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Population Genetics (BIOL 4366, BIOL 5366)
Spring 2003 Dr. Aldemaro Romero Arkansas State University
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1. Course Objectives 1.1. Introduction
The main objective of this course is to introduce you to the study of genetics at the population level in order to better understand evolution as a process. Emphasis will be placed on ecological population genetics rather than on a pure mathematical population genetics. Yet, we will cover in extenso both theory and experimental approaches including mathematical / statistical / computer methods. The essentials for understanding the theoretical foundations for population processes such as genetic drift, selection, and gene flow will be covered throughout the course. The knowledge gained with the study of those concepts will be used to address the mechanisms for the maintenance of variation. We will also take a look of the neutral theory of evolution. Assignments will include basic problems that can be solved with a hand calculator but also those that will require computer statistical and other programs. Many simulations will be accomplished using software programs. Although there is no laboratory connected with this course, realistic examples will be given where possible to illustrate the use of population genetics in solving/explaining/pursuing biological problems.
1.2. Methodology
You will be trained on the basic concepts and principles of population genetics and to further develop the knowledge and skills required of the research scientist, skills which are also required in many other professions. Whether you enter (and/or pursue further) into graduate school, pursue a teaching career, or follow some other career path, you will be compelled to understand and integrate a large body of knowledge, to think analytically, identify and critically evaluate pertinent literature, to communicate effectively, and to work with others
This is how this course aims to develop those abilities.
A. Solid foundation in the knowledge of Population Genetics. You will be introduced to the content of the course in the classroom. B. Application of scientific methods of inquiry, search and, critically read the scientific literature. We will examine the diverse approaches used by researchers to uncover the basic concepts of the study of population genetics. C. Development of analytical thinking skills. Population genetics is a highly integrative field of biology. To make your approach as scientific as possible you will need to rely heavily on critical thinking. The true test of understanding comes when you use your knowledge in different situations.
1.3. Expected Outcome
By the end of the semester, you should have a general knowledge of the basic concepts and processes related to the genetic dynamics of populations. Additionally, you should have further developed your skills in planning a population genetics research program, conducting field and laboratory studies, analyzing information, and critically reviewing the scientific efforts of others.
1.4. Prerequisites
Prerequisites for this course are Genetics (BIOL 3313) and Laboratory for Genetics (BIOL 3311). No exceptions will be made.
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2. Instructor
Dr. Aldemaro Romero, (B.S.: University of Barcelona, Spain, 1977; Ph.D.: University of Miami, 1984). I am Professor and Chair of the Department of Biological Sciences at Arkansas State University. I have published more than 420 papers, abstracts, and books in different areas of biology, but many of them are on evolution, an area for which population genetics is a critical component. Here are some of the most recent:
Romero, A. 1999. Useless abilities. New Scientist 162(2190):54-55. Romero, A. 2001. Evolution is opportunistic, not directional. BioScience 51(1):2-3. Romero, A., A. Singh, A. McKie, M. Manna, R. Baker, K. M. Paulson, & J. E. Creswell. 2002. Replacement of the troglomorphic population of Rhamdia quelen (Pisces: Pimelodidae) by an epigean population of the same species in the Cumaca Cave, Trinidad, W.I. Copeia 2002(4):938-942. Romero, A. 2003. Adaptation: Behavior. Encyclopedia of Cave and Karst Science. (J. Gunn, ed.). London: Fitzroy Dearborn (In Press). Romero, A. 2003. Evolution of hypogean fauna. Encyclopedia of Cave and Karst Science. (J. Gunn, ed.). London: Fitzroy Dearborn (In Press).
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3. Textbook and Supplies 3.1. The Textbook Daniel L. Hartl & Andrew G. Clark. 1997. Principles of Population Genetics, Third Edition.Sunderland, MA: Sinauer Associates.
undergraduate and graduate levels. It introduces the principles of genetics and statistics that are relevant to population studies, and examines the forces affecting genetic variation from the molecular to the organismic level. Integrated throughout the book are descriptions of molecular methods used to study variation in natural populations, as well as explanations of the relevant estimation theory using actual data. Chapter 1 presents the fundamental genetic and statistical concepts in population genetics. Chapter 2 reviews the types and prevalence of genetic variation in natural populations. This is followed in Chapter 3 by a detailed examination of the implications of random mating for one locus and multiple loci. Chapter 4 examines population subdivision and its consequences for the distribution of genetic variation among subpopulations, including the hierarchical F statistics used in estimating these effects. Chapters 5 through 7 deal with mutation, migration, natural selection in all its varieties, and the consequences of random genetic drift. Molecular population genetics, including coalescent theory, is the subject of Chapter 8. Quantitative genetics is covered in Chapter 9, from the standpoint of genetic variance and covariance components as well as with respect to molecular markers used to detect quantitative trait loci (QTLs). Applications of principles discussed in the text are illustrated by numerous examples of worked problems, using actual data. Each chapter end, in addition to a complete summary, offers several problems for solution, to reinforce and further develop the concepts.
3.2. Other Supplies I recommend that you obtain a zip-disk or a CD-ROM disk to download the electronic material I will be e-mailing you.
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4. Other Resources 4.1. Library Resources: ASU’s Library has various scientific periodicals and books and I also have a private library with numerous books, journals, and reprints on the subject; you are welcome to use those resources in my lab under the appropriate supervision. 4.2. Computer Resources: All officially enrolled students have access to the E-mail system. I heavily use the system to communicate with you (up to several times a week). Please check your email regularly for class announcements. You can also send me email to ask me questions or to engage in discussions with your colleagues.
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5. Academic Approach I give the best of myself in each one of my classes in order to offer you the opportunity to maximize your chances of learning lasting lessons in science. I consider myself motivational, challenging, and enthusiastic. I encourage questions during lectures and will stop lecture until you are satisfied that your question has been answered. I greatly appreciate students who come to me for further discussion and inquiring. Please do not hesitate to see me to discuss the subject as well any problem that may arise regarding class schedule and grading. At the same time, I have high expectations for your personal growth and success as a student in this semester. If you cannot figure something, I expect you to see me so we can seek a solution to the problem. I will do my best to ensure that you learn the maximum and that your effort is rewarded with good grades. I take a great deal of pride on how much my students learn and on the well-earned grades they receive. Your total effort per week should average 9 hours. This will include approximately 3 hours of lecture and at least 6 hours of outside work. |
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6. Recording and Duplication of Course Materials Lecture presentations, lecturer's notes and outlines, handouts, and exam materials are the property of the instructor and may not be recorded or duplicated for commercial use or sale without the permission of the instructor. Students are permitted to record lectures for individual use only. Commercial note-taking services are expressly prohibited. |
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7. Office Hours
My policy regarding office hours is that if I am in my office or my lab, I am available. If you need to discuss something that requites a lot of time, please make an appointment. Office: Biology Office; Lab: LSW 443 Phone Number: (870) 972-3082 Email address: aromero@astate.edu
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8. Evaluation Criteria
Your performance will be evaluated totaling 500 points as follows: a) Tests: two 100-point exams will be given. They will consist of critical thinking/problem oriented questions about the material covered in the lectures. POINTS = 200 b) Class participation: POINTS = 100 c) Paper: Each student is expected to complete a minimum typed, double-spaced 10 page paper (not counting literature cited list). By February 8th you will be submit a title and a one page outline of the project. By February 24th an annotated bibliography will be submitted. By March 23 an electronic copy of the paper will be submitted. Each paper will be reviewed. These critiques will be returned by April 11 with a re-submission of a final manuscript by April 27th. Oral presentations of the project and discussion of those projects will take place during the last two class meetings. POINTS = 200 TOTAL = 500
No make-up exams will be given under any circumstances. If a student misses a scheduled examination s/he will receive a grade of zero. All deadlines must be met. No excuses will be accepted.
The grading scale is as follows: % Grade 450-500 A 400-449 B 350-399 C 300-349 D 299 or below F
Incomplete grades will be given only in rare cases where the student suffers from some type of physical disability or illness that prevents the completion of the second half (that is after the first exam) of the semester. Medical documentation will be required.
Also, if you feel I have erred in grading, please let me know, and I will regrade your entire exam. You might get points back, but then again, I might see something I missed before...
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9. Letters of Recommendations Those students that have excelled in my class can always count on strong letters of recommendation upon request.
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10. Attendance Attendance is expected at all lecture sessions. Attendance will be taken at the beginning of each class. I can be flexible if in a very occasional fashion you are late and I will give you an "attended" mark for that day. However, regular tardiness will not be excused. Since there is not textbook, students are expected to come to all sessions. I reserve the right to penalize those who do not attend by not granting favors. Class attendance is one of the major characteristics that employers are interested in when hiring new employees because it tells a lot about one's commitment to assigned tasks and the ability to deal with varying life situations. For example, there is an increasing tendency for some students to miss a class in one course in order to study for a test scheduled later in the day. Although there might be times when such decisions are necessary, studies suggest this is usually not a valid decision. Not only does it seldom result in a significant increase in the test score, it is considered an indication of lack of confidence and/or poor time management. The problem is usually magnified when one is later tested without adequate notes (or no notes) from the missed class. If you must miss class for any reason, you should get notes from two classmates, review the notes, and then see me to clear up any questions about the missed class. It is best to do this by the next class period since the importance of the missed notes often quickly diminishes with time only to resurface the day before an exam or perhaps during the exam. The university remains open for academic classes and all other services during inclement weather except in extreme circumstances determined solely by the president of the university. Regional and local news media will publicize the closing.
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11. Academic Honesty To ensure the highest standards of academic honesty and ethical behavior, the Honor Code will be strictly enforced. In other words, do not even think about any behavior that may be construed as academic dishonesty, plagiarism, misrepresentation, or cheating. Academic dishonesty includes, but is not limited to the following: A. Cheating on an examination, taking information or allowing information to be taken from tests. B. Receiving help from others in work to be submitted, if contrary to the stated rules of the course. C. Plagiarizing, i.e., taking and passing off as one's own the ideas, writings or work of another, without citing the source. This is true whether the material used is only a brief excerpt or an entire paper or article and whether the original source is the work of another student or some publication. D. Submitting work from another course. E. Stealing examinations or course material. F. Falsifying data and/or records. G. Assisting anyone to do any of the above. The honor code protects the honest student, the reputation of ASU, and the value of degrees earned here. We should all support it both by personal honesty in all things and by refusing to tolerate dishonesty in others. Any graded work must be performed completely unaided. Students must report to me any suspected cheating. If you have any questions about your assignment, plagiarism, or the Honor Code, please contact me. The following are not allowed in class: tobacco usage, active pagers or cell phones.
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12. Withdrawals You are the sole responsible for fulfilling all necessary steps to formally withdraw from this course.
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13. Students with Special Instructional Needs If you have any special needs related to learning or testing in this course, please let me know as soon as possible so I can address those needs.
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14. Course Outline Week Topic Chapter
1 Genetic and statistical background 1
2 Review of probability and hypothesis testing 1
3 Genetic and Phenotypic variation 2
4 Hardy Weinberg rule of gene frequencies 3
3 Extension of Hardy Weinberg 3
4 Inbreeding 4 Random drift 7
5 Wright's Shifting Balance Theory 7
6 Assortative Mating 4
7 Sources of Variation 5
8 Natural Selection and Genetics 6
9 Natural Selection and Genetics. Sexual Selection 6
10 Molecular population genetics 8
11 Molecular population genetics 8
12 Quantitative Genetics 9
13 Nature vs nurture. Heritability Handouts
14 Presentations of graduate students
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HOW TO SUCCEED IN MY CLASS Every professor has his/her own values on how to judge students. This ranges from knowledge to attendance, from attitude to hard work. Each one of us is different in his/her methods and approaches, but all of us want our students to succeed by learning and getting good grades. What follows are a series of recommendations that, if pursued, would put you pretty much on the path to success: 1. Show up. My lectures and discussion sessions contain the information you should know. Attending class and taking notes will help you focus on what is really important, in what I consider to be essential. I use a lot of visuals in my presentations. I also like to challenge my students, to engage in discussions, to make the class a truly participative experience. You cannot get this information from another student's notes. You need to observe my delivery: you need to know not only what was said but also how it was said. Besides, when you study without having been in class, you are learning the material for the first time. When you study after you have been to class, you are reviewing. 2. Attendance record. Make no mistake about it: in the subjective realm of grading, attendance always counts. I respond positively towards students who come to class regularly. Repeated absences will lose you the benefit of the doubt when it comes to grading, and you might very well need that benefit. For this class, learning is accumulative, with each class building on the previous one. If you fall behind, it becomes increasingly difficult to catch up. 3. Prepare for class. The schedule included in this syllabus tells you exactly what topics will be covered and I will email you notices on the reading material before hand. I will ask questions during the class; your class performance will be evaluated. Know the scientific vocabulary and terminology and practice critical thinking. 4. Choosing the right seat. I use a lot of visuals for this class. Thus, try to seat in the very first rows. That will allow you to read the visuals without difficulty, it would let me notice you (leading me to believe that you are involved and conscientious), and will ensure your participation. 5. Take notes. Unless you have a photographic memory you should take notes, but do not confuse taking notes with stenography. I try to make you think during the class and you cannot listen, think, and respond if you are busy playing secretary. Most of the things that are written on the board and/or shown in transparencies tend to be very important. Many of my past students have told me that they have found that the best way to follow my classes is by tape-recording my lectures and just taking notes on the information written on the board or the transparencies. Since it is not practical to have 40 tape recorders on my desk while I am lecturing, I strongly suggest that you form study groups where one student per group is responsible for recording and sharing the tape (see "Recording and Duplication of Course Materials policies," above). Do not hesitate to come to me with questions or concerns about past lecture material. Try to understand why we know what we know in science. Establish connections and links between concepts and ideas covered throughout the course. Know how the information presented is used, and why it is useful in the real world. Extend and relate your knowledge and understanding into new contexts and situations. 6. Class participation. I seek, need, and appreciate student involvement in my class. Animated discussions are one of the best rewards I can receive as an instructor. Some class sessions will be specifically aimed at discussion of reading material. I know that speaking before a group is a scary experience for many. Survey after survey, it has been shown that what people fear most (even more than death, accident, or even losing their job) is to speak in public. Do not think that by participating you are annoying others, that you have nothing to contribute, or that by asking a fundamental question people will judge you negatively. They will not judge you: they are too busy thinking about their own comments. However, as much as I encourage participation, there is one and only one question I do not like to hear, and that is: "Do we need to know that?" Make no mistake about it: you are not paying tuition (and the University is certainly not paying me) in order to use the class time to engage myself into idle talk and/or irrelevant material. Everything I say, everything I point out to, is because I feel is important for you to know, and in consequence it can be asked in a test. I will use the review sessions, however, to point out to those aspects that I consider really relevant for you to prepare for the exam. 7. Form study groups. My most successful students form study groups. Talking about the material, quizzing each other, and sharing time exploring the material builds your interest and comprehension, and makes learning fun. Disclaimer: The information contained in this syllabus is as accurate as possible, but may be subject to change with reasonable advance notice. The schedule and content of lectures and assignments may be changed at the discretion of the instructor upon oral notification in class. Changes may involve additions, deletions, substitutions, or changes in sequence or due date.
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FAILURE TO FOLLOW THE DIRECTIONS CONTAINED IN THIS SYLLABUS COULD CAUSE YOU TO GET A POOR GRADE IN POPULATION GENETICS
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Cover illustration: In 1926 the cave fish population in the Cumaca Cave of Trinidad, W.I., was described as a new troglomorphic genus and species, Caecorhamdia urichi, due to its reduction in eyes and pigmentation. Later studies indicated that this was just a cave population of the widely distributed epigean form of Rhamdia quelen. Beginning in the 1950's a number of specimens were collected in the cave showing variability in eye size and pigmentation. In 2000 and 2001 myself and some of my students conducted field studies that included direct observation of individuals using infrared equipment (video cameras and night-vision goggles), fish echo-sounders, and collecting. We also studied all available specimens of the cave population that have been deposited in museums. Our results strongly suggest that the troglomorphic population has been completely replaced by an epigean one in a period of time as little as 50 years. We hypothesized that some of the reasons for this replacement included, but are not limited to, a new and continuous gene flow from the surface population into the cave one and the adaptations to nocturnal life among individuals of the cave population of R. quelen. This illustration is from Romero, A., A. Singh, A. McKie, M. Manna, R. Baker, K. M. Paulson, & J. E. Creswell. 2002. Replacement of the troglomorphic population of Rhamdia quelen (Pisces: Pimelodidae) by an Epigean population of the same species in the Cumaca Cave, Trinidad, West Indies Copeia 2002(4):938-942. |
| Recent Student Evaluations: These are the evaluations for the last time I taught this course, i.e., Spring 2004: Sample size: Six students registered for that class; five filled out the students' evaluations and four wrote comments. Below is the information: Scale: 5= high; 1 = low Instructor is organized and well prepared: 4.5 Grading System is a fair measure of learning: 4.0 Examinations are relevant to the course activities: 4.0 The instructor is helpful when the students have difficulty: 4.5 I do not have trouble understanding the instructor language: 3.7 The instructor explains difficult material clearly: 3.5 The instructor is among the best I have had: 3.7 The course is among the best I have had: 3.3 Comments: "This course has been challenging and enjoyable. It has greatly increased my ability to think, reason, and solve problems rationally." "Just about any genetics class I will like. I think Dr. Romero does a good job." "Al is excited and very helpful when you ask for assistance. Al's accent is often hard to understand. Al uses powerpoint which allows him to move thru the material too quickly." "While the explanations of the topics related to general ecology are adequate, the instructor (illegible) the work difficult molecular/genetic material is still hard to grasp. I realize we "attempt" to go slow over the difficult material, it is still hard to grasp. I really do not like the use of powerpoint as a teaching tool. It makes us cover material too rapidly and we don't get the "in depth" time that we need. I also do not want to see a bunch of slides that we are supposed to (illegible). If the material is enough to portray with slides, then we should go over it. Not a bad class or material." |
