Biology 545: Advanced Evolutionary Biology

University of Indianapolis Spring 2004

"nothing in biology makes sense except in the light of evolution"

-Theodosius Dobzhansky

Instructor: Dr. Sandra Davis

Lilly Hall 130C

788-3289

sdavis@uindy.edu

Office Hrs: Mon. & Wed. 10:00-11:00am, Tues. & Thurs. 2:00-3:00pm, or by appt. Feel free to drop by my office, if the door is open, I will be most likely willing to talk to you.

Textbook: Evolutionary Analysis 3^nd Edition, by Scott Freeman and Jon C. Herron, 2003, Prentice Hall Publishing Company

Locations: This course will meet concurrently with Biology 280: Evolutionary Biology. Lectures will meet in Lilly Hall 126 from 11:00am-12:00pm on MWF. This will provide background and a basic introduction to the topics covered. In addition, students enrolled in Biology 545 will meet on Wednesday from 2:00-3:50pm in Lilly Hall 123 to further explore these topics in greater depth.

Course Objectives: As the often-quoted statement by Dobzhansky emphasizes, evolution, and its primary mechanism natural selection, is the major unifying theory of all the biological sciences. Like Newton's theories in physics and plate tectonics in geology, evolution makes sense of a huge variety of observations in such disparate fields as genetics, physiology, anatomy, ecology, and paleontology. In this course, we will explore the principles of evolutionary theory and the processes of evolutionary change, and why they are considered the "grand unified theory" of biology.

This course focuses on the processes of evolution and the patterns generated by these processes. Our aim is to develop a scientific way of thinking about biological diversity rather than attempting to memorize the history of living things. Evolutionary biology addresses such questions as: Why are there males and females? How on earth did some insects come to look so much like sticks? Why do we grow old and die? We will seek explanations for such patterns of diversity and for the apparent "good fit" of organisms to their environment. Topics covered include population genetics, the theory of evolution by natural selection, concepts of fitness and adaptation, genetic bases of evolutionary change, modes of speciation, molecular evolution, principles of systematic biology, paleontology and macroevolutionary trends in evolution, extinction and human evolution.

Evolutionary biology and the concepts of genetics are strongly intertwined. Therefore, the prerequisite for this course is Biology 225: Introduction to Genetics. If you feel you do not have an adequate background in genetics or an understanding of basic genetic principles, please see the instructor.

Course components:

Lecture: Class periods meeting with Biology 280 will consist of lecture, discussion, and group work. Attendance will be taken according to University policy, but will not count towards your final grade. You are responsible for all material covered in lecture, whether or not it is covered in the textbook. Therefore, it is very important and expected that you attend all lectures.

Readings / Discussion: Graduate students are expected to read all material assigned to students in Biology 280, and come to class prepared to discuss them.

Wednesdays will be devoted to discussion of topics in greater depth. Readings from outside sources and primary literature will be assigned for each week. Readings will be discussed during class on Wednesday and will be led by students. For each discussion, a name will be drawn from a hat to determine who will lead that day's discussion. That name will then be put back into the hat and will be available for selection at the next discussion. Therefore, there is a possibility that one student will be picked to lead every discussion during the semester, or will never be picked at all. This is to encourage everyone to come to class prepared to lead the discussion, and should reduce the amount of "work" that the discussion leader has to do to get discussion rolling. A good way to prepare for leading discussions is to think about / make a list of some of the following as you are reading: the most interesting things you learned, something you didn't understand, a cool way that the material was presented, something that rubbed you wrong, doubts that were raised, ways in which the reading made you think about something in your world differently.

Term Paper and Presentation: You will be required to write one term paper that is approximately 10-15 pages, double-spaced with one-inch margins. The topic is open for your choice, but must deal with evolutionary biology and must be approved by me before you start. You will then be required to give a 20-30 min. presentation to the class on the topic of your term paper. The term paper will be worth 100pts., the presentation will be worth 50 pts.

I also reserve the right to periodical give out additional assignments in addition to the paper and presentation. Some may involve working problems. Others may involve writing a short essay. Some may be graded and others may receive credit just for being turned in on time. I also may assign points for participation during discussions.

Other Assignments: I also reserve the right to periodical give out additional assignments in addition to the paper and presentation. Some may involve working problems. Others may involve writing a short essay. Some may be graded and others may receive credit just for being turned in on time. I also may assign points for participation during discussions.

Exams: Graduate students will not be required to take the in-class exams with Biology 280. Instead, all students enrolled in Biology 545 will be required to complete 3 take home exams. These will be 3 exams worth 100pts each. The last of these 3 exams will be held during the last week of classes. This last exam will not be comprehensive. The dates are fixed, even if we get behind in the lecture schedule, so this allows you to plan. The format of all exams will be essay. I curve only in one case: if the exams have been, in my opinion, too difficult. I will NOT use a curve if I feel that people just didn't try. I have no problem with giving everyone in the class an A if they all score above 90%, but I've yet to see it happen. Exam questions will be handed out in class and you will have until the exam date listed on the course schedule to complete it and turn it in. Since you are not being curved, it will be of benefit to you to study with your peers. Being able to logically explain a concept to another student equates with at least partial understanding of the topic. However, once you start work on an exam, you are expected to complete it independently. If I find evidence of collaboration on exams, the parties involved will split the points for one grade. I will try to return exams as promptly as possible. If you feel I have erred in grading, please let me know, and I will regrade your entire paper. You might get points back, but then again, I might see something I missed before...

Grading: your grade for the course will be based on the points you earn on the following:

Assignment	Points Possible
3 Lecture exams, 100 pts. each	300
Term paper	100
Presentation	50
Total	450

Letter grades will be assigned according to the percentage of points accumulated out of the total possible using the following scale:

98-100%	A+	77-79.9	C+
93-97.9	A	73-76.9	C
90-92.9	A-	70-72.9	C-
87-89.9	B+	67-69.9	D+
83-86.9	B	63-66.9	D
80-82.9	B-	60-62.9	D-
		Below 60	F

Web page: In order to make study materials and myself more accessible, I have put together a web page for the course. You can find the page at: pages.uindy.edu/~sdavis.

Here you will find important announcements, worksheets, study materials, etc.

Finally, CHEATING: If I suspect cheating, I WILL pursue it according to UINDY policy (see your student handbook). Nuff said.

Lecture Schedule

Week	Monday	Wednesday	Friday	Text Readings
1	08/30- Introduction	09/01- History of evolutionary thought	09/03- Evolutionary thought today: AIDS, SSE’s white paper	Ch. 1	Introduction: AIDS, SSE’s white paper
2	09/06- Labor Day: No Classes!!	09/08- Evidence for Evolution	09/10- Evidence for Evolution	Ch. 2	Darwin: Origin, Paper TBA
3	09/13- Overview of the Evolutionary Process	09/15- The Nature of Natural Selection	09/17- Carry-over/review	Ch. 3, 4	Dawkins: Watchmaker, Paper TBA
4	09/20- Exam I	09/22- Variation in Natural Populations	09/24- Variation in Natural Populations	Ch. 5, 6
5	09/27- Mechanisms of Evolution I: Mutation and Selection	09/29- Mechanisms of Evolution I: Mutation and Selection	10/01- Mechanisms of Evolution II: migration, drift, nonrandom mating	Ch. 5, 6	Take home exam distributed
6	10/04- Mechanisms of Evolution II: migration, drift, nonrandom mating Quantitative Genetics	10/06- Development and Evolution	10/08- Agents of selection	Ch. 18, 9	Take- home exam II due
7	10/11- Agents of selection	10/13- Carry-over/review	10/15- Exam II	Ch. 9
8	10/18- Fall Break: No Classes!!	10/20- Quantitative genetics: heritability	10/22 – Quantitative genetics: modes of selection	Ch. 7
9	10/25- Quantitative genetics: modes of selection	10/27 – Why have sex?	10/29 – Why have sex?	Ch. 9
10	11/01 – Sexual Selection	11/03- Sexual Selection	11/05- Evolution of Life History Strategies	Ch. 10
11	11/08- Evolution of Life History Strategies	11/10- Catch up / review	11/12- Exam III	Ch. 11	Take home exam distributed
12	11/15- What is a species?	11/17- The process of Speciation	11/19- The process of Speciation		Take- home exam II due
13	11/22- The process of Speciation	11/24- Thanksgiving Break NO CLASSES!!	11/26- Thanksgiving Break NO CLASSES!!	Ch. 12	Oral Presentations
14	11/29- Creating Phylogenies	12/01- Creating Phylogenies	12/03- Creating Phylogenies	Ch. 12	Oral Presentations
15	12/06- Evolution of Social Behavior	12/08- Evolution of Social Behavior	12/10- Catch up/ review	Ch. 13	Oral Presentations
16	Final Exam: Wednesday, Dec. 15, 10-11:55pm				Final Exam Due: NOON, Wed. Dec. 15

This schedule is tentative, and lecture subjects may change. Dates of Exams however are fixed, and will only change with regards to the subject matter covered. Additional outside readings are not listed, but will be assigned in class.