IBS 8012 Spring 2013

Integrated Evolutionary Processes

 

Dr. Julie R. Etterson

 

 

Office:

153B SSB 

Lab:

180 SSB 

Phone:

726-8110

Email: 

jetterso@d.umn.edu

Class hours:

8:00-8:50 M,W 207A SSB

Readings:

Listed on syllabus and web page

Office hours:

After class or by appointment

 

Purpose:

 

This course will present current thinking on the mechanisms and consequences of evolution at all levels of biological organization from the molecule to the ecosystem

.  

Class format:

Mondays - Lectures

8:00-8:50

Introduction of new material

 

 

Wednesdays - Student presentations

 

8:00-8:05

 

Closed book essay question on the reading from the primary literature (QQQ)

 

 

8:05-8:20

Student presentation on the reading

 

 

8:20-8:40

Small group discussion on the reading

 

 

8:40-8:50

Large group wrap up

 

Lectures:

 

Lecture material will be drawn from the primary literature.  PowerPoint presentations will be handed out at the beginning of each lecture and will include all tables and figures.

 

Essay Questions:

Quick Quiz Questions (QQQ) will consist of 3-5 five essay questions on the weekly reading assignment will be posted on the web in advance of class.  Students are expected to prepare answers to each question and will be expected to write a 5-10-minute essay in class on one of the QQQ prior to the student presentation on the reading and discussion.  Essays should be written in paragraph form and provide specific examples from the assigned reading to justify your answer.

 

Journal article presentation and discussions:

A pair of students will be assigned to present each journal article and facilitate the small-group and large-group discussions. The students will give a brief PowerPoint presentation (15-20 min).  Presentations should include the following elements:

 

  • Objectives of the paper
  • The study system (pictures of organisms are always nice)
  • Methodological approach
  • Major results (include ALL figures and tables from the paper)
  • Major conclusions

 

The presentation should conclude with a list of thought-provoking questions (5-10) that will be discussed in small groups (~20 min).  The final question on this list should always be "How does this paper illustrate the integrative nature of evolutionary processes?"  In the last 10 minutes of class, the assigned pair of students will facilitate discussion of any remaining issues and summarize the major points. 

Students will be graded on:

  • clarity of presentation of the major results and conclusions
  • quality of their discussion questions
  • ability to facilitate the group discussion and summarize the major points

 

Research paper:

The goal of this assignment is for you to explore how your thesis question relates to the major themes of this course.  For some of you, the relationship will be obvious because your research question is inherently evolutionary.  For others, I encourage you to think about how evolutionary processes underlie your research question.  In either case, I would like you write a review paper (~15-20 pages double spaced not including the literature cited, 1-inch margins, 12-point font) that explores how evolutionary processes integrate aspects of your field of study.  You should include evolutionary hypotheses and a section that describes experiments to test these hypotheses.  The first draft of your paper will be reviewed by me and two of your peers and draft will be due at the end of the semester.

Peer   evaluations: 

Peer evaluation is an essential component of a scientific career.  Scientists need to be able to competently evaluate the work of others and learn how to improve their own work by incorporating constructive criticisms.  A scientist receives peer evaluations in many aspects of their work including: grant proposals, manuscripts, delivery of courses, annual performance reviews, and overall evaluations of their contributions of their field through the process of tenure and promotion.  Learning how to provide and utilize constructive criticism is an extremely important but often neglected part of graduate education.  As a part of this course, you will be asked to provide an anonymous peer review on the first draft of a research paper of two of your classmates.  You will also receive three reviews, two from students and one from me.  You will be expected to take the suggestions of these reviews into account in the final draft of your research paper. 

 

Class participation: 

Active participation is expected during lectures and discussions and will be considered in the computation of your final grade.  Attendance is mandatory

 

Grading: 

Grading will be based on weekly in-class essay quizzes, journal article presentations, one research paper on the topic of your choice, peer evaluation of classmates' research papers, and participation in lecture and discussion.

 

Assignment

Points per assignment

% of final grade

Weekly essay questions (15) and paragraph on 2/4

10

15

Journal article presentation (2)

10

20

First draft of research paper

10

20

Peer evaluation of research paper (2)

10

15

Final draft of research paper

10

20

Class participation

10

10

 

TENTATIVE SYLLABUS

 DAY

 DaTE

Lecture Topic

TENTATIVE

Assigned Reading

 Student Presentations

 Other assignments

W

1/23

The process of Evolution

 Open discussion on the process of Evolution

 

M

1/28

Evolution as an integrating principal

Guide to critical thinking

Elements of a successful grant proposal

NSF preproposal model

 
W
1/30
AIDs research illustrates the integrative nature of evolutionary biology
Discussion - where do you fit in?

Variation - a central concept

M
2/4
Origins of variation
    Turn in a one-paragraph description of  the relationship between your thesis topic and evolutionary processes

W

2/6

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

QQQ

Yvette Ibrahim

Hannah Panci

M

2/11

Signifcance of variation

 

W

2/13

 

Gu et al. 2003. Role of duplicate genes in genetic robustness against null mutations. Nature 421:63-66

QQQ

        Sara Prince

Lisa Wiesen

 

M 2/18

Jared Strasburg

Detecting selection at the molecular level

 

 

W 2/20 Jared Strasburg

Barrier et al. 2001. Accelerated regulatory gene evolution in an adaptive radiation. PNAS. 98: 10208–10213.

QQQ

Jacob Stevens

Volunteer

 
M

2/25

Use of variation to construct phylogenies and test hypotheses

 

 

W

2/27

Lukas et al. 1999. Replicated evolution of trophic specializations in an endemic cichlid fish lineage from Lake Tanganyika. PNAS. 96:10230–10235

QQQ

Trevor Keyler

Chelsea Hatzenbuhler

Integrating from genes to phenotypes in nature

M 3/4 What is a species?      
W 3/6  

Sauders. 2009. Routine DNA barcoding of Canadian Gracilariales
(Rhodophyta) reveals the invasive species Gracilaria
vermiculophylla
in British Columbia. Molecular Ecology Resources 9:140–150

QQQ

Chelsea Hatzenbuhler Julian Terry  

M

3/11

What is Evo-devo?

W
3/13

Abzhanov et al. 2006. The calmodulin pathway and evolution of elongated beak morphology in Darwin's finches

QQQ

    Kayla Devoll   

Sara Prince  

     
Spring Break
   
M 3/25 Plasticity and constraint      

W

3/27

Sigalov. 2012. Evolution of immunity: no development without risk.  Innol Res 2012 52:176-181

QQQ

Jacob Stevens

Tim Cyr

M 4/1  

Caceres et al. 2003. Elevated gene expression levels distinguish human from non-human primate brains. PNAS 100:13030-13035

QQQ

Kayla Devoll

Magie Jia


W 4/3  

Nasrallah et al 2004 . Natural variation in expression of self-incompatibility
in Arabidopsis thaliana: Implications for the evolution
of selfing.

QQQ

      Lisa Wiesen         Magie Jia

Turn in a paragraph about your grant proposal incuding the research question and hypothesis

                                                                       Life history

M 4/8

Life history trade-offs

 

 
W 4/10

Reznek et al. 1990. Experimentally induced life-history evolution in a natural population. Nature 346:357-359

QQQ

Mihn Tran

Jo Jo Nemec

M
4/15

Evolution and behavior

Turn in an outline and bibliography
W

4/17

Ashleigh et al. 2004. Cooperation and competition in pathogenic bacteria. Nature 430: 1024-1027

QQQ

Trevor Keyler

Yvette Ibrahim

M

4/22

Evolution and competition

Turn in first draft for peer review.  Etterson will tell you who to email your paper to for review (two people).  Please email one copy to Etterson and put a hard copy in my mailbox.

W

4/24

Grant and Grant. 2006. Evolution of character displacement in Darwin's finches. Science 313:224-226.

QQQ

Hannah Panci

Volunteer

Benos et al. 2003. How to review a paperAdvan Physiol Educ 27:47-52, 2003.

Reviewer Guidelines to follow modified from ESA

Communities and ecosystems

M  4/29 Coevolution      
W

5/1

Lively & Dybdahl. 2000. Parasite adaptation to locally common host genotype. Nature 405: 679-681

QQQ

Tim Cyr

Juliann Terry

Peer evaluations due

M

5/6

Evolution and ecosystem properties

W

5/8

Lennon and Martiny. 2008. Rapid evolution buffers ecosystem impacts of viruses in a microbial food web. Ecology Letters 11: 1178–1188

QQQ


Jo Jo Nemec

Minh Tran

 Turn in response to reviewers letter and final draft Example of a letter that responds to reviewer comments

   

Schweitzer et al. 2008. Microorganism interations: heritable relatinoship between plant genotype and associated soil microorganisms. Ecology 89;773-781

QQQ

Mooney and Cleland. 2001 The evolutionary impact of invasive species
PNAS 98:5446–5451

QQQ

Dufay and Anstett. 2003. Conflicts between plants and pollinators that reproduce within inflorescense: evolutionary variations on a theme. Oikos 100:3-14.

QQQ

Heath et al. 2003. Rapid evolution of egg size in captive salmon. Science 299:1738-1740

QQQ

Benkman 1999.  The selection mosaic and diversifying coevolution between crossbills and lodgepole pine. Am.Nat. 153:S75-91

My advice on writing a scientific paper

Beldade et al. 2002. Developmental constraints versus flexibility in morphological evolution. Nature 416:844-847

QQQ

Anderson et al. 2005. The latitudinal cline in the In(3R)Payne inversion polymorphism has shifted in the last 20 years in Australian Drosophila melanogaster populations. Molecular Ecology 14: 851-858

QQQ

Elena and Lenski. 2003.  Evolution experiments with microorganisms: the dynamics and genetic basis of adaptation.  Nature Reviews Genetics 4:457-469.

QQQ

Inoue et al. 2005. Structural and Functional Evolution of Three Cardiac Natriuretic Peptides.  Mol. Biol. Evol. 22(12):2428–2434.                    QQQ

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. 

 

 

Not included in 2011

Hairston et al. 1999. Rapid evolution revealed by dormant eggs. Nature 401:446

Weider et al. 1997. Long-Term Genetic Shifts in a Microcrustacean Egg Bank Associated with Anthropogenic Changes in the Lake Constance Ecosystem. Proceedings: Biological Sciences 264:1613-1618

QQQ

Hughes, K.A. et al. 2002.  A test of the evolutionary theories of aging. PNAS 99:14286

QQQ

Hinkle et al. 1994. Phylogeny of attine ant fungi based on analysis of small subunit ribosomal RNA gene sequences

QQQ

or

Colosimo et al. 2005.
Widspread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. Science 307: 1928-1933.

QQQ

Bolnick 2004. Can intraspecific comeptition drive disruuptive selection? An experimental test in natural populations of sticklebacks. Evolution, 58: 608–618