Overview
What can molecular data tell us about the history of life? This course provides a review of current knowledge in molecular evolution, with attention to evolutionary theory, the patterns and mechanisms of molecular change, the reconstruction of evolutionary trees from gene sequences, the evolution of gene families and their functions, and the evolution of development.
Prerequisites
This is a course for undergraduates with some background in biology. A year of introductory biology covering basic genetics, molecular biology, and cell biology (Bio C2005/2006, Bio-Anthro W2001/2002, or equivalent) is required. No specific background in evolutionary biology is expected.
Requirements
The best way to learn about molecular evolution is to understand basic concepts and techniques and then see how they are implemented in published research papers on important subjects. To that end, this will be a seminar-style class with a mix of lectures, student presentations of seminal papers from the scientific literature, and discussion. In the process, we will address interesting and sometimes revolutionary findings in the evolution of major lineages of organisms, including including humans.
Students grades will be determined as follows: class participation, including presentation (30%), mid-term examination (30%), final examination (40%). I will supply some homework exercises and their solutions; these will not be collected or graded, but they are the best (and in some cases) the only way to prepare for exams. Exams will be based on lecture material; the reading alone does not substitute for the material taught in class.
Class participation includes your presentation (see below) and involvement in the discussion every day. This is a small class: you can (and must) ask questions and make comments during the lectures and the discussions of the papers. Presentation and discussion of papers is not a one-way lecture by the student but a learning exercise for the whole class, a chance to work through the findings and logic of an important piece of research. During and after the presentation, anyone in the class may (and should) ask for clarification of anything they don’t understand about the paper and venture additional comments and criticisms about it.
A student presentation is a brief (15 to 20 minute) critical summary of the paper assigned by the instructor. Be sure to practice your presentation in advance to be sure you can present it smoothly and that it does not run overtime. I strongly encourage you to use overheads, which are available from me. The papers are scheduled for several days after the lecture that covers the major techniques and topics in the paper, but there may still be some terms or techniques we haven’t learned in class: please meet with me in advance to go over anything in the paper that you don’t understand. Every presentation should have the following general structure:
1. A short statement of what the purpose of the paper is, why this is interesting, what the conclusion is, and the extent to which you consider it a sound paper. (1-2 minutes)
2. A short summary of the general research strategy (1-2 minutes)
3. A brief overview of the important findings, not necessarily including everything presented in the paper. Any major problems you find in any of these items should be mentioned as you go along. (6-10 minutes)
4. Overall assessment of the paper: Do the data support the interpretations? Are there other interpretations that are equally supported by the data? Do you know of any other methods that would have been appropriate to use? Do the interpretations provide adequate support for the overall conclusions? Are assumptions made that may not be true? What other research could be done to shed further light on the issue? Assigned background reading will often give hints that can guide your assessment. Some of the papers we will read have serious weaknesses, but others are very well done. If you think the paper is great, say so, but think hard about all the questions above first. (2-5 minutes)
The primary textbook for the course is
The following books are recommended to clarify topics in the lectures that are not well covered in Graur and Li,. Specific chapters are listed in the syllabus. "Highly recommended" refers to subjects on when Graur and Li do a grossly inadequate job, so these are the only useful references.
All three books are available for purchase at Labyrinth Books and are on reserve in the bio library.
Readings must be completed before the class in which they will be discussed.