BIOL 5240 Fall 2007
Ecological Genetics
Dr. Julie R. Etterson
Office: 252B Swenson Science Building
Lab: 180 Swenson Science Building
Phone : 726-8110
Email: jetterso@d.umn.edu
Graduate Student Lab Volunteer: Kyle Snell Email: snel0048@d.umn.edu
Lecture: 9:00 - 9:50 am MW, SSB 212
Lab: 9:00-11:50 am F, SSB 212
Text: A Primer of Ecological Genetics by Jeffrey K. Conner and Daniel L. Hartl (2004)
Other Readings: Journal articles from the primary literature are l isted on syllabus and web page.
Office hours: Immediately after lecture on Monday or by appointment
Links to websites I mentioned in class:
Purpose: Ecological genetics is at the interface of three important subdisciplines of biology: ecology, evolution, and genetics. In this course, students will explore basic concepts in population and quantitative genetics focusing on techniques that reveal the genetic structure and adaptive value of ecologically relevant traits. This course will provide a conceptual link between courses focused on genetics and molecular biology and courses focused on whole organisms and their ecology.
Attendance: Lecture and lab attendance is expected and will be considered in the computation of your final grade.
Lectures: Because much material in this course will be drawn from the primary literature, PowerPoint presentations will be handed out for each lecture that include tables and figures not found in the textbook.
Labs: Until the snow flies, labs will be conducted outdoors where we will do experiments and collect data that will be analyzed in subsequent labs during the winter. Evaluation of your understanding of the labs will be tested in problem sets and exams. On Friday 9/28/07, the lab has two meetings, one in the morning and a second meeting after dark. Please let me know if this schedule poses a problem for you. There will not be any formal lab reports. Attendance to labs is mandatory. Of course, things happen. however, you must tell me in advance if you cannot attend.
Discussion sections conducted during lecture and lab time: There are nine journal articles from the primary literature assigned for this course. Groups of students will be assigned to lead discussions for these articles. Each discussion section will begin with a short quiz on the assigned reading given by me. These "Quick Quiz Questions" will be made available to you in advance of the quiz and are designed to be a study guide that will direct you to the most important points of the paper. After the quiz, the group of students assigned to the reading will give a brief overview and provide more questions for small group discussion. The students assigned to the reading will then wrap up with a classroom-wide discussion of the journal article. These discussions will start midway through the course and will become more frequent toward the end. See syllabus for your specific assignment. Guidelines for leading a discussion section
Computer Simulations: Computer simulations using the freeware package POPULUS will be used to illustrate points in lecture and for exercises in one lab. Students may wish to download this program to work on problems at home. Below are directions for downloading POPULUS.
Directions for downloading POPULUS
Download Java
http://www.java.com/en/index.jsp
Click on green box that says "manual download"
Click on free download
Download POPULUS
http://www.cbs.umn.edu/populus/
Click on download
Chose correct operating system
Double click on downloaded file to install
The program should now be on your desktop.
Problem sets: There will be seven problem sets during the course that will provide students with an opportunity to practice using equations presented in lecture and to estimate various genetic parameters. Problems sets will also include questions that pertain to the labs. Problem sets that are turned in late will have 1/2 of the points deducted.
Exams: All exams will be in a take-home format. Exams will cover required readings from the text, lecture material, problem sets, computer simulations, labs, and discussions. Exam questions will include problems using equations learned in class, short answer questions, and essays. Exams that are turned in late will have 1/2 of the points deducted.
Grading : The percentage toward the final grade of each course component is shown in the table below.
|
% of Grade |
Two midterms |
25 |
Final exam |
25 |
Journal article quizzes (9) |
15 |
Problem sets (7) |
15 |
Presentation and discussion |
10 |
Class participation |
10 |
Academic Dishonesty: Academic dishonesty tarnishes UMD's reputation and discredits the accomplishments of students. UMD is committed to providing students every possible opportunity to grow in mind and spirit. This pledge can only be redeemed in an environment of trust, honesty, and fairness. As a result, academic dishonesty is regarded as a serious offense by all members of the academic community. In keeping with this ideal, this course will adhere to UMD's Student Academic Integrity Policy, which can be found at www.d.umn.edu/assl/conduct/integrity. This policy sanctions students engaging in academic dishonesty with penalties up to and including expulsion from the university for repeat offenders.
Student Conduct Code: The instructor will enforce and students are expected to follow the University's Student Conduct Code (http://www.d.umn.edu/assl/conduct/code). Appropriate classroom conduct promotes an environment of academic achievement and integrity. Disruptive classroom behavior that substantially or repeatedly interrupts either the instructor's ability to teach, or student learning, is prohibited. Disruptive behavior includes inappropriate use of technology in the classroom. Examples include ringing cell phones, text-messaging, watching videos, playing computer games, doing email, or surfing the Internet on your computer instead of note-taking or other instructor-sanctioned activities."
Access for Students with Disabilities: Individuals who have any disability, either permanent or temporary, which might affect their ability to perform in this class are encouraged to inform the instructor at the start of the quarter. Methods, materials or testing may be modified to provide for equitable participation.
Promotion of Bias-free Instruction: The University of Minnesota is committed to the policy that all of its students shall have equal educational opportunities. The University expressly forbids discrimination on the basis of race, color, gender, sexual orientation, disability, veteran's status, ethnicity, religion, creed, national origin or marital status. If you believe that your Biology instructor has not followed this policy, you are invited to bring this to the attention of the Biology Department Head (211 Life Science; 726-7263) or the Associate Dean of the College of Science and Engineering (140 Engineering; 26-7585). Your conference will be kept confidential.
Syllabus: Ecological Genetics
Fall 2007
Day |
Date |
Topic |
Reading |
W |
9/5 |
Introduction to the course |
CH 1 |
F lab 1 |
9/9 |
Getting a handle on variance and ways to measure it Tansy: Variation from the beach to the hilltop Problem set #1 |
|
M |
9/10 |
What is ecological genetics and what can it tell us? Problem set #1 due |
CH 1 |
Part I. Population Genetics
|
|||
W |
9/12 |
How to measure genetic variation at the molecular level |
CH 2 |
F lab 2 |
9/14 |
Molecular genetic variation in an invasive aquatic species. Collecting spiny water flea, Bythotrephes longimanus, at Island Lake |
|
M |
9/17 |
Detection of evolutionary processes with molecular data - Deviations from Hardy-Weinberg Handout problem set # 2 |
CH 2 |
W |
9/19 |
Nonrandom mating and inbreeding |
CH 2 |
F lab 3 |
9/21 |
Fitness in small populations vs. large populations. Seed collections from populations that differ in size. Keller and Waller. 2002. Inbreeding effects in wild populations. TREE 17:230-241 PDF |
|
M |
9/24 |
Testing ecological hypotheses with paternity analysis. Guest lecture by Dr. Matthew Etterson, U.S. EPA. Questions you should be able to answer from this lecture Problem set #2 due. Handout problem set #3. |
CH 2 |
W |
9/26 |
Mutation, migration and drift |
CH 3 |
F lab 4 |
9/28 |
Gene flow in natural communities AM: fluorescent marking of pollen and seed PM: tracking movement of genes through pollen and seed Campbell and Waser. 1989. Variation in pollen flow iwthin and among populations of Ipomopsis aggregata. Evolution 43:1444-1455 PDF |
|
M |
10/1 |
Drift and effective population size Problem set #3 due. |
CH 3 |
W |
10/3 |
Measuring population structure with F-statistics |
CH 3 |
F lab 5 |
10/5 |
Quantitative genetic variation - Measuring morphological traits of Solidago clones Handout problem set #4. |
|
M |
10/8 |
Natural selection on genotypes |
CH 3 |
W |
10/10 |
Synthesis of the four fundamental evolutionary forces Problem set #4 due. |
CH 3 |
F lab 6 |
10/12 |
Computer simulations POPULUS Take-home EXAM handed out. Material from 9/5- 10/10. Due on Wednesday 10/17 |
|
Part II. Quantitative Genetics
|
|||
M |
10/15 |
Quantitative genetics |
CH 4 |
W |
10/17 |
Turn in Take Home Exam Quantitative genetics |
CH 4 |
|
F lab 7 |
10/19 |
Guest lecture by Don Branstrator: Tracing the invasion history of Bythotrephes longimanus using molecular markers A Good Example: Quick Quick Question Essay Branstrator, D.K. 2005. Contrasting life histories of the predatory cladocerans Leptodora kindtii and Bythotrephes longimanus. Journal of Plankton Research. 27:569-585. PDF Discussion - Quick Quiz Questions Colautti RI, Manca M, Viljanen M, Ketelaars HAM, Burgi H, Macisaac HJ, Heath DD. 2005. Invasion genetics of the Eurasian spiny waterflea: evidence for bottlenecks and gene flow using microsatellites. Molecular Ecology 14 (7): 1869-1879 PDF |
Kyle Snell |
M |
10/22 |
Quantitative genetics |
CH 4 |
W |
10/24 |
Estimating heritabilities |
CH 4 |
F lab 8 |
10/26 |
Allozymes electrophoresis on Bythotrephes longimanus samples collected on Rice Lake |
|
M |
10/29 |
Estimating heritabilities Handout Problem Set #5 |
CH 4 |
W |
10/31 |
Estimating heritabilities
|
CH 4 |
F lab 9 |
11/2 |
Allozyme electrophoresis on Bythotrphes longimanus samples.
|
|
|
M |
11/5 |
Discussion - Quick Quiz Questions Gutierrez-Rodriguez and Lakser. 2004. Microsatellite variation reveals high levels of genetic variability and population structure in the gorgonian coral Pseudopterogorgia elisabethae across the Bahamas. Molecular Ecology 13:2211-2221. PDF |
Kyle Benkofske Clifford Bronniche |
W |
11/7 |
Phenotypic plasticity Problem Set #5 Due. |
CH 5 |
|
F lab 10 |
11/9 |
Analysis of allozyme data Heritability: Analysis of Solidago clone data Discussion - Quick Quiz Questions Laurila et al. 2002 Adaptive phenotypic plasticity and genetics of larval life histories in two Rana temporaria populations. Evolution. 56:617-627. PDF Handout Problem Set #6 . |
James Hurst Jennifer Kiewatt Jodi Baker |
|
M |
11/12 |
Correlations among traits |
CH 5 |
|
W |
11/14 |
Artificial selection Problem Set #6 Due |
CH 5 |
F lab 11 |
11/16 |
Lecture: Natural selection Analysize Tansy data from lab 1 and Solidago clone data from Lab 5 Handout Problem Set #7 |
CH 6 |
M |
11/19 |
Response to selection - predicting evolutionary change Problem Set #7 Due |
CH 6 |
W |
11/21 |
Pick up graded Problem Set #7 Distribute take-home exam. Material from 10/15- 11/19. Due on Wednesday Nov 30. |
|
Part III. Topics in Applied Ecological Genetics
|
|||
M |
11/26 |
Lecture: Evolution of invasive species |
CH 7 |
W |
11/28 |
Turn in take-home exam Discussion- Quick Quiz Questions Parker, Rodriguez and Loik. 2003. An evolutionary approach to understanding the biology of invasions. Local adaptation and general-purpose genotypes in the weed Verbascum thapsus . Conservation Biology 17:59-72. PDF |
Brent Mathison Thomas Pevan |
F lab 12 |
11/30 |
Set up germination experiment of invasive Campanula populations Discussion - Quick Quiz Questions Lee CE. 2002. Evolutionary genetics of invasive species. Trends in Ecology and Evolution.17 (8): 386-391 PDF |
Mark Wickre Kyle Benkofske |
M |
12/3 |
:Lecture: Conservation genetics |
CH 7 |
W |
12/5 |
Discussion- Quick Quiz Questions Stockwell CA, Hendry AP, Kinnison MT. 2003. Contemporary evolution meets conservation biology . Trends in ecology and evolution 18 (2): 94-101 PDF |
Clifford Bronniche James Hurst |
F lab 13 |
12/7 |
Collect data on germination experiment Discussion- Quick Quiz Questions Heschel and Paige. 1995. Inbreeding depression, environmental stress, and population size variation in scarlet gilia ( Ipomopsis aggregata ). Conservation Biology 9:126-133. PDF Lecture: Transgene Escape |
CH 7 |
M |
12/10 |
Discussion- Quick Quiz Questions Klinger, Elam and Ellstrand. 1991. Radish as a model system for the study of engineered gene escape rates via crop-weed mating. Conservation Biology 5:531-535. PDF |
Jennifer Kiewatt Brent Mathison
|
W |
12/12 |
Lecture: Evolution of resistance to pesticides and antibiotics |
CH 7 |
|
F lab 14 |
12/14 |
Collect and analyze data on germination experiment Discussion- Quick Quiz Questions Snow et al. 2003. A Bt transgene reduces herbivory and enhances fecundity in wild sunflowers. Ecological Applications 13:279-286. PDF |
Thomas Pevan Mark Wickre Jodi Baker |
|
|
FINAL EXAM Take Home - distributed on Friday December 14. Due on Tuesday December 18 by noon! |
|