Genes, Pedigrees, and Populations Investigations In to the World of Genetics. Name

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1 Genes, Pedigrees, and Populations Investigations In to the World of Genetics Name Objectives The purpose of this exploration is to review the terms gene, allele, phenotype, genotype, heterozygous, and homozygous, and practice using them correctly; 2. analyze several human pedigrees to determine the type of inheritance exhibited by the trait; and 3. predict the likelihood that particular individuals in the families will have the trait that is the focus of the pedigrees. 4. understand the significance of the Hardy-Weinberg law in predicting that allele frequencies remain the same from generation to generation; 5. determine gene frequencies under the conditions of codominance and recessive inheritance; and 6. explore the impact of effects such as selection and migration on allele frequencies. Part 1 Genes and You. The example we will explore in class today, PTC taste testing, is an example of alleles that exhibit dominance/recessiveness. Pedigree studies of human families have indicated that the ability to taste phenylthiocarbamide (PTC) is due to the presence of a dominant allele (T) and that the inability to taste the chemical occurs in homozygous recessive individuals (tt). There are two phenotypes (tasters and non-tasters), but three genotypes (TT, Tt, and tt). Procedure Part 1 You will be given a small piece of filter paper that has been lightly saturated with PTC. Before you place the PTC paper on your tongue, take a piece of untreated paper and taste it. This wills serve as a control so that you can readily determine the difference between the taste of the paper and the taste of PTC. Fill out the questions for Part 1 on your worksheet now. Most hereditary traits in humans and other species are controlled by multiple genes with multiple alleles that utilize complex gene interactions to result in the organisms phenotype. The following human characteristics are controlled by a single gene with two alleles. Determine your phenotype for each of the following traits. Also determine your genotype if possible. If you have the dominant phenotype, you will not know whether you are heterozygous or homozygous. What procedures could you use to determine whether or not you are homozygous? Other traits that are easily observed and controlled by a single gene are listed below. Try to identify both your genotype and phenotype for each of these. BIO 101 Genes and You 1

2 Trait 1. Bent Pinky (B,b) Dominant allele causes distal segment of fifth finger to bend distinctly inward toward fourth (ring) finger 2. Tongue Rolling (R,r) Dominant allele in heterozygous or homozygous condition allows people to roll their tongues into a tubelike shape. 3. Blue eyes (E,e) Homozygous recessive individuals lack pigment in the iris, others have iris pigment color determined by other genes. 4.Widows Peak (W,w) Dominant allele causes individuals to have V-shaped front hairline. 5. Thumb crossing (T,t) In relaxed interlocking of fingers, the left thumb over the right indicates the dominant allele is present; homozygous recessives naturally place right thumb over left. 6. Attached Earlobe (A,a) Dominant allele causes individuals to have detached ear lobes. 7. Hitchhiker Thumb (H,h) Homozygous recessives can bend the distal joint of the thumb backward to nearly a 90 angle. 8. Red-green colorblind (C,c)Sex linked trait (on the X chromosome). Recessive allele on the X chromosome causes the color blindness. 9. Hairy Ears (M,m) Sex linked trait (on the Y chromosome). Dominant allele causes individual to have hair growing on the outside edge of the ears. 10. Pattern Baldness (P,p) A sex influenced trait. Dominant allele causes premature loss of hair on top and front of head in heterozygous or homozygous dominant males. 11. Finger length (F,f) A sex influenced trait that involves the length of the index finger relative to the ring finger. In males, the allele for short index finger is dominant; in females it is recessive BIO 101 Genes and You 2

3 Part 2 Human Pedigree Analysis Introduction The inheritance of human traits is typically determined using a technique called pedigree analysis. Pedigrees are family trees that show which individuals in a family exhibit a particular trait and how they are related to other affected and nonaffected family members. This information, plus a basic understanding of Mendelian genetics, is used to make hypotheses about the inheritance of the trait and to make predictions about the probability that a child will have the trait. Genetic counselors use pedigree analysis, among other skills, in their work. In a pedigree, circles represent females, while squares represent males. A diamond indicates that the sex of the individual is unknown. Shaded symbols indicated that the individual exhibits the phenotype under consideration. For example, in a pedigree that examines the inheritance of sickle cell disease in a family, a shaded symbol indicates an individual with this disease. A horizontal line connects parents; the vertical line from them leads to their offspring. All of their offspring are sibs and are connected by a horizontal sibship line. They are placed from left to right in order of birth. Connected diagonal lines indicate twins. Analyzing inheritance patterns revealed in pedigrees A pedigree is typically used to determine the type of inheritance involved for a trait and the probability that a specific family member will exhibit the trait in question. Inherited traits due to a single gene may be inherited in one of four general ways: Autosomal recessive inheritance. The trait is due to a gene on an autosomal chromosome (chromosomes 1 to 22) and is expressed only in the homozygous recessive condition. Pedigree tip-offs for this kind of inheritance: both males and females are affected; unaffected parents have an affected child. Autosomal dominant inheritance. The trait is due to a gene on an autosomal chromosome and is expressed whenever the gene is present (either homozygous dominant or heterozygous condition). As a rule of thumb, most individuals with a dominant trait are heterozygous (unless information in the pedigree reveals otherwise). Pedigree tip-offs: both males and females are affected; affect individuals have at least one parent who also exhibits the trait. X-linked inheritance (also known as sex-linked inheritance ). The trait is due to a gene on the X chromosome. Most traits of this type are recessive and are expressed in males who receive an X chromosome carrying the gene from their mothers. Traits of this type are expressed in females only if they are homozygous, that is, if they received X chromosomes carrying the gene from both parents. Thus, males exhibit the trait far more often than females in fact, most pedigrees of this type will show only males with the trait. BIO 101 Genes and You 3

4 Y-linked inheritance. This type of inheritance is due to a gene carried on the Y chromosome and, except for genes that cause an individual to be male, is very rare. Pedigrees for traits with this type of inheritance will show that only males exhibit the trait and that all affected males have fathers who also have the trait. In this lab, you will work in pairs to analyze several pedigrees. This is an opportunity for you to review several genetics terms and concepts. Keep in mind that real life situations are often more ambiguous that those described above. For example, penetrance is a phenomenon that makes pedigree interpretation difficult. It refers to the likelihood that an individual who has the genotype for a particular trait will actually have the phenotype for the trait. If a dominant trait has 100 percent penetrance, then every individual who has a dominant allele will exhibit the trait associated with it. If a dominant trait has 90 percent penetrance, then 90 percent of the individuals who have the allele will have the corresponding phenotype, but 10 percent of them will not show the trait (it does not penetrate in them). Procedure Part 2 1. Obtain a set of pedigrees from your instructor. 2. In pairs, discuss the pedigrees and answer the following questions for each one: a. Is the gene associated with the trait on an autosomal chromosome or the X chromosome? Explain. b. Is the trait conferred by a dominant or recessive gene? Explain. c. What is the probability that individual A will have the trait? Explain your reasoning. d. What is the probability that individual B will have the trait? Explain your reasoning. Fill out the table for Part 2 on your worksheet now. Part 3. Genes in Populations, the Hardy-Weinberg Equilibrium Introduction The English mathematician G.H. Hardy, and the German physician, W. Weinberg formulated the basic law of population genetics independently in It is called the Hardy-Weinberg equilibrium in their honor. This principle allows population geneticists to calculate the frequency of alleles of a gene in a randomly interbreeding group of plants or animals. Hardy and Weinberg demonstrated that in such natural populations allele frequencies reach equilibrium (that is, the frequencies of the different alleles of a gene remain constant generation after generation), provided that no disturbing effects occur such as those caused by mutation, migration, BIO 101 Genes and You 4

5 selection pressure, non-random mating, or random genetic drift (which occurs in small populations). For example, consider a gene that has two alleles, A and a. Let p equal the frequency, or percent, of the A alleles in a population and q equal the frequency, or percent, of the a allele. Then, p + q = 1. If random mating occurs, the population should consist of p 2 AA individuals, 2pq Aa individuals and q 2 aa individuals (see the Punnett square below). Alleles carried by sperm in the population Alleles carried by ova in population p = A q = a p = A q = a p 2 = AA pq = Aa pq = Aa q 2 = aa If the table above is confusing to you, try substituting values for p and q. For example, instead of p sperm/ova with the A allele and q with the a allele, substitute 0.7 sperm/ova with A and 0.3 with a. Then, what percent of offspring with the genotype aa would you expect? The generation offspring represented in the Punnett square will consist of p 2 (AA) + 2pq (Aa) + q 2 (aa) individuals. According to the Hardy-Weinberg law, the next generation should consist of exactly the same frequencies of each genotype. If a population is in Hardy-Weinberg equilibrium, it will stay in equilibrium, generation after generation. Neither the allele frequencies nor the genotype frequencies will change as long as the following apply: random mating occurs; there is no selection for particular genotypes; there is no migration into or out of the population; and the population is relatively large. Determining gene frequencies when alleles exhibit dominance/recessiveness When dominance and recessiveness affect a pair of alleles, it is impossible to detect all three genotypes by their phenotypes and to calculate gene frequencies directly. However, if you assume the population to be in Hardy-Weinberg equilibrium, you can estimate gene frequencies using the Hardy-Weinberg equations. You know that q 2 represents that frequency of homozygous recessive individuals. The square root of this frequency is q; knowing q you can determine p using the p + q = 1 equation. Once you have determined the values for p and q, you can calculate the frequencies of homozygous dominant individuals (p 2 ) and heterozygous individuals (2pq). BIO 101 Genes and You 5

6 For example, if you know that 16 percent of a particular population is made up of Rhnegative people (dd): q 2 = 0.16; q = 0.40 = frequency of the recessive allele d. Then, p = 1 q = = 0.60 = frequency of the dominant allele D. The 84 percent of the population that is Rh-positive can be divided as follows: 2pq = 2 x 0.6 x 0.4 = 0.48 = 48% of the population expected to be heterozygous Dd; and p 2 = 0.6 x 0.6 = 0.36 = 36% of the population expected to be homozygous DD. Procedure Part 3 Using the information gained about PTC tasting in Part 1 complete the table for your lab section. Fill out the questions for Part 3 on your worksheet now. Determining gene frequencies when alleles exhibit codominance The Hardy-Weinberg equations are not needed to calculate gene frequencies in the case of codominant inheritance. In these cases, gene frequencies can be determined directly from the phenotypes of the individuals involved. Suppose you wish to determine the frequencies of the alleles A (for normal hemoglobin) and S (for sickle cell hemoglobin) in an African American population consisting of 343 AA (normal), 294 AS (sickle cell trait), and 63 SS (sickle cell disease) individuals. (Heterozygous individuals those with sickle cell trait can be determined by microscopic examination of their red blood cells; under conditions that reduce the oxygen tension in the environment of the cells, some proportion of their cells will exhibit the characteristic sickle shape. These conditions do not ordinarily occur within the body of a heterozygous individual, although heterozygotes may experience some sickle cell disease symptoms at high altitudes.) BIO 101 Genes and You 6

7 Suppose you want to know whether the population is in Hardy-Weinberg equilibrium. There are 1400 alleles for the hemoglobin gene in the total population of 700 people (each individual carries two alleles of the gene). The number of A alleles is 980: 343 people have two A alleles and 294 have one A allele. The frequency of A is 0.7: (343 x 2) = 1400 = 1400 = 0.7 Similarly, the frequency of S is 0.3: (63 x 2) = 1400 = 1400 = 0.3 If this population is in Hardy-Weinberg equilibrium, then the frequency of homozygous dominant (AA) individuals is 0.7 (the probability of having one A allele) x 0.7 (the probability of having a second A allele) = Thus, you would expect that 49 percent of the population would have the AA genotype. Similarly, 2pq, or 2 x 0.7 x 0.3 = 0.42, or 42 percent of the population should be heterozygous. You would expect only 9 percent (0.3 x 0.3 = 0.09) of the population to have sickle cell disease (SS). Applying these percentages to the population of 700 individuals reveals that it is in perfect Hardy-Weinberg equilibrium: 49% x 700 = % x 700 = 294 9% x 700 = 63 Part 4. Revisiting the Micro-evolutionary Process and the Hardy-Weinberg Equilibrium In 1950 Atlantic Puffins were introduced to two islands that are 763 miles apart, San Carlos and Nola Rei. Every 6 years more puffins were released on the San Carlos, but not on Nola Rei due to lack of funding. No puffins were observed moving between islands. In 2000 researchers noticed that nearly all the puffins on Nola Rei had completely orange beaks instead of the striped ones puffins usually have, both populations appear to be stable with 75 breeding pairs Using the information above and the H-W equations, complete the information on the worksheet. Fill out the questions for Part 4 on your worksheet now. BIO 101 Genes and You 7

8 Part 5. Incomplete dominance and Co-dominant and models Cats generally have long tails controlled but one gene in a incomplete dominance model where LL are long-tailed, Ll are bobtails, and ll are stump-tailed cats. Blood types in humans follow a co-dominant model. There are three alleles involved yielding 4 phenotypes Using the information above, complete the information on the worksheet. Fill out the questions for Part 5 on your worksheet now. BIO 101 Genes and You 8

9 Part 6 Multiple Genes in Action The following gel electrophoresis is for Labrador retrievers. Coat color arises through interactions among alleles of two gene pairs. One gene pair codes for melanin production (B) the dominant form allows production of black pigment and the recessive form(b)allows for brown or chocolate color. The other gene codes for melanin deposition (E) in order to place pigment in the hair the dominant form must be present, if only the recessive allele (e) is present the dog will have yellow coat color. Procedure Part 5 Using the information above, complete the information on the worksheet. Fill out the questions for Part 6 on your worksheet now. BIO 101 Genes and You 9

10 BIO 101 GENETICS Name Part 1 Genes and You 1. Are you a taster of PTC? If you are a taster, what did it taste like? Was it sweet, sour, salty, bitter, etc.? 2. You now know your phenotype. Do you know your genotype? a. If no, why not? b. If no, how might you be able to determine what your genotype is? 3. Fill out the chart below for yourself and one or more people. Trait Your Traits Other Person Bent Pinky Tongue rolling Phenotype Possible Genotype Phenotype Possible Genotype Blue Eyes Widows Peak Thumb Crossing Attached Earlobe Hitchhiker Thumb Redgreen Colorblind Hairy Ears Pattern Baldness Finger length BIO 101 Genes and You 10

11 Part 2 Human Pedigree Analysis Complete the table below for the traits exhibited in the six pedigrees you analyzed in class. Pedigree Autosomal or X-linked? Dominant or Recessive? Probability A will have trait Probability B will have trait BIO 101 Genes and You 11

12 Part 3. Genes in Populations, the Hardy-Weinberg Equilibrium 1. Record your phenotype on the table on the board or overhead projector. After all the data for the class is recorded, copy the total call data below: Phenotype Number Frequency (Percent) Taster Non-taster TOTAL 2.Calculate the frequency of the recessive allele, t, in your class by applying the Hardy-Weinberg equations to the class data: 3. Use the equations to determine the frequency of the T allele: 4. According to the Hardy-Weinberg equations, the frequency of TT individuals is: and the frequency of Tt individuals is: Part 4. Microevloutionary Process and the Hardy Weinberg Equilibrium 1. As you may expect, the conditions for Hardy-Weinberg equilibrium do not always exist five factors disturb genetic equilibrium in natural populations they are: BIO 101 Genes and You 12

13 2. If we assume a single dominant gene controls that beak-stripping allele (S) and that the recessive allele is (s) causes a non-striped completely orange beak. Given the following data calculate the Hardy-Weinberg Equilibrium: Phenotype Stripped Beaks Orange Beaks Total p freq q freq Initial Releases San Carlos Nola Rei Part 5. Incomplete and Co-dominant and models 1.What are the possible outcomes and probabilities from the following cross? Ll x Ll (Please show your work.) 2.What are the possible outcomes and probabilities from the following cross? Ll x ll(please show your work.) 3.What are the possible outcomes and probabilities from the following cross I A i x I B i (Please show your work.) BIO 101 Genes and You 13

14 4.What are the possible outcomes and probabilities from the following cross I A I Bi x ii (Please show your work.) 5. Could a marriage between the individuals list in question #4 have a Type-O child? Part 6. Multiple Genes in Action 1.What is the probability of getting a yellow lab from the cross listed below EEBb x EeBb (Please show your work.) 2. What is the probability of getting a chocolate lab from the cross listed below EeBb x eebb (Please show your work.) 3. What is the probability of getting a black lab from the cross listed below Eebb x eebb (Please show your work.) BIO 101 Genes and You 14

15 NAMES DATE Analysis Question 1 Examine the pedigree below for a rare trait found in a particular family: Gen I Gen II Gen III Analyze this pedigree below Give specifics on the type of inheritance and How you know, use genetically appropriate language. Is it dominant or recessive? How you know? Is it autosomal or sex-linked? How you know? BIO 101 Genes and You 15

16 Analysis Question 2 The Hardy-Weinberg law applies not only to human populations, but also to plant populations and other animal populations. T and N represent two alleles of the gene for venom found in a population of gaboon vipers. A study of 2000 vipers from the population revealed the following: 100 were genotype NN (non-venomous), 800 were genotype TN (mildly venomous), and 1100 were TT (deadly venomous). Analyze this group of gaboon vipers, from a population genetics perspective. (Hint your need to use the codomiant model) Show your work. BIO 101 Genes and You 16