Population genetics lab

.docx

School

Austin Peay State University *

*We aren’t endorsed by this school

Course

MISC

Subject

Biology

Date

Dec 6, 2023

Type

docx

Pages

Uploaded by ProfJellyfishPerson1838

Population Genetics Lab NOTE: Bring a flash drive with you to lab! Pre-lab activity (please inform your instructor if any links are nonfunctional) : - The following PBS site has many interesting short video clips and other information regarding evolution: http://www.pbs.org/wgbh/evolution/library/index.html . If your instructor does not assign anything specific, then check out whatever sounds interesting! Lab Objectives After completing this lab topic, you should be able to: 1. Describe the conditions required for “Hardy-Weinberg equilibrium”. 2. Know and use the Hardy-Weinberg and allele frequency equations to solve population genetics problems. 3. Describe the genetic effects of evolutionary forces such as natural selection and random genetic drift on large and small populations. List of Lab Activities: Activity 1. Using class data for Hardy-Weinberg calculations ( pages 4-5 ): - PTC tasting ( p. 4 ) - earlobe condition ( p.5 ) Note: We will collect data for this in lab, and you will complete it as homework, filling in the spreadsheet posted on D2L. Check with your instructor whether you should submit the spreadsheet to the appropriate D2L assignment folder, OR whether you should send it as an email attachment. Activity 2. Bean simulation activity (beans, 2 people per group) ( pages 6-10 ). Activity 2A: Genetic Drift: Bottleneck Effect (pages 6-7 ) Activity 2B: Hardy-Weinberg conditions for one generation ( pages 8-10 ) Activity 3. Computer simulations using Populus software ( pages 11-17 ) Note: If you can’t finish during lab, this software can be downloaded for free at: www.cbs.umn.edu/populus . (If you have problems downloading or getting this program to work at home, be sure to make arrangements to complete it at school!)

Population Genetics Lab 2 Assignment to complete for Population Genetics lab report 1. Submit a Word document with the following (in this order) : 1. Bean data experiment for Activity 2A (Genetic Drift: Bottleneck Effect): a. Excel graph of allele frequencies (both allele frequencies on same graph) b. Table 1 ( page 7 of this handout) c. Summary statement about what happened (a few sentences, typed ). Be sure to state what caused your results to turn out as they did. 2. Populus activity: The 7 labeled graphs you were told to copy (see Populus instructions). ALSO do the following: 3. Take the D2L quiz for the Populus worksheet. Note that D2L will not grade several of the questions – your instructor or TA will have to go in and grade those manually. 4. Download and fill in the spreadsheet for the PTC tasting / earlobe condition data. Submit the completed spreadsheet file to the appropriate D2L assignment folder, unless your instructor tells you to email it as an attachment (CHECK). Be sure you submit it BEFORE lab (at the usual D2L pre-lab quiz deadline time).

Population Genetics Lab 3 Introduction In this lab you will practice doing calculations using equations relevant to population genetics and carry out simulations of populations being affected by various evolutionary forces. A population “at equilibrium” for any particular gene is a population where no evolutionary forces are changing allele and genotype frequencies for that gene as generations pass. The Hardy-Weinberg genotype frequency equation (see Activity 1) predicts the next generation’s genotype frequencies under equilibrium conditions, and under these conditions there will be no changes in the genotype frequencies. Evolutionary forces that can disrupt “Hardy-Weinberg equilibrium conditions” (and thus must not be happening for Hardy-Weinberg to accurately predict the next generation’s genotype frequencies) are the following: natural selection (“survival of the fittest”), mutation, nonrandom mating, gene flow (i.e. migration of individuals or gametes between populations), and random genetic drift (changes in allele frequencies due only to random, chance events). The smaller the population, the stronger the effects of random genetic drift, which means that large populations are much less affected by random genetic drift. When populations that used to be large suddenly become small they are said to have gone through a “ genetic bottleneck ” causing a loss of alleles and thus a decrease in genetic variability when they became small. This is because a small number of individuals cannot contain as many different alleles for genes as a very large number of individuals can. Large populations may become small if a disaster (e.g. a hurricane) causes high mortalities. Alternatively, a few individuals from a large population may start a new population which would then be a small population (e.g. a few birds blown off course in a storm may land on an island where no other birds of that species exist and so start a new population on the island). The decrease in genetic variation caused by such a colonization event is referred to as the “ founder effect ”. Of course, many times one or more evolutionary forces are changing allele frequencies for certain genes, so that the Hardy-Weinberg equation does not accurately predict the genotype frequencies of the next generation. Nonetheless, the equation’s predictions still provide a “baseline” with which to compare actual genotype frequencies, and any discrepancies revealed may lead to investigations to elucidate what evolutionary force(s) could be causing the changes. See Chapter 23 of your text for more background information on these topics, including a derivation of the Hardy-Weinberg equation.

Population Genetics Lab 4 Activity 1: Using Class Data for Hardy-Weinberg Calculations Review of equations: If p is the frequency of the dominant allele and q is the frequency of the recessive allele: Hardy-Weinberg equation (= the genotype frequency equation): p 2 + 2pq + q 2 = 1 Allele frequency equation: p + q = 1 NOTE for all work below: - Use decimal numbers for frequencies (rather than %). - Write your answers to three (3) decimal places . Data from PTC test : Your individual results: Taster or Nontaster ? (write what you are on the board up front) Class data: total # of students in class = 20 phenotype counts for class: T # of tasters (TT and Tt genotypes) = 5 # of nontasters (tt genotype) = 15 NOTE: the non-tasting phenotype is the only phenotype for which we know exactly what the genotype is. (The tasting phenotype is a mixture of two genotypes.) Calculating frequencies of genotypes and alleles: q 2 = frequency of nontasters = (# of nontasters) / (total # of students) = .75 Question: Can we just calculate p 2 (the frequency of homozygous tasters) instead of q 2 ? Why or why not? We don’t know q = frequency of t allele = _0.86_______ p = frequency of T allele = 1 - q = 0.14 p 2 = frequency of TT genotype = 0.02 2pq = frequency of Tt genotype = 0.23 Questions: If you choose a person at random from this class, what is the chance (probability) that he/she will be 1. a taster? 1/4 2. a taster who is a “carrier” for the t allele? 23/100 3. Which allele is more common in this case — the dominant or the recessive? Recessive

Population Genetics Lab 5 (Using Class Data for Hardy-Weinberg Calculations, cont.) Data for earlobe condition: Your individual results: Attatched or Unattached earlobes? (write what you are on the board up front) Class data: total # of students in class = __20______ phenotype counts for class: # with unattached (free) earlobes (EE and Ee genotypes) = ___13_____ # with attached (no lobe) earlobes (ee genotype) = ___7_____ Calculating frequencies of genotypes and alleles: q 2 = frequency of attached = (# with attached) / (total # of students) = 0.35 q = frequency of e allele = 0.59 p = frequency of E allele = 1 - q = 0.41 p 2 = frequency of EE genotype = 0.17 2pq = frequency of Ee genotype = 0.48 Question: 4. Which allele is more common in this case — the dominant or the recessive? Dominant allele . The dominant

Population Genetics Lab 6 (bean simulations) Activity 2: Simulating population genetics using beans In Activity 2, we will be using dark and light beans to simulate alleles. We will say that the dark bean represents the dominant allele and the light bean represents the recessive allele. Remember that every diploid individual has TWO alleles for a gene, so every pair of beans will represent one diploid individual. We will be placing beans into a bag, and our bag of beans will represent the “gene pool” – the alleles from our randomly mating population. Activity 2A : Simulating an evolutionary force at work: Random Genetic Drift, via the Bottleneck Effect In this experiment you will be simulating the effects of random genetic drift on your population. The random genetic drift in this experiment is due to some disaster (e.g. a hurricane) causing your population to become very small in the next generation (i.e. the “bottleneck effect”). Procedure: 1. Establish a population of 50 individuals (how many beans total?) with a frequency of 0.5 for each allele (so how many dark beans and how many light beans?). This will be “Generation 0”. 2 . Without replacement (NOTE!), randomly select 5 individuals (survivors), two alleles at a time, leaving each pair of beans out on the table (because you are sampling without replacement). This represents a drastic reduction in the population size as only 10% of the population has survived. 3. Record the genotypes of the five survivors in Table 1 below. Also calculate the frequency of each genotype (observed # of individuals divided by a total of 5 survivors) as well as the frequency of each allele in this population of survivors. 4. Complete the rest of this row in Table 1 by calculating the frequency of each genotype that would be expected in the next generation IF the population were under Hardy-Weinberg equilibrium conditions. Note that we do NOT actually think our next generation is going match Hardy-Weinberg expectations very well, because our population is not experiencing equilibrium conditions (recall: Hardy-Weinberg assumes that no random genetic drift is occurring). We aren’t going to carry out any goodness of fit test to determine this statistically, but nonetheless we can notice how the actual observed frequencies we get for our next generation compare with the Hardy-Weinberg predictions (and we won’t be surprised if they are fairly different). 5. Using the new allele frequencies that you calculated in step 3, determine how many of the 100 beans in your bag should now be dark beans and how many should be light beans. Report these numbers to the instructor before you actually count out the beans if this is the first time you are carrying out this step! 6. Place the proper number of light and dark beans in your bag.

Your preview ends here

Eager to read complete document? Join bartleby learn and gain access to the full version