Notes for Franklin Xie -------------------------------------------------------------------------Results of Cross #1 Parents (Female: +) x (Male: EY) Offspring Phenotype Female: + Male: + Total Number 45 59 104 Proportion 0.4327 0.5673 Ratio 1.000 1.311

-------------------------------------------------------------------------Chi Square Hypothesis Using Cross #1 Phenotype Female: + Male: + Total Observed 45 59 104 Hypothesis 1.0000 1.0000 2.0000 Expected 52.0000 52.0000 104.0000 Chi-Square Term 0.9423 0.9423 1.8846

Chi-Squared Test Statistic = 1.8846 Degrees of Freedom = 1 Level of Significance = 0.1698 Recommendation: Do not reject your hypothesis -------------------------------------------------------------------------Results of Cross #2 Parents (Female: +) x (Male: +) Offspring Phenotype Female: + Male: + Female: EY Male: EY Number 3753 3783 1321 1255 Proportion 0.3711 0.3741 0.1306 0.1241 Ratio 2.990 3.014 1.053 1.000

Franklin Xie February 11, 2013

Total 10112

-------------------------------------------------------------------------Chi Square Hypothesis Using Cross #2 Phenotype Female: + Male: + Female: EY Male: EY Total Observed Hypothesis 3753 3.0000 3783 3.0000 1321 1.0000 1255 1.0000 10112 8.0000 Expected 3792.0000 3792.0000 1264.0000 1264.0000 10112.0000 Chi-Square Term 0.4011 0.0214 2.5704 0.0641 3.0570

Chi-Squared Test Statistic = 3.0570 Degrees of Freedom = 3 Level of Significance = 0.3829 Recommendation: Do not reject your hypothesis -------------------------------------------------------------------------The F1 generation population consists of 104 flies. This generation is the outcome of the cross between homozygous individuals for variations of the same trait. I hypothesized that the offspring will express the dominant trait (wild type eye shape) on a ratio of 1:0. Even with such a limited number of offspring, the data is completely predictable because the cross between homozygous parents must produce heterozygous offspring at a 100% rate. In these different experiments (a, b, and c), the result of the different crosses is more predictable when the offspring population is larger because with more offspring, there is more opportunity for the result to even out towards what is probable. 3. Flylab Lab Notes for Franklin Xie -------------------------------------------------------------------------Results of Cross #1 Parents (Female: E) x (Male: VG) Offspring Phenotype Female: + Male: + Total Number 492 497 989 Proportion 0.4975 0.5025 Ratio 1.000 1.010

-------------------------------------------------------------------------Chi Square Hypothesis Using Cross #1 Phenotype Female: + Male: + Total Observed Hypothesis 492 1.0000 497 1.0000 989 2.0000 Expected 494.5000 494.5000 989.0000 Chi-Square Term 0.0126 0.0126 0.0253

Chi-Squared Test Statistic = 0.0253 Degrees of Freedom = 1 Level of Significance = 0.8737 Recommendation: Do not reject your hypothesis

Franklin Xie February 11, 2013

-------------------------------------------------------------------------Results of Cross #2 Parents (Female: +) x (Male: +) Offspring Phenotype Female: + Male: + Female: VG Male: VG Female: E Male: E Female: VG;E Male: VG;E Total Number 282 271 98 90 89 108 41 27 1006 Proportion 0.2803 0.2694 0.0974 0.0895 0.0885 0.1074 0.0408 0.0268 Ratio 10.444 10.037 3.630 3.333 3.296 4.000 1.519 1.000

-------------------------------------------------------------------------Chi Square Hypothesis Using Cross #2 Phenotype Female: + Male: + Female: VG Male: VG Female: E Male: E Female: VG;E Male: VG;E Total Observed Hypothesis 282 9.0000 271 9.0000 98 3.0000 90 3.0000 89 3.0000 108 3.0000 41 1.0000 27 1.0000 1006 32.0000 Expected 282.9375 282.9375 94.3125 94.3125 94.3125 94.3125 31.4375 31.4375 1006.0000 Chi-Square Term 0.0031 0.5037 0.1442 0.1972 0.2992 1.9865 2.9087 0.6264 6.6689

Chi-Sqaured Test Statistic = 6.6689 Degrees of Freedom = 7 Level of Significance = 0.4642 Recomendation: Do not reject your hypothesis -------------------------------------------------------------------------F1: wwNN (ebony, normal wings) x WWnn (wild type, vestigial wings) F2: WwNn x WwNn wN wN wN wN Wn WwNn WwNn WwNn WwNn WN Wn wN Wn Wn WwNn WwNn WwNn WwNn WN WWNN WWNn WwNN WwNn Wn WwNn WwNn WwNn WwNn Wn WWNn WWnn WwNn Wwnn Wn WwNn WwNn WwNn WwNn wN WwNN WwNn wwNN WwNn Outcome: 100% WwNn (1:0 ratio) wn WwNn Wwnn wwNn Wwnn (All wild type bodies and wings) Wild Type, Normal: 9 Ebony, Normal: 3 Wild Type, Vestigial: 3 Ebony, Vestigial: 1

Franklin Xie February 11, 2013

9:3:3:1 ratio The outcomes for my F1 and F2 crosses can be explained by the dihybrid punnett squares. The F1 punnett square shows that, by crossing two homozygous individuals, only one genotype and phenotype can be achieved within offspring (WwNn). When the offspring reproduce, however, They will provide an F2 generation with roughly the ratio of 9:3:3:1 [wild (color), normal (wild wings): ebony, normal: wild, vestigial: ebony, vestigial]. The actual ratio for the F2 generation was approximately 8.1:2.7:2.9:1. There is a small difference from the predicted and the actual outcome. This is due to the randomness of genetic crosses that occurs because, after the alleles segregate and assort independently during gamete formation, the flies sperm and egg randomly combine. It only likely, not certain, that the final result of the cross will produce offspring with phenotypes based on a 9:3:3:1 ratio. The actual ratio will even out due to principles of probability if more offspring are made from the F1 parents. 4. Flylab Lab Notes for Franklin Xie -------------------------------------------------------------------------Results of Cross #1 Parents (Female: +) x (Male: SV;DP;E) Offspring Phenotype Female: + Male: + Total Number 501 522 1023 Proportion 0.4897 0.5103 Ratio 1.000 1.042

-------------------------------------------------------------------------Chi Square Hypothesis Using Cross #1 Phenotype Female: + Male: + Total Observed Hypothesis 501 1.0000 522 1.0000 1023 2.0000 Expected 511.5000 511.5000 1023.0000 Chi-Square Term 0.2155 0.2155 0.4311

Chi-Squared Test Statistic = 0.4311 Degrees of Freedom = 1 Level of Significance = 0.5115 Recommendation: Do not reject your hypothesis -------------------------------------------------------------------------Results of Cross #2 Parents

Franklin Xie February 11, 2013

(Female: +) x (Male: +) Offspring Phenotype Female: + Male: + Female: SV Male: SV Female: DP Male: DP Female: SV;DP Male: SV;DP Female: E Male: E Female: SV;E Male: SV;E Female: DP;E Male: DP;E Female: SV;DP;E Male: SV;DP;E Total Number 213 215 57 68 69 67 30 25 66 69 28 27 31 29 10 8 1012 Proportion 0.2105 0.2125 0.0563 0.0672 0.0682 0.0662 0.0296 0.0247 0.0652 0.0682 0.0277 0.0267 0.0306 0.0287 0.0099 0.0079 Ratio 26.625 26.875 7.125 8.500 8.625 8.375 3.750 3.125 8.250 8.625 3.500 3.375 3.875 3.625 1.250 1.000

-------------------------------------------------------------------------Chi Square Hypothesis Using Cross #2 Ignoring Sex Phenotype + SV DP SV;DP E SV;E DP;E SV;DP;E Total Observed Hypothesis 428 27.0000 125 9.0000 136 9.0000 55 3.0000 135 9.0000 55 3.0000 60 3.0000 18 1.0000 1012 64.0000 Expected 426.9375 142.3125 142.3125 47.4375 142.3125 47.4375 47.4375 15.8125 1012.0000 Chi-Square Term 0.0026 2.1061 0.2800 1.2056 0.3757 1.2056 3.3268 0.3026 8.8052

Chi-Sqaured Test Statistic = 8.8052 Degrees of Freedom = 7 Level of Significance = 0.2669 Recomendation: Do not reject your hypothesis _____________________________________________________________________________ The F1 generation, as always, would result in offspring that exhibit the dominant traits at a 1:0 (100%) ratio. That is why my hypothesis for the Chi-square analysis of the F1 generation is correct.

Franklin Xie February 11, 2013

The punnett square on the next page was used to predict the outcome of the F2 generation. A,B,C represent the dominant, or wild type, traits. a,b,c represent the traits, respectively, for dumpy wing shape, ebony body, and shaven bristles.

ABC ABc AbC Abc aBC aBc abC abc

ABC AABBCC AABBCc AABbCC AABbCc AaBBCC AaBBCc AaBbCC AaBbCc

ABc AABBCc AABBcc AABbCc AABbcc AaBBCc AaBBcc AaBbCc AaBbcc

AbC AABbCC AABbCc AAbbCC AAbbCc AaBbCC AaBbCc AabbCC AabbCc

Abc AABbCc AABbcc AAbbCc AAbbcc AaBbCc AaBbcc AabbCc Aabbcc

aBC AaBBCC AaBBCc AaBbCC AaBbCc aaBBCC aaBBCc aaBbCC aaBbCc

aBc AaBBCc AaBBcc AaBbCc AaBbcc aaBBCc aaBBcc aaBbCc aaBbcc

abC AaBbCC AaBbCc AabbCC AabbCc aaBbCC aaBbCc aabbCC aabbCc

abc AaBbCc AaBbcc AabbCc Aabbcc aaBbCc aaBbcc aabbCc aabbcc

The expected phenotypic ratio: All dominant traits:wild,wild,shave:wild,ebony,wild:dumpy,wild,wild:wild,ebony,shaven: Expected Phenotype Ratio of F2 generation W=Wild (dominant) D=Dumpy Wings E=Ebony Body S=Shaven Bristles WWW WWS WEW DWW WES DWS DEW DES 27 9 9 9 3 3 3 1 The actual phenotypic ratio was approximately: 24:7:8:8:3:3:3:1. The randomness of genetic crosses occurs because, after the alleles segregate and assort independently during gamete formation, the flies sperm and egg randomly combine. It only likely, not certain, that the final result of the cross will produce offspring with phenotypes based on a 27:9:9:9:3:3:3:1 ratio. The actual ratio will even out due to principles of probability if more offspring are made from the F1 parents. Assignment 2 Flylab Lab Notes for Franklin Xie -------------------------------------------------------------------------Results of Cross #1 Parents (Female: BW) x (Male: E) Offspring Phenotype Female: + Male: + Total Number 5016 5030 10046 Proportion 0.4993 0.5007 Ratio 1.000 1.003

-------------------------------------------------------------------------Chi Square Hypothesis Using Cross #1 Phenotype Female: + Male: + Total Observed Hypothesis 5016 1.0000 5030 1.0000 10046 2.0000 Expected 5023.0000 5023.0000 10046.0000 Chi-Square Term 0.0098 0.0098 0.0195

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Franklin Xie February 11, 2013

Chi-Squared Test Statistic = 0.0195 Degrees of Freedom = 1 Level of Significance = 0.8889 Recommendation: Do not reject your hypothesis -------------------------------------------------------------------------Results of Cross #2 Parents (Female: +) x (Male: BW;E) Offspring Phenotype Female: + Male: + Female: BW Male: BW Female: E Male: E Female: BW;E Male: BW;E Total Number 1237 1170 1269 1262 1253 1183 1247 1182 9803 Proportion 0.1262 0.1194 0.1295 0.1287 0.1278 0.1207 0.1272 0.1206 Ratio 1.057 1.000 1.085 1.079 1.071 1.011 1.066 1.010

-------------------------------------------------------------------------Chi Square Hypothesis Using Cross #2 Phenotype Female: + Male: + Female: BW Male: BW Female: E Male: E Female: BW;E Male: BW;E Total Observed Hypothesis 1237 1.0000 1170 1.0000 1269 1.0000 1262 1.0000 1253 1.0000 1183 1.0000 1247 1.0000 1182 1.0000 9803 8.0000 Expected 1225.3750 1225.3750 1225.3750 1225.3750 1225.3750 1225.3750 1225.3750 1225.3750 9803.0000 Chi-Square Term 0.1103 2.5024 1.5531 1.0947 0.6228 1.4654 0.3816 1.5354 9.2656

Chi-Sqaured Test Statistic = 9.2656 Degrees of Freedom = 7 Level of Significance = 0.2341 Recomendation: Do not reject your hypothesis

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Franklin Xie February 11, 2013

The F1 wild-type female is double-heterozygous. The female cannot be double homozygous, otherwise all of the offspring would have exhibited the dominant trait. A cross between double heterozygous females and double homozygous recessive males will produce a phenotype ratio of 1:1:1:1.

Test Cross (aabb male) x (AaBb female) ab ab ab ab AB AaBb AaBb AaBb AaBb Ab Aabb Aabb Aabb Aabb aB aaBb aaBb aaBb aaBb ab aabb aabb aabb aabb
This punnett square illustrates the outcome of the cross that I described. The actual outcome of the parent cross of the F1 generation created offspring on a 1:1:1:1 ratio (Wild eyes, Wild body: Brown eyes, wild body, Wild eyes: ebony body: Brown eyes, Ebony body). That is the predicted outcome of a test cross between a double homozygous recessive individual and double heterozygous individual (shown in the punnett square). The data proves that the female was almost certainly double-heterozygous.

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