Evolution (Biol 4802)

 Spring 2013
 

Dr. Julie R. Etterson (Professor)

Matt Jahnke (GTA) 

Office:

153B SSB         

Office hours in:

 339 Life Science

Lab:

180 SSB

Lab:

 180 SSB

Phone :

726-8110

Phone :

  726-7963 

Email:  

jetterso@d.umn.edu

Email:  

 jahnk083@d.umn.edu

                                                      

Purpose:

The purpose of this course is to introduce biology students to the fundamental

concepts that underlie the process of evolution.  Students will learn how this

discipline is relevant to all aspects of biology from the level of the molecule to

the level of the ecosystem. 

Office Hours:

Dr. Etterson - immediately after class on T and Th or by appointment

Matt Jahnke - Mondays 10:00-11:00 and Thursdays 11:00-12:00.

Lecture:

2:00-3:15, T and Th, 175 Life Science Building

Text:   

Evolution, 2nd Edition by Douglas J. Futuyma (2009).  Lectures will also include the figure numbers from the 1st edition of this text.

Software:

EvoBeaker SimBiotic software disk and workbooks from UMD bookstore.  You must purchase this packet.  When exercises are turned in to be graded, the original publisher’s workbook must be submitted. Photocopies will not be accepted.

Populus - simulations of population biology (D. N. Alstad, U of MN, 2007), is available for free download at http://www.cbs.umn.edu/populus

Readings:

Articles from the primary literature are listed on syllabus and can be downloaded if you would like to follow up on a topic of interest.

Attendance:

Attendance is expected.  Activities conducted during class periods will be considered in the computation of your final grade.  Unexcused absences from any exam will result in a grade of zero.

EvoBeaker Software & Workbooks:

Check out this recent NPR story on the ineffectiveness of the traditional lecture for student learning and you will begin to understand my rationale for the unusal format for this course.  Rethinking the way college students are taught

Lectures don't work!

We will use five EvoBeaker computer simulation exercises in this course to deepen your understanding of evolutionary concepts.  These exercises were developed with funding from the National Science Foundation to help introduce evolutionary thinking and provide opportunities to develop your skills in hypothesis generation and testing.  A packet is available in the bookstore which includes the software disk and workbooks for each simulation exercise. 

If you have a laptop, please bring it to class to submit answers to in-class simulation exercises and discussion questions.  We need one lap top for each 2-5 students to use in class for simulation exercises.  Students are free to change groups on a weekly basis.

 

There will be three kinds of assignments in the course (2 kinds of in-class assignments and one out-of-class weekly assignment):

In-class assignments - either 1. or 2. every class period : 

1.  Answer a problem in class

    • Etterson will project or pass out a problem on paper
    • Students will work in small groups (2-5 people) to solve the problem and upload their answer as a single file in Moodle. 
    • Only one upload is necessary per group but the names of all students who contributed to the answer must be clearly indicated at the top of the file.
    • Answers must be uploaded by 3:50 pm.
    • These answers will be graded by the TA and will be considered a component of "class participation." See grading matrix below.

2.  Answer a discussion question (a), peer review (b), and revise (c)

  • This is a three-part exercise that will be completed over the course of one week.

(a) On Tuesday in class Etterson will project a discussion question.

  • Students get into small groups (2-5 people) and write a short essay question directly into Moodle

(b) Between Tuesday at 4:00pm and Thursday at 2:00pm, each individual student will:

  • Open an answer in Moodle and write a short review of one of the other groups answers. Ttry to make one good substanative point (not spelling or grammar).  Each answer must get at least three reviews.  If a answer already has three reviews, then move on to the next one.

(c) On Thursday in class, the original Tuesday group will get back together and:

  • Rate the usefulness of the peer reviews they recieved. Tthese ratings will go into your Moodle gradebook and are considered a component of "class participation."  See grading matrix below
  • Rewrite the disucssion question answer taking peer reviews into consideration.
 

Outside of class:

3. Weekly Assignments

    • Students work in small groups to develop hypothesis, design experiments, and interpret their meaning following the instructions in the EvoBeaker packets. 
    • There will be an assignment from this group work due every week on Tuesdays that should be uploaded onto Moodle by 11:55 pm.Click here for uploading DIRECTIONS.Most of assignments will be the sythesis questions from the EvoBeaker workbooks.  Assignments should be prepared in a standard word processing program, like MS Word. 
    • A single group submission is encouraged.  Please clearly list all students who have participated in preparing the submission. 
    • These will be graded by the TA and will constitute 25% of your grade.

When we are finished with the exercises in the workbook:

  • Three times during the semester, you will be requested to turn in completed EvoBeaker workbooks that will be graded on a pass/fail basis (complete or not complete).  You must turn in the original publisher’s workbook at this time.  Photocopies will not be accepted.

 

Grading:

To calculate your final grade, the percentage of points obtained for each assignment and exam will be recorded, averaged across categories, and then weighted according to the table below.

 

Component of Course

% of Grade

Two midterms

40

Final exam

20
Class participation: In-class problems and discussion questions
15

Weekly assignment: EvoBeaker workbooks

25
 Interesting Links  
 MN Twins study - raised together and apart Bouchard et al. 1990
 Genetic detail on spontaneous mutation in Arabidopsis Ossowski et al. 2010
 Nature article on Lake Vostok Story in Nature Feb 2012
 Discovery of bacteria in ice during drilling to Lake Vostok Lavire et al. 2006
 Deviations from H-W identification of genes associated with disease Neilson et al. 1999
 Evolution in response to temperature in E. coli Bennett and Lenski 1992
 How to build phylogenies with protein data Chang et al. 2008

 1st diploid human sequence of an individual

Levy et al. 2007

 Inheritance of environmental effects

Galloway and Etterson 2007

 Evolution of guppy coloration

Endler 1980
 Evolution of squirrels in response to climate change Reale et al. 2000
 Specialism to generalism in brood parasitism Lanyon 1992
 Paramorphosis in flightless birds Cubo and Arthur 2001
 Early tetrapod fossil that fills a gap Clack 2002
 Differences between pathogenic and benign E. coli Perna et al. 2001
 Fragments of early Ordovician plants Wellman et al. 2003
 Relationship between bacteria, eukarya, and archaea Pace 2006
 Glacial refugia of Jack Pine in North America Godbout et al. 2005
 Optimal inbreeding in humans Helgason et al. 2008
 Positive frequency dependent selection Mallet and Barton 1989
 Intense natural selection due to invasion of green crabs Seeley 1986
 Review of QTL mapping in Drosophila Mackay 2001
 Recognition of parasitic eggs Lyon 2003
 Female fur seals chose heterozygous and unrelated males Hoffman et al. 2007
 Hyrbid speciation in sunflowers Rieseberg et al. 1996

 

                                        Syllabus Spring 2013

Date

Day

Book

Lecture topic & EvoBeaker

Assignment due on this date
1/22

T

1

Intro to the course: Darwin’s theory of evolution.

Lecture 1 Notes

 
1/24
TH

new 1, 23

(old Ch 22)

Evidence for Evolution

Lecture 2 Notes

EvoBeaker: Guppies

In-class assignment Moodle
1/29

T

2

inferring phylogenetic history

Lecture 3 Notes

No weekly assignment due because EvoBeaker did not come into the bookstore on time

In-class tree building exercise
1/31

TH

2

Problems in phylogeny construction

Lecture 4 Notes

EvoBeaker: Dogs 

Supplemental notes on tree building methods

In-class assignment Moodle
2/5
T
5

Guest Lecture - Jared Strasburg - pdf of powerpoint lecture

History of life on earth: Archean to Cambrian Explosion

Lecture 7 Notes

Assignment 1: EvoBeaker: Guppies  Questions 1.1 (page 6) and 1.3 (page 7), Questions 1.1 (page 12) and 2.1 (page 13)

2/7

TH

5

History of life on earth: Cambrian extinction to Cenozoic

Lecture 8 Notes

 

In-class assignment Moodle
2/12

T

3

Patterns of evolutionary change

Guess thet embryo

Lecture 5 Notes

EvoBeaker: Dogs

Assignment 2: EvoBeaker: Dogs Question 14.1 (page 7) and Question 8.4 (page 9)

In-class assignment Moodle
2/14
TH
4

The fossil record

Lecture 6 Notes

In-class assignment Moodle
2/19

T

Movie: Dogs, dogs and more dogs

Assignment 3: EvoBeaker: Dogs

Question 25.1 (page 15) Modified questions from Exercise 6 (see Moodle for specifics about question on page 20)

In-class assignment Moodle
2/21

TH

1-5, 23 (old 22)

Midterm Exam 1 - includes the movie

 

2/26
T
6

Evolutionary approaches to biogeography

Lecture 9 Notes

EvoBeaker: HIV

Assignment 4: EvoBeaker: Dogs

Exercise 5

In-class assignment Moodle
2/28

TH

7

Evolution of biodiversity

Extinction and environmental change

Lecture 10 Notes

In-class assignment Moodle
3/5

T
8

Origins of genetic variation: mutation, and other sources

Lecture 11 Notes

 

Assignment 5: Turn in two completed publisher-issued EvoBeaker workbooks (Guppies & Dogs). Photocopies will not be accepted.

Assignment 6: EvoBeaker: HIV  The table on page 11 and supporting graphs, Question 32.2 (page 12), Question 8.2 (page 14)

In-class assignment Moodle
3/7
TH
8, 9

Impact of mutation on phenotype

Lecture 12 Notes

 In-class assignment Moodle
3/12
T
9

Decting evolutionary change - Hardy-Weinberg

Lecture 13 Notes

Hardy-Weinberg Problem

Assignment 7: EvoBeaker: HIV Questions 9.1 and 9.2 (page 16) Question 1.1 (page 20) In-class assignment Moodle
3/14

TH
9

Discrete vs. polygenic traits

Lecture 14 Notes

In-class assignment Moodle
   
Spring Break  
3/26
T

9, 10

Random evolutionary processes: Genetic drift

Lecture 15 Notes

Assignment 8: Turn in one completed publisher-issued workbook (EvoBeaker HIV). Photocopies will not be accepted

In-class assignment Moodle
3/28

TH
10

Gene flow and neutral theory

Lecture 16 Notes

 In-class assignment Moodle
4/2
T
11

Adaptation

Lecture 17 Notes

Assignment 9: POPULUS. Please details on Moodle

In-class assignment Moodle
4/4

TH

Opportunity for you to ask questions about Midterm Exam 2

Movie: The first flower

 In-class assignment Moodle
4/9

T

6-11

Midterm Exam 2 including the movie

  
4/11
TH
12

Natural selection and population genetic theory

Lecture 18 Notes

EvoBeaker: Sickle Cell

In-class assignment Moodle

4/16

T
12

Examples of the forms of selection

Lecture 19 Notes

Assignment 10: EvoBeaker Sickle Cell Modified versions of these two questions: Question 7.1 (page 8), Question 4.1 (page 10), Question 2.3 (page 13)  

In-class assignment Moodle

4/18
 TH
13

Predicting evolutionary change

Lecture 20 Notes

In-class assignment Moodle

4/23

T

Conflict and cooperation: theories

Lecture 21 Notes

Supplementary slides on reciprocity

 

Assignment 11:  EvoBeaker Sickle Cell Question 4.1 (page 16), Question 5.5 (page 18) and More things to try (page 19)

In-class assignment Moodle
4/25
TH

16 new

(14 old)

Sexual selection

Lecture 22 Notes

In-class assignment Moodle
4/30

T

15 new

(14 old)

Species concepts

Lecture 23 Notes

 

 

 Assignment 12: EvoBeaker Snails Question 12.1 (page 7),  Question 6.1 (page 9), Question 13.1 (page 10), and Question 23.2 (page 12) In-class assignment Moodle
5/2

TH

17 new

(15 old)

Reproductive barriers and molecular divergence

Lecture 24 Notes

In-class assignment Moodle
5/7
T

18 new

(old 16)

Speciation - allopatry

Lecture 25 Notes

Assignment 13: EvoBeaker: Snails Question 1.1 (page 13), and Question 5.1 (page 16)

Question 1.2 (page 17) and Question 2.1 (page 19)

In-class assignment Moodle
5/9

TH

18 new

(16 old)

Other mechanims of speciation

Lecture 26 Notes

 In-class assignment Moodle
if we have time
?

 19 new

(18 old)

Coevolution

Lecture 27 notes

 
5/14

T

12-19 

Final Exam Tuesday May 14 2:00-3:55pm

 

 

Assignment 14:  Turn two completed publisher-issued workbooks,EvoBeaker: Sickle Cell & Snails Photocopies will not be accepted

  

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.