Genetics 2450

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Introductory Material

 

Instructions for PopGenLab Research Paper  (from pages 9-11 of printed manual)

Overview of Assignment

This assignment has two purposes. You will use the Online lab called PopGenLab to explore the basic concepts of population genetics and evolution. You will also write a scientific paper about the simulation experiments you perform with the PopGenLab. Consequently, there are two parts to this assignment:

1. Conduct the simulation experiments for assignments 1-6 from the PopGenLab and answer the questions for each assignment. These questions are indicated in bold in the text for each assignment. You will turn in the answers to these questions at the beginning of lab two weeks from today.

2. After completing the assignments, you will develop research questions and hypotheses relating to the themes of three of the assignments. Your lab instructor will tell you which three assignments to work on.  You will then design an experiment to test your hypotheses using the PopGenLab simulations and conduct that experiment. Your new questions/hypotheses, the data from your simulation experiments and the conclusions you draw from them will form the foundation for your PopGen paper. This will require some thought. Some hints for developing ideas for your research are provided in the next section. On the due date three weeks from today, you will be expected to hand in a well-crafted scientific paper describing your research using the PopGenLab.

Developing Research Questions and Hypotheses

While you are working on the assignments, think about what you are doing and what is interesting to you. Try to formulate new questions and write them down as you work through the assignments. You can then look over these questions to formulate research ideas and hypotheses.

The best questions will be ones that are interesting to you and the ones for which you can formulate a testable hypothesis. As you think about your hypotheses, think also about how you could test them. Here is some advice:

1. Keep things relatively simple if possible. Try to design experiments that require manipulation of only one, or at most, two of the input variables. Do not try, for instance, to manipulate stand size, migration rate and mating pattern at the same time. Those kinds of experiment will be difficult to manage. Keep it simple.
2. When formulating your hypothesis, don�t worry about its originality. If you want to test a hypothesis that you heard about somewhere else and you can design a good experiment, go for it. Extensions and modifications of the assignments are completely acceptable. The point is to explore population genetics and evolution with the simulations.
3. Make sure the hypothesis is worth testing. Consider the following examples:

    

   Example Research Question 1: How does variation in starting allele frequencies affect the rate of fixation in small populations?

   
   Poor Hypothesis: Genetic drift will have no effect on a population that is fixed for one allele. (This is just not interesting.)
   

   Better Hypothesis: The average time to fixation of the A allele in a population is faster in populations with higher starting frequencies of that allele.
   

   Example Research Question 2: How does natural selection affect heterozygosity in populations?
   

   Poor Hypothesis: Natural selection will change heterozygosity within a population.
   

   Better Hypothesis: Natural selection will increase heterozygosity within a population.
   

   (Notice that the type of selection has not been specified in this hypothesis. Notice also that the time scale of the experiment (number of generations) has also not been specified.)

   
   Even Better Hypothesis: Diversifying selection will increase heterozygosity within a population over time.

   
   Example Research Question 3: How does the strength of selection influence the rate of change in allele frequencies?

    

   Poor Hypothesis: Strong selection will affect the rate of change in allele frequencies.

   
   Better Hypothesis: Strong directional selection will cause fixation of the favored allele to occur in fewer generations compared to weaker selection.

   
   Even Better Hypothesis: Increasing the selection coefficient, s, by a factor of 2 will cause fixation of the favored allele to occur in half the time.

The point here is to think carefully about your questions and resulting hypotheses and to formulate an experiment which will clearly test your hypothesis. You will then write a scientific paper that describes your methods (experimental designs) and your results as well as a discussion of the conclusions you draw from your simulation experiments. Feel free to discuss your hypotheses with other students, your lab instructor or the course instructor. However, the work you turn in must be original. No plagiarism will be tolerated.

General Instructions For Writing Your Paper

• Papers are due at the beginning of class on the due date.  Late papers will NOT be accepted and will be given a grade of zero.  Lack of planning on your part does not constitute an emergency. 
• You must include a minimum of 10 peer-reviewed references.  Try JSTOR, Science Direct or BIOSIS under the TSU, San Marcos (Alkek) library�s journal databases.  If it�s not peer-reviewed, it will not count towards the minimum requirement. (Hint: you may use these references as sources of ideas for your questions and hypotheses.)
• Papers will be turned in as 1) hard copy and 2) digital copy saved to 3.5� floppy disk.  Disk should be labeled with your full name and TSU ID number as personal identification.  Failure to turn in both hard copy and digital copy result in grade of zero.  You will not get this disk back since it goes into a permanent collection of digital genetics papers to test for similarities with other genetics papers.  There should be ONE file on this disk, and filename saved as �TSU ID number, 2450, Spring 2004, PopGen� (example: 785489,2450,Spring2004,PopGen).  All papers should be written in Microsoft Word format.  
• Follow the instructions on page 3 of your lab book for �General rules for genetics lab papers.�  Also use the book you purchased for Freshman Biology entitled Writing Papers in the Biological Sciences by J. A. Pechenik.   If you are still unsure about writing a paper, the English Department and SLAC at the Alkek library offer assistance.
• Papers will follow scientific paper format.  This includes labeled sections of Abstract, Introduction, Methods, Results, Discussion, and Literature Cited.   Double-space the entire document, use 12 point font, and use a common font (Times, Arial, etc).  Write at the level of your college biology peers.
• Separate thoughts = separate paragraphs.  No single paragraph should be more than a page long.  Ever. Write in paragraphs.  Do not bullet or outline methods.
•  Write in past tense, use correct grammar and use complete sentences. Use the required peer-reviewed papers as a guide to writing style.
• Saving graphics to put in your paper. This includes any figures or tables that illustrate your results. DO NOT INCLUDE RAW DATA. If you collect data on allele frequencies over 500 generations, do not include the actual numbers in your paper. Instead, use a simple graph figure to illustrate the data.
  • for PC users, just click export button, then copy graphics and paste in MS Word.
  • for Mac users, export in PopGen lab, then click and hold (same as right click but there�s only one button) on image, and you can either a) �download image to disk�, open image, copy, paste in Word, or, b) �copy image� and paste in Word

Outline

 

You should follow the following general outline when writing your paper:

 

Abstract (10%)

Should be one or two sentences summarizing each section of Intro, Methods, Results, Conclusions/Discussion, and should be concise.

Introduction (15%)

A) Introduce topic�population genetics; frequency of alleles; genotype frequency vs. allele frequency

B) Overall - factors affecting the genetic structure of populations

Describe the Hardy-Weinberg Equilibrium Theory. What is the purpose of the Theory? Describe the HW conditions and their meanings. Discuss each of the following topics and the theoretical effects of each factor:

1. Genetic Drift
   a) what is genetic drift, carrying capacity
   b) how does genetic drift relate to HW
   c) how, when, and why does genetic drift affect populations over time

2. Influence of Mating Patterns on a population
   a) what are random, assortative, and disassortative mating
   b) how do mating patterns relate to HW
   c) how do mating patterns in a population affect populations over time

3. Modes of Natural Selection
   a) Define: natural selection, fitness (w) and selection coefficient(s)
   b) fixation and extinction of alleles
   c) directional, stabilizing, and diversifying selection
   d) how do modes of natural selection relate to HW
   e) how do modes of natural selection effect a population over time

4. Migration
   a) what is migration
   b) smaller population size � greater impact
   c) how does migration relate to HW
   d) how does migration effect a population over time

5. Population bottlenecks
   a) what is a population bottleneck
   b) disasters and disaster frequency
   c) how do population bottlenecks relate to HW
   d) how do population bottlenecks effect a population over time

B) Moths and Industrial Revolution

C) PopGenLab

a) describe PopGenLab program briefly and the parameters you can manipulate (give appropriate citation for PopGenLab software)
b) describe the general objectives of your three experiments

Methods (15%)

Go through each of your three experiments and list the steps and what you did. Do not give any results yet � save results for the next section of the paper.
For each section:

1) describe your research question and hypothesis
2) describe the input variables that you manipulated and how you changed them for your experiment, including their values.

Results (20%)

For each of the three sections: Clearly describe the results of your experiment and the data you collected. Use Tables and/or figures whenever necessary. Place all tables and figures at the end of your paper in numerical order. Do not embed the figures and tables in the text.

 

Discussion (25%)

1) discuss EACH section and determine how the factors you manipulated affected the outcome of your experiments. Discuss what you learned from each experiment
2) report any errors or failures that occurred and suggest why they may have occurred

Literature Cited

 

Single spaced, alphabetized, follow style on pages 5 and 6 of your lab manual

 

 

Appendix

1) tables and figures for results (follow Writing Papers in the Biological Sciences by J. A. Pechenik if you need more instruction)
2) turn-in stuff for pop gen. (figures and answers to questions)

Legends for Figures (Charts and graphs)

1) label ALL as figures whether they are charts or graphs or pictures
2) put everything you can in legend: genotype frequencies for all three, tree freqs. for all 3 trees, stand carrying capacity, number of stands, migration rate, mating pattern, and disaster frequency. Add any other distinguishing information.

Figures

1) should have �Label. Explanatory title. Complete description where the figure can stand alone without having to look back to the text.� See the figures in your peer-reviewed papers for examples of how figures should look.