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BIO Virtual fly lab (final draft)

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IB Bio HL Virtual Fly Lab OMG

IB Bio HL Virtual Fly Lab OMG

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  • 1. Virtual Fly Lab<br />Introduction<br />Gregor Johann Mendel’s experiments with garden peas dramatically influenced the field of biology. Mendel’s results became the foundation for the discipline known as genetics, which is the study of variation and inheritance. Mendel’s experiments were done by using varieties of pea plant. He crossed those varieties of pea together by transferring the male pollen from one variety to the female parts in flowers of another variety artificially. He considered seven different characters including flower color, flower position, seed color, seed shape, pod color, pod shape, and stem length. Variations of a given character are known as traits. Then, he collected the seeds and grew them to find out what their characteristics looked like. Later his results were surprising; characteristics from the original parents had disappeared or reappeared in their offspring. During his experiments, he discovered that there were particles of inheritance factors, which are now called genes. Specifically, genes are heritable factors that control a specific characteristic. Mendel also thought that were alternative forms of a gene which were responsible for variations in inherited characters. Those forms of a gene are now called alleles. After he got surprising results, he observed that the ratio of pea plants was always close to 3:1, dominant alleles : recessive alleles. For instance, in the pea plants that Mendel used have two alleles for stem length, a tall stem and a dwarf stem. With true-breeding homozygous parents called the P generation, he first crossed a tall plant with a dwarf plant. The first offspring, called the F1 generation, were all tall. This is because a tall stem is a dominant character in pea plant and a dwarf stem is a recessive character. In F2 generation from the self-pollination of F1 plants, the phenotype ratio of tall plants to dwarf plants was approximately 3:1. Here, Mendel discovered that this ratio was made from a cross between heterozygotes. He also used dihybrid crosses in order to explain his law of independent assortment, which is that alleles for different characters segregate into each gamete independently. In a dihybrid cross, the phenotype ratio of heterozygous F1 cross is approximately 9:3:3:1 in F2 generation. Furthermore, Punnett square is useful to predict the genotypes and phenotypes from a genetic cross. <br />Chi-square analysis is a statistical test that makes a comparison between the data collected in an experiment and expected data. In genetics, the Chi-square analysis used to evaluate data from experimental crosses to determine if the assumed genetic explanation is supported by the data. <br />The person who originally proposed the use of the fruit fly was Thomas Hunt Morgan while he worked at Columbia University in the early 1900’s. For his genetics work with fruit fly, he received the Nobel Prize in Medicine in 1933. In this virtual Fly Lab, fruit flies, also called Drosophila melanogaster, will be used. In addition, with Punnett square, Chi-square analysis, and other basic knowledge, it will be easy to simulate basic principles of genetic inheritance based on Mendel’s genetics by performing crosses between fruit flies. The Chi-square analysis will be used so that I can accept or reject my hypothesis for the expected phenotype ratio of offspring for each cross. The tasks of this lab are to investigate traits of fruit flies and to show proof that I have found traits which are inherited in the following five manners: a dominant allele, a recessive allele, a recessive sex-linked allele, a dominant lethal allele, and dihybrid cross.<br />In this lab, there will be also used some genetic abbreviations. The normal “wild type” version will be represented as “+”. A table of the genetic abbreviations used in this lab appears below. <br />Table 1) The Genetic AbbreviationsAbbreviationPhenotypeAbbreviationPhenotypeAbbreviationPhenotypeAPApterous WingsEYEyeless EyesSESepia EyesARAristapedia AntennaeDPDumpy WingsSNSinged BristlesBBar EyesFForked BristlesSSSpineless BristlesBLBlack BodyLLobe EyesSTStar EyesBWBrown EyesMMiniature WingsSVShaven BristlesCCurved WingsPRPurple EyesTTan BodyCVCrossveinless WingsRIRadius Incompletus WingsVGVestigial WingsCYCurly WingsSSable BodyWWhite EyesDDichaete WingsSBStubble BristlesYYellow BodyEEbony BodySDScalloped Wings<br />A dominant allele (Eye shape Bar Female x Wild type Male)<br />A dominant allele is an allele that has the same effect on the phenotype whether it is present in the homozygous or the heterozygous state. To test for a dominant allele, the character of lobe eyes is used because this character is assumed as a dominant allele. In this cross, one of the parents must have identical lobe eyes allele and another must be a wild fruit fly. <br />F1<br />--------------------------------------------------------------------------<br />Results of Cross #27<br />Ignoring Sex<br />Parents<br />(Female: B) x (Male: +)<br />Offspring<br />Phenotype Number Proportion Ratio<br /> B 1016 1.0000 1.000<br /> Total 1016<br />--------------------------------------------------------------------------<br />Chi Square Hypothesis Using Cross #27<br />Ignoring Sex<br />Phenotype Observed Hypothesis Expected Chi-Square Term<br /> B 1016 1.0000 1016.0000 0.0000<br /> Total 1016 1.0000 1016.0000 0.0000<br /> Chi-Squared Test Statistic = 0.0000<br /> Degrees of Freedom = 0<br /> Level of Significance = 1.0000<br /> Recommendation: Do not reject your hypothesis<br />--------------------------------------------------------------------------<br />Explanation:<br />From this data, it is shown that when a fly with homozygous bar eyes mates with a fly with wild type eyes, the resulting offspring only has bar type eyes. This evidence can suggest that bar eye shape is the dominant allele over wild type because in order for the offspring to have only have bar eye shape from parents that have different homozygous allele, the bar eye shape must be the dominant allele. This is shown in the Punnett square below:<br />B = Bar Eyes+ = Wild Type<br />Table 2) Punnett Square for a Cross between Bar Eyes Female and Wild Eyes MaleBB+B+B++B+B+<br />Genotype of the offspring = B+<br />Phenotype of the offspring = All Bar eyes (supported by the result of cross #27)<br />F2 <br />--------------------------------------------------------------------------<br />Results of Cross #28<br />Ignoring Sex<br />Parents<br />(Female: B) x (Male: B)<br />Offspring<br />Phenotype Number Proportion Ratio<br /> + 251 0.2505 1.000<br /> B 751 0.7495 2.992<br /> Total 1002<br />--------------------------------------------------------------------------<br />Chi Square Hypothesis Using Cross #28<br />Ignoring Sex<br />Phenotype Observed Hypothesis Expected Chi-Square Term<br /> + 251 1.0000 250.5000 0.0010<br /> B 751 3.0000 751.5000 0.0003<br /> Total 1002 4.0000 1002.0000 0.0013<br /> Chi-Squared Test Statistic = 0.0013<br /> Degrees of Freedom = 1<br /> Level of Significance = 0.9709<br /> Recommendation: Do not reject your hypothesis<br />----------------------------------------------------------------------------------------------------------------<br />Explanation:<br />From Cross #28, it further supports that bar eye is the dominant allele for eye shape. As suggested from the previous Punnett Square, the F1 generation only has a bar eye shape phenotype with genotype of B+. When these heterozygotes cross together, they are expected to produce F2 generation with a phenotype ratio, 3:1 for bar eye shape to wild eye shape, as shown in the Chi-Square #28 above. According the Chi-squared test, the result is not statistically significant because the result is nearly accurate compared to the expected data. This can only suggest that bar eye shape is the dominant allele and this is shown in the Punnett square below:<br />B = Bar Eyes+ = Wild Type<br />Table 3) Punnett Square for a Cross between Heterozygous Bar Eye ParentsB+BBBB++B+++<br />Genotype ratio of the offspring – BB : B+ : ++ = 1:2:1<br />Phenotype ratio of the offspring – Bar Eyes : Wild Eyes = 3:1<br />A recessive allele (Wing shape Dumpy Female x Wild type Male)<br />A recessive allele is an allele that only has an effect on the phenotype when it is present in the homozygous state. In this case, dumpy wing shape is assumed as a recessive allele. Therefore, if dumpy wing shape female and wild type male cross together, they will breed offspring that has all phenotype with wild wing shape. <br />F1<br />--------------------------------------------------------------------------<br />Results of Cross #3<br />Ignoring Sex<br />Parents<br />(Female: DP) x (Male: +)<br />Offspring<br />Phenotype Number Proportion Ratio<br /> + 1004 1.0000 1.000<br /> Total 1004<br />--------------------------------------------------------------------------<br />Chi Square Hypothesis Using Cross #3<br />Ignoring Sex<br />Phenotype Observed Hypothesis Expected Chi-Square Term<br /> + 1004 1.0000 1004.0000 0.0000<br /> Total 1004 1.0000 1004.0000 0.0000<br /> Chi-Squared Test Statistic = 0.0000<br /> Degrees of Freedom = 0<br /> Level of Significance = 1.0000<br /> Recommendation: Do not reject your hypothesis<br />--------------------------------------------------------------------------<br />Explanation:<br />From this data, it is shown that when a fly with homozygous dumpy wings mates with a fly with wild type wings, the resulting offspring only has wild type wings. This evidence can suggest that dumpy wing shape is the recessive allele over wild type wing because in order for the offspring to have only wild wing shape from parents that have different homozygous allele, the dumpy wing shape must be the recessive allele. This is shown in the Punnett square below:<br />DP = Dumpy Wings+ = Wild Type<br />Table 4) Punnett Square for a Cross between Dumpy Wings Female and Wild Wings MaleDPDP+DP+DP++DP+DP+<br />Genotype of the offspring = DP+<br />Phenotype of the offspring = All Wild Wings (supported by the result of cross #3)<br />F2<br />--------------------------------------------------------------------------<br />Results of Cross #4<br />Ignoring Sex<br />Parents<br />(Female: +) x (Male: +)<br />Offspring<br />Phenotype Number Proportion Ratio<br /> + 741 0.7647 3.250<br /> DP 228 0.2353 1.000<br /> Total 969<br />--------------------------------------------------------------------------<br />Chi Square Hypothesis Using Cross #4<br />Ignoring Sex<br />Phenotype Observed Hypothesis Expected Chi-Square Term<br /> + 741 3.0000 726.7500 0.2794<br /> DP 228 1.0000 242.2500 0.8382<br /> Total 969 4.0000 969.0000 1.1176<br /> Chi-Squared Test Statistic = 1.1176<br /> Degrees of Freedom = 1<br /> Level of Significance = 0.2904<br /> Recommendations: Do not reject your hypothesis<br />--------------------------------------------------------------------------<br />Explanation:<br />From Cross #4, it further supports that dumpy wing is the recessive allele for wing shape. As suggested from the previous Punnett Square, the F1 generation only has wild wing shape phenotype with genotype of DP+. When these heterozygotes cross together, they are expected to produce F2 generation with a phenotype ratio, 3:1 for wild wing shape to dumpy wing shape, as shown in the Chi-Square #4 above. According the Chi-squared test, the result is statistically significant because the result is not that accurate compared to the expected data and the hypothesized rate. This can only suggest that dumpy wing shape is the recessive allele over wild wing shape and this is shown in the Punnett square below:<br />DP = Dumpy Wings+ = Wild Type<br />Table 5) Punnett Square for a Cross between Heterozygous Wild Wing ParentsDP+DPDPDPDP++DP+++<br />Genotype ratio of the offspring – DPDP : DP+ : ++ = 1:2:1<br />Phenotype ratio of the offspring – Wild Wings : Dumpy Wings = 3:1<br />A recessive sex-linked allele (Wild type Female x Body color Sable Male)<br />A recessive sex-linked allele is an allele which appears in sex chromosome, X chromosome. Crossing a wild type female with a sable color male is the first step to find a recessive sex-liked allele. <br />F1<br />--------------------------------------------------------------------------<br />Results of Cross #5<br />Parents<br />(Female: +) x (Male: S)<br />Offspring<br />Phenotype Number Proportion Ratio<br /> Female: + 488 0.4905 1.000<br /> Male: + 507 0.5095 1.039<br /> Total 995<br />--------------------------------------------------------------------------<br />Chi Square Hypothesis Using Cross #5<br />Phenotype Observed Hypothesis Expected Chi-Square Term<br /> Female: + 488 1.0000 497.5000 0.1814<br /> Male: + 507 1.0000 497.5000 0.1814<br /> Total 995 2.0000 995.0000 0.3628<br /> Chi-Squared Test Statistic = 0.3628<br /> Degrees of Freedom = 1<br /> Level of Significance = 0.5469<br /> Recommendation: Do not reject your hypothesis<br />--------------------------------------------------------------------------<br />Explanation:<br />From this data, it is shown that when a fly with normal color crosses with a fly having homozygous sable color, the resulting offspring only has wild body color. This evidence can suggest that sable body color is included in the recessive sex-linked allele over the wild body color because in order for the offspring to have only wild body color from parents that have different homozygous allele, the sable body color must be the recessive sex-linked allele. This is shown in the Punnett square below:<br />S = Sable Body+ = Wild Body<br />Table 6) Punnett Square for a Cross between Wild Body Color Female and Sable Color MaleXSYX+XSX+X+YX+XSX+X+Y<br />Genotype of the offspring = XSX+, X+Y<br />Phenotype of the offspring = All Wild Body Color (supported by the result of cross #5)<br />F2<br />--------------------------------------------------------------------------<br />Results of Cross #6<br />Parents<br />(Female: +) x (Male: +)<br />Offspring<br />Phenotype Number Proportion Ratio<br /> Female: + 509 0.4947 2.004<br /> Male: + 254 0.2468 1.000<br /> Male: S 266 0.2585 1.047<br /> Total 1029<br />--------------------------------------------------------------------------<br />Chi Square Hypothesis Using Cross #6<br />Phenotype Observed Hypothesis Expected Chi-Square Term<br /> Female: + 509 2.0000 514.5000 0.0588<br /> Male: + 254 1.0000 257.2500 0.0411<br /> Male: S 266 1.0000 257.2500 0.2976<br /> Total 1029 4.0000 1029.0000 0.3975<br /> Chi-Squared Test Statistic = 0.3975<br /> Degrees of Freedom = 2<br /> Level of Significance = 0.8198<br /> Recommendation: Do not reject your hypothesis<br />--------------------------------------------------------------------------<br />Chi Square Hypothesis Using Cross #6<br />Ignoring Sex<br />Phenotype Observed Hypothesis Expected Chi-Square Term<br /> + 763 3.0000 771.7500 0.0992<br /> S 266 1.0000 257.2500 0.2976<br /> Total 1029 4.0000 1029.0000 0.3968<br /> Chi-Squared Test Statistic = 0.3968<br /> Degrees of Freedom = 1<br /> Level of Significance = 0.5287<br /> Recommendation: Do not reject your hypothesis<br />--------------------------------------------------------------------------<br />Explanation:<br />From Cross #6, it further supports that sable body color is the recessive sex-linked allele for body color. As suggested from the previous Punnett Square, the F1 generation only has wild body color phenotype with genotype of S+. When these heterozygotes cross together, they are expected to produce F2 generation with a phenotype ratio, 3:1 for wild body color to sable body color, as shown in the Chi-Square #6 above. According the Chi-squared test, the result is not statistically significant because the result is nearly accurate compared to the expected data and the hypothesized rate. This can suggest that sable body color is the recessive sex-linked allele over wild body color and this is shown in the Punnett square in next page:<br />S = Sable Body+ = Wild Body<br />Table 7) Punnett Square for a Cross between Heterozygous Wild Body Color ParentsX+YXSXSX+XSYX+X+X+X+Y<br />Female genotype ratio of the offspring – XSX+ : X+X+ = 1:1<br />Female phenotype ratio of the offspring – All Wild Body Color<br />Male genotype ratio of the offspring – XSY : X+Y = 1:1<br />Male phenotype ratio of the offspring – Sable Body Color : Wild Body Color = 1:1<br />A dominant lethal allele (Wing angle Dichaete Female x Wing angle Dichaete Male)<br />A lethal allele is an allele that can cause death if organisms have homozygous dominant allele. For fruit flies, dichaete wing angle is one of the lethal alleles. The reason is that when two fruit flies with the same trait, dichaete wing angle, are mated, the ratio is 2:1, dichaete wing angle : wild wing angle. Here, the one that survives and that will be used for mating has to be carrier because homozygous dichaete wing angle fly cannot live anymore. <br />--------------------------------------------------------------------------<br />Results of Cross #13<br />Ignoring Sex<br />Parents<br />(Female: D) x (Male: D)<br />Offspring<br />Phenotype Number Proportion Ratio<br /> + 350 0.3418 1.000<br /> D 674 0.6582 1.926<br /> Total 1024<br />--------------------------------------------------------------------------<br />Chi Square Hypothesis Using Cross #13<br />Ignoring Sex<br />Phenotype Observed Hypothesis Expected Chi-Square Term<br /> + 350 1.0000 341.3333 0.2201<br /> D 674 2.0000 682.6667 0.1100<br /> Total 1024 3.0000 1024.0000 0.3301<br /> Chi-Squared Test Statistic = 0.3301<br /> Degrees of Freedom = 1<br /> Level of Significance = 0.5656<br /> Recommendation: Do not reject your hypothesis<br />--------------------------------------------------------------------------<br />Explanation:<br />From this data, it is shown that when two flies with the same trait, dichaete wing angle, the resulting offspring only has wild wing angle and dichaete wing angle. However, we can know that by drawing a Punnett square, the homozygous dichaete wing angle flies are dead because the trait is a lethal allele. This evidence can suggest that dichaete wing angle is included in the lethal allele because in order for the offspring to have the ratio of 2:1, dichaete wing angle : wild wing angle, the dichaete wing angle must be the lethal allele. This is shown in the Punnett square below:<br />D = Dichaete Wings+ = Wild Wings<br />Table 8) Punnett Square for a Cross between two dichaete wing angle parentsD+DDD (died)D++D+++<br />Genotype of the offspring = DD (died), D+, ++<br />Phenotype of the offspring = Dichaete Wing, Wild Wing (supported by the result of cross #13)<br />Genotype ratio of the offspring – DD (died) : D+ : ++ = 1:2:1<br />Phenotype ratio of the offspring – Dichaete Wing : Wild Wing = 2:1 (because one dichaete wing fly is dead)<br />Dihybrid Cross (Wild type Female x Wing size Apterous & Eye color Sepia Male)<br />The 9:3:3:1 ratio is often found when parents that are heterozygous for two genes are crossed together. The dihybrid cross follows Mendel’s Law of Independent Assortment because the genes are unlinked.<br />F1<br />--------------------------------------------------------------------------<br />Results of Cross #7<br />Ignoring Sex<br />Parents<br />(Female: +) x (Male: SE;VG)<br />Offspring<br />Phenotype Number Proportion Ratio<br /> + 1011 1.0000 1.000<br /> Total 1011<br />--------------------------------------------------------------------------<br />Chi Square Hypothesis Using Cross #7<br />Ignoring Sex<br />Phenotype Observed Hypothesis Expected Chi-Square Term<br /> + 1011 1.0000 1011.0000 0.0000<br /> Total 1011 1.0000 1011.0000 0.0000<br /> Chi-Squared Test Statistic = 0.0000<br /> Degrees of Freedom = 0<br /> Level of Significance = 1.0000<br /> Recommendation: Do not reject your hypothesis<br />--------------------------------------------------------------------------<br />Explanation:<br />From this data, it is shown that when a fly with wild type crosses with a fly having sepia eye and vestigial wings, the resulting offspring only has wild type. This evidence can suggest that this cross is dihybrid cross because in order for the all offspring to have only wild type from parents that have different characteristics, the cross between the wild type and sepia eye and apterous wing must be the dihybrid cross. This is shown in the Punnett square below:<br />SE = Sepia Eyes+ = Wild TypeVG = Vestigial Wings<br />Table 9) Punnett Square for a Cross between a wild type female and a vestigial wing / sepia eye maleSEVG+SE+VG++SE+VG+<br />Genotype of the offspring = SE+, VG+<br />Phenotype of the offspring = All Wild Eye Color / Wild Wing (supported by the result of cross #7)<br />F2<br />--------------------------------------------------------------------------<br />Results of Cross #8<br />Ignoring Sex<br />Parents<br />(Female: +) x (Male: +)<br />Offspring<br />Phenotype Number Proportion Ratio<br /> + 561 0.5571 9.508<br /> SE 195 0.1936 3.305<br /> VG 192 0.1907 3.254<br /> SE;VG 59 0.0586 1.000<br /> Total 1007<br />--------------------------------------------------------------------------<br />Chi Square Hypothesis Using Cross #8<br />Ignoring Sex<br />Phenotype Observed Hypothesis Expected Chi-Square Term<br /> + 561 9.0000 566.4375 0.0522<br /> SE 195 3.0000 188.8125 0.2028<br /> VG 192 3.0000 188.8125 0.0538<br /> SE;VG 59 1.0000 62.9375 0.2463<br /> Total 1007 16.0000 1007.0000 0.5551<br /> Chi-Squared Test Statistic = 0.5551<br /> Degrees of Freedom = 3<br /> Level of Significance = 0.9066<br /> Recommendation: Do not reject your hypothesis<br />--------------------------------------------------------------------------<br />Explanation:<br />From Cross #8, it further supports that a cross between a wild type and sepia eye / apterous wing is a dihybrid cross. As suggested in previous Punnett square, the F1 generation only has wild heterozygous type. When these heterozygotes cross together, they are expected to produce F2 generation with a phenotype ratio, 9:3:3:1 for wild body color to sepia eye color to vestigial wing shape to mixture of sepia eye and vestigial wing, as shown in the Chi-Square #8 above. According the Chi-squared test, the result is not statistically significant because the result is nearly accurate compared to the expected data and the hypothesized rate. This can suggest that this cross is a dihybrid cross and this is shown in the Punnett square in next page:<br />SE = Sepia Eyes+ = Wild TypeVG = Vestigial Wings<br />Table 10) Punnett Square for a Cross between two heterozygous flies++VG+SE+VGSE++VG+++ ++VG+ ++SE+ ++VGSE ++VG+ ++VGVG ++VGSE ++VGVG SE+SE+VGSESE+ ++VGSE ++SESE ++VG+ SESEVGSE ++VGVG SE+VG+ SESEVGVG SESE<br />Genotype ratio of the offspring – ++ ++ : VG+ ++ : SE+ ++ : VGSE ++ : VGVG ++ : VGVG SE+ : SESE ++ : VG+ SESE : VGVG SESE = 1:2:2:4:1:2:1:2:1<br />Phenotype ratio of the offspring – 9 Wild type : 3 vestigial-winged : 3 sepia-eyed : 1 vestigial-winged sepia eyed<br />