Wecome to Ecological Genetics!

BIOL 5240 Spring 2012

 

Dr. Julie R. Etterson

Office: 153B Swenson Science Building

Office hours: Immediately after lecture on Monday or by appointment

Lab: 180 Swenson Science Building

Phone: 726-8110

Email:  jetterso@d.umn.edu

Graduate Student Volunteer: Katie Winkler

Lecture:  11:00-11:50am; M,W,F; SSB 115

 

Text: A Primer of Ecological Genetics by Jeffrey K. Conner and Daniel L. Hartl (2004)

Other Readings: 17 Journal articles from the primary literature are assigned reading (pdf links below).  

 

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 attendance is expected and will be considered in the computation of your final grade.

 

Discussion sections:  More than 1/3 of the course will be based on discussions from the primary literature.  One or two 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," (aka QQQ) 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. Click here for an example of a nice QQQ answer.  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. See syllabus for your specific assignment. Click here for guidelines for leading the discussion section.

 

Computer Simulations: Computer simulations using the freeware package POPULUS will be used to illustrate points in lecture and for exercises in one lecture period. Students may wish to download this program to work on problems at home. Populus - simulations of population biology (D. N. Alstad, U of MN, 2007), is available for free download at http://www.cbs.umn.edu/populus/index.html

 

Problem sets: There will be four 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. 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, 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                              30

Final exam                                  15

Journal article quizzes (16)           15

Problem sets (5)                          15

Presentation and discussion         15

Class participation                       10

 

Papers that came up in class

Links to websites I mentioned in class:

Syllabus: Ecological Genetics

Spring 2012

Overview of Ecological Genetics

W

1/18

Lecture 1. Introduction to the course

CH 1

F

1/20

Lecture 2. What is ecological genetics?

CH 1

M

1/23

Read and discuss: Reed and Frankham 2001.  How closely are molecular and quantitative genetic measures of genetic variation? A meta-analysis. Evolution 55:1095-1103.PDF

QQQ

Etterson provides example of journal article presentation

Part I. Population Genetics

W

1/25

Lecture 3. Continue survey of Ecological Genetics, start survey of genetic markers

CH 2

F

1/27

Lecture 4. Clay Carter - Molecular approaches for understanding the genotype-phenotypic map

 

M

1/30

Lecture 5. Molecular markers  - the toolkit

CH 2

W
2/1
Lecture 6. H-W, Nonrandom mating and inbreeding
             CH 2

F

2/3

Read and discuss: 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

QQQ

Jahnke,Matthew GRAD                  Durand,Nathaniel

UGRD

M

2/6

Lecture 7. 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 #1 due

Ch 2 from book

2.1a&b, 2.3a,

2.5 a&b

W

2/8

Lecture 8. Finish inbreeding - Mutation, migration and drift

CH 3

F

2/10

Read and discuss:  Ficetola et al. 2011. Rapid selection against inbreeding in a wild population of a rare frog.  Evolutionary applications 4:30-38. PDF

QQQ

Toldo,Jessalyn     GRAD      Knudsen,Andrew UGRD

M

2/13

Lecture 9. Drift and effective population size
CH 3

W

2/15

Lecture 10. Measuring population structure with F-statistic

CH 3

F

2/17

Read and discuss: Bailey et al. 2007. Beyond the point of no return? A comparison of genetic diversity in captive and wild populations of two nearly extinct species of Goodeid fish reveals  that one is inbred in the wild. Heredity 98:360–367. PDF

QQQ

Fellman,Timothy UGRD

Olson,Dena UGRD

M

2/20

Lecture 11. Finish F-statistics, start Natural selection on genotypes

CH 3

W

2/22

Lecture 12. Synthesis of the four fundamental evolutionary forces

CH 3

F
2/24

Read and discuss: Colautti et al. 2005. Invasion genetics of the Eurasian spiny waterflea: evidence for bottlenecks and gene flow using microsatellites.  Molecular Ecology 14:1869-1879. PDF

QQQ

Wagner,Angela   UGRD     

Rice,Wesley UGRD

M

2/27

Computer simulations POPULUS

Take-home Exam 1 handed out. Material from 1/18-2/27.  Due on Monday 3/5

Distribution of scores from Midterm Exam 1

Problem set #2 due

Part II. Quantitative Genetics

W

2/29

Lecture 13. Quantitative genetics

 CH 4

F

3/2

Read and discuss: Kojola et al. 2003. Rescue of a severely bottlenecked wolf (Canis lupus) population by a single immigrant. Proc. R. Soc. Lond. B. 270:91-97. PDF

QQQ

Katie Winker        GRAD     

Sloan,Caitlin GRA

M

3/5

Turn in Take Home Exam 1

Lecture 14. Quantitative genetics

Populus simulation exercises

CH 4

W

3/7

Lecture 15. Quantitative genetics

 

F

3/9

Read and discuss: Young and Pickup. 2010. Low S-allele numbers limit mate availability, reduce seed set and skew fitness in small populations of a self-incompatible plant.  Journal of Applied Ecology 47:541–548. PDF

QQQ

Toldo,Jessalyn GRAD        Wagner,Angela   UGRD

 

Spring Break

M

3/19

Lecture 16. Estimating heritabilities

Problem set #3 due

CH 4

W

3/21

Lecture 17. Estimating heritabilities

CH 4

F

3/23

Read and discuss: Evans and Sheldon 2012.Quantitative genetics of carotenoid-based color: heritability and persistent natal environmental effects in the Great Tit. The American Naturalist 179:74-94. PDF

QQQ

Sloan,Caitlin GRAD            Rice,Wesley UGRD

M

3/26

Lecture 18. Phenotypic plasticity

CH 5

Problem set #4 due

Problems 4.1, 4.2 4.3

W
3/28
Lecture 19. Phenotytic plasticity and genetic correlations across environments CH 5
F
3/30
No class - more than 1/2 students gone on field trip

M

4/2

Read and discuss: Laurila et al. 2002 Adaptive phenotypic plasticity and genetics of larval life histories in two Rana temporaria populations. Evolution. 56:617-627. PDF

QQQ

Jessalyn Toldo GRAD  

 

W
4/4
Lecture 20. Artificial selection
CH 5
F
4/6

Read and discuss: Burgess et al. 2007. Artificial selection shifts flowering phenology and other correlated traits in an autotetraploid herb.

Heredity 99:641–648. PDF

QQQ

 

Knudsen,Andrew UGRD

M

4/9

Lecture 21. Natural selection

W
4/11
Lecture 22. Response to selection - predicting evolutionary change
CH 6

F

14/3

Read and discuss: .Change to Etterson, J.R. and R.G. Shaw. 2001. Constraint to adaptive evolution in response to global
warming. Science 294:151-154. PDF

QQQ

Olson,Dena UGRD             Fellman,Timothy UGRD

Problem set #5 due

Chapter 5, 1 & 2

Part III. Topics in Applied Ecological Genetics

M

4/16

Distribute take-home exam 2. Material from 2/29-4/11

Lecture 23. Evolution of invasive species

CH 7

W

4/18

Read and discuss: Parker et al. 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

QQQ

 Jahnke,MatthewGRAD

Wagner,Angela UGRD 

F

4/20

Lecture 24: Conservation genetics

CH 7

M

4/23

Read and discuss:  Houde et al. 2010. Reduced anti-predator responses in multi-generational hybrids of farmed and wild Atlantic salmon (Salmo salar L.) Conservation Genetics 11:785-794. PDF

QQQ

Turn in take-home exam 2 - Distribution of scores

Olson,DenaUGRD              Durand,NathanielUGRD

W

4/25

Read and discuss: Vernooy et al. 2010. Barcoding life to conserve biological diversity: beyond the taxonomic imperative.  PLoS Biology 8:e1000417. PDF

QQQ

Sloan,Caitlin GRAD Rice,Wesley UGRD  

F

4/27

Lecture 25: Transgene Escape

 

M

4/30

Read and discuss: Warwick et al. 2008. Do escaped transgenes persist in nature? The case of an herbicide resistance transgene in a weedy Brassica rapa population. Molecular Ecology 17:1387–1395. PDF

QQQ

Knudsen,Andrew UGRD  

Fellman,Timothy UGRD

W

5/2

Lecture 26: Evolution of resistance to pesticides and antibiotics

CH 7

F

5/4

Read and discuss: Snow et al. 2003. A Bt transgene reduces herbivory and enhances fecundity in wild sunflowers. Ecological Applications 13:279-286. PDF

QQQ

Jahnke, Matthew GRAD

Durand,Nathaniel UGRD

 

 

FINAL EXAM

Take Home - distributed on Friday May 4

Due on Tuesday May 8 by noon!

 

 

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: It is the policy and practice of the University of Minnesota Duluth to create inclusive learning environments for all students, including students with disabilities. If there are aspects of this course that result in barriers to your inclusion or your ability to meet course requirements – such as time limited exams, inaccessible web content, or the use of non-captioned videos – please notify the instructor as soon as possible. You are also encouraged to contact the Office of Disability Resources to discuss and arrange reasonable accommodations. Please call 218-726-6130, 218-726-6130 or visit the DR website at www.d.umn.edu/access for more information.   

 

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.