Evolution and Development

EVOLUTION AND DEVELOPMENT BIOL 514H

Location: Wilson 202 Time: Tuesdays and Wednesdays, 11:00 AM – 12:15 PM Instructors: Dr. David Pfennig Dr. Bob Goldstein Email: [email protected] Email: [email protected] Office: 320 Wilson Hall Office: 616 Fordham Hall Office Hours: by appointment Office Hours: by appointment

Course Description Living things are amazingly diverse! Species differ (you would not be confused for a dandelion), and individuals within species differ (e.g., you and your neighbor are each unique). Individuals even differ over time: i.e., your summer tan will be a distant memory by the end of term. Much of this variation helps adapt organisms to their environments, and over time has fostered major evolutionary transitions like the origin of vertebrates or the colonization of land from water. In this course, we will discover how and why such a remarkable and vast diversity of forms and functions has evolved. We will also consider why all possible forms do not exist: i.e., don’t blame your parents for being born without wings.

To gain a comprehensive understanding of how biodiversity arises, we will explore the intersection of concepts and mechanisms from development, evolution, and ecology, as these processes are inextricably linked. The developmental systems by which seeds turn into trees or larvae turn into butterflies are the products of past evolution. However, as the palette upon which new mutations appear, developmental systems can bias or constrain what mutations are beneficial or even visible to natural selection and thus what new forms can arise. Finally, because the environment acts both as a source of cues that guide how development proceeds and as the source of selective pressures that drive or frustrate evolutionary change, a consideration of the ecological context is frequently critical to understanding both processes.

Learning Objectives By fully engaging with the material and class assignments, at the end of the semester you will be able to: • Explain how an interdisciplinary approach involving genetics, development, evolutionary biology, and ecology can be used to understand the processes that generate patterns of biodiversity. • List and describe major questions, findings, and experimental approaches in the field of ecological and evolutionary developmental biology. • Discuss biological research using specialized terminology and defend your opinions. • Critically evaluate and interpret the primary scientific literature. • Combine factual material with deductive reasoning to propose hypotheses and future research directions

Course Format This course is a hybrid lecture and seminar course. Generally, Tuesday meetings will be in lecture format, though these classes may often involve breakout group activities in the course of the lecture as appropriate. The goals of the lectures will to be to introduce you to conceptual frameworks, historical context, and biological information relevant to the week’s theme(s). Thursday class meetings will be focused on discussions of the classic and recent papers from the scientific literature on the week’s theme(s).

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Course Prerequisites There are three prerequisites for this course. You must have already achieved a passing grade in Biology 201 (Ecology and Evolution), Biology 202 (Molecular Biology and Genetics), and Biology 205 (Cell and Developmental Biology).

Textbooks & Readings This course has two texts, which reflect the different perspectives of the two instructors. Both texts are recommended but not required (meaning that no exam material will be taken solely from the textbooks). These texts are:

Gilbert, S. F. & D. Epel. 2009. Ecological Developmental Biology. Sinauer Associates (highly recommended to complement the lecture material in the first half of the course)

Wilkins, A. S. 2002. The Evolution of Developmental Pathways. Sinauer Associates (highly recommended to complement the lecture material in the second half of the course)

Both texts should be available in the student stores. If not, then they can be purchased online (e.g., Amazon.com). In addition to these texts, there will be weekly discussion readings (see below). Links to these readings are on the Sakai site.

Student-led Discussions As noted above, each week this class will include a lecture by one of the instructors (always on Tuesdays) and student-led class discussions (always on Thursdays). Your participation in these discussions is mandatory, meaning that a significant portion of your final course grade will be determined by your performance during these discussions (see below).

Each of you will be asked to participant in a team (of 2-4 students) that leads TWO different discussions during the semester (the team need not be the same for both discussions). Your responsibilities will vary, depending on whether or not you are a discussion participant or discussion leader.

Responsibilities of discussion participants: For the days when you are not part of a team charged with leading a discussion, you should come to class prepared to participate actively in the discussion. It’s important that you read the material carefully and be prepared to discuss it in class, as 10% of your final course grade will be based on your class participation (we presume that everyone will speak up in every discussion). To help you prepare, and to assist the discussion leaders in their presentation, you will be asked to post at least two questions based on each week’s reading assignment on the Sakai Discussion Board no later than 5 pm the day before the discussion (please post your questions on the appropriate discussion forum, which are listed by the date of the discussion). Note that 5% of your final course grade will be based on your turning in satisfactory questions each week.

Responsibilities of discussion leaders: On days when you are leading a discussion, you (and your group) will be in control of class for that particular day. Your group will be engaged in two types of activities:

First, your group should spend no more than 20 minutes at the outset of the class period presenting an overview of the reading material. During this time, you should tell the class why the material is important, and what the central messages of the reading were. In doing so, you may wish to use a Powerpoint presentation, handouts, and/or the chalkboard. A good way of conducting these overviews is to have each member of the team present a different aspect of the paper(s) being discussed that day (in other words, everyone should take a turn presenting before the class).

2 Second, after the overview, the remainder of the class period will be devoted to the discussion team reading their classmates' questions and leading a discussion on each of their questions. Here are some tips on how to lead a successful discussion:

1) Use your classmates’ submitted questions to get the discussion rolling and to keep it rolling. It is a good idea to put these questions into your powerpoint or handouts, so that everyone can see the questions while thinking about them. It can also help to put basic questions that get everyone onto the same page first, and the most interesting questions just after them, leaving other questions to the end if time allows.

2) Once the discussion gets started, ease up and let your classmates talk. You do not need to respond to everything that others say; in the best discussions, everyone is speaking to each other rather than solely to the discussion leaders. Be prepared to redirect the conversation if we become bogged down on meaningless argumentation, but don't be too eager to shift topics if the class is confused.

3) Be fair to the author’s arguments. Present the author's position first before voicing your personal beliefs.

4) Avoid jargon. If it's necessary to use special terms, make sure you define them.

5) Be prepared to support your arguments. The best way to do so is to read the material carefully. It also helps to consult additional, outside readings for opposing views or to clarify points made in the assigned reading. If you find useful outside readings, provide these additional references in your synopsis (see below).

Written synopsis of the discussion After the class period during which your discussion takes place, your group of should prepare a written 1- 2 page synopsis of the reading assignment, in which you summarize (1) the week's reading and (2) the major issues that we discussed and how we resolved these issues. The group should also prepare (3) a bibliography of no fewer than 10 references for those who want to read more on the topic. After you have prepared this material, email it the instructor responsible for that week’s lecture by the deadline, which is the following Monday at noon. We will post your synopsis on the Sakai Discussion Board (in the same folder as the discussion questions for that week).

Please note that 25% of your course grade will be determined by your class presentation (12.5% for each presentation).

Exams There will be one mid-term exam and a final exam. Exams will stress concepts, and they may contain multiple-choice, short answer, problem-solving, and essay questions.

Make-up exams will be given only at our discretion. To be eligible for a make-up exam, you must have an "official" excuse (i.e., a note from the Dean’s office).

Final Course Grade Exams and class presentations/participation are worth the following percentage of your final grade:

Exam 1 - 30% of final grade Exam 2 - 30% of final grade

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Class Presentation - 25% of final grade (12.5% for each of two presentations) Class Participation - 10% of final grade Questions for Discussions - 5% of final grade

Your course grade will be determined as follows:

A final course average of 93 or above will earn you an A/H* A final course average of 90 to 92 will earn you a grade no lower than A-/P A final course average of 87 to 89 will earn you a grade no lower than B+/P A final course average of 83 to 86 will earn you a grade no lower than B/P A final course average of 80 to 82 will earn you a grade no lower than B-/P A final course average of 77 to 79 will earn you a grade no lower than C+/L A final course average of 73 to 76 will earn you a grade no lower than C/L A final course average of 70 to 72 will earn you a grade no lower than C-/L A final course average of 67 to 69 will earn you a grade no lower than D+/L A final course average of 63 to 66 will earn you a grade no lower than D/L A final course average of 60 to 62 will earn you a grade no lower than D-/L

*(undergraduate/graduate student grading scheme; please note that undergraduate and graduate students will be graded separately)

Your final grade may be "curved" upward, depending on: 1) evidence of improvement in your exam performance, 2) the performance of your classmates, and 3) your attendance and participation in class.

How to Succeed in this Class: 1) Come to all classes, including the lectures, and participate by asking questions. 2) While reading papers for discussion, summarize the question being addressed and the take home message of each figure in your own words. 3) Reconsider the readings in light of discussion questions posted by your classmates before class so you will be prepared to talk about them. 4) Make connections with others in the class so you can work together to understand the assigned readings and swap notes in the event of an absence from class. 5) Dig deep into one or more topics/systems/approaches that excite you. 6) Help me (and the rest of the class), help you (and each other)! Bring your questions about the material to class, and if they go unanswered, speak up during the class or come talk to one of the instructors.

4 BIO 514H Syllabus Fall 2015

Date Lecturer Lecture*/Activity Reading**

Aug. 18 DP 1. BASIC PRINCIPLES OF EVOLUTIONARY G&E-Ch. 1 DEVELOPMENTAL BIOLOGY Aug. 20 Student activity: visit Pfennig’s lab

Aug. 25 DP 2. THE ORIGINS OF VARIATION: G&E-Ch. 2, 8 GENETIC CHANGE Aug. 27 Student-led Discussion #1

Sept. 1 DP 3. THE ORIGINS OF VARIATION: G&E-Ch. 10, ENVIRONMENTAL CHANGE Appendix A, D Sep. 3 Student-led Discussion #2

Sep. 8 DP 4. PHENOTYPIC PLASTICITY AND THE ORIGINS OF NOVELTY G&E-Ch. 9, Sakai Sep. 10 Student-led Discussion #3

Sep. 15 DP 5. THE HISTORY OF LIFE: WHAT, HOW, Sakai AND WHY? Sep. 17 Student-led Discussion #4

Sep. 22 DP 6. THE MAJOR TRANSITIONS Sakai IN EVOLUTION Sep. 24 Student-led Discussion #5

Sep. 29 DP 7. HUMAN EVO-DEVO Sakai (we will also conduct evaluations for the 1st half of the course) Oct. 1 Student-led Discussion #6 Oct. 6 Exam 1 ______* lecture outlines or Powerpoint presentations are on the course Sakai site ** “W-Ch.” refers to the chapters in the Wilkins text; “G&E-Ch.” refers to the chapters in the Gilbert and Epel text; “Sakai” refers to readings available on the course Sakai site

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BIO 514H Syllabus Fall 2015

Date Lecturer Lecture*/Activity Reading** Oct. 8 Student-led Discussion #7

Oct. 13 BG 8. THE BIRTH OF EVO-DEVO W-Ch. 1 Oct. 15 NO CLASS – FALL BREAK

Oct. 20 BG 9. COMPARATIVE DEVELOPMENTAL W-CH. 3 BIOLOGY Oct. 22 Student-led Discussion #8

Oct. 27 BG 10. CONSERVATION OF DEVELOPMENTAL W-Ch. 5 PATHWAYS Oct. 29 Student-led Discussion #9

Nov. 3 BG 11. EVOLUTION OF ARTHROPOD W-Ch. 7 SEGMENTATION PATHWAYS Nov. 5 Student-led Discussion #10

Nov. 10 BG 12. EVOLUTION OF PATHWAYS FOR W-Ch. 8 FORMING ORGANS Nov. 12 Student-led Discussion #11

Nov. 17 BG 13. EVOLUTION OF SEX DETERMINATION W-Ch. 6 Nov. 19 Student-led Discussion #12 Nov. 24 Student activity: building low-power microscopes Nov. 26 NO CLASS – THANKSGIVING BREAK

Dec. 1 BG REVIEW SESSION (we will also conduct evaluations for the 2nd half of the course) Thur. Dec. 10 Exam 2 12:00 pm (noon) (covering material from Goldstein’s lectures and discussions only) ______* lecture outlines or Powerpoint presentations are on the course Sakai site ** “W-Ch.” refers to the chapters in the Wilkins text; “G&E-Ch.” refers to the chapters in the Gilbert and Epel text; “Sakai” refers to readings available on the course Sakai site