Molecular Evolution by hcj


									                                BSCI 247 – Molecular Evolution
                                   Spring 2007, Tu/Th 11:00–12:15
                                    SC Math building room 1120

Dr. Daniel Funk, Associate Professor
Office: Biological Sciences 7260A
Office Hours: Tu/Th 12:30-1:30 or by appointment
Phone: 322-2214 (2-2214)

    This is an upper level course that builds on information covered in previous courses within the
Biological Sciences Department. Of particular importance are BSCI 205 (Evolution) and BSCI 210
(Principles of Genetics). Successful completion of these courses prior to enrollment in BSCI 247 is
required. If you have not yet successfully completed both of these courses, I urge you to speak to me
about this issue immediately.

The Course:
     The field of molecular evolution has two primary goals: (1) documenting and understanding
evolutionary mechanisms, rates, and patterns with respect to genes, genomes, and proteins, and (2) using
molecular data to reconstruct the evolutionary history of genes and taxa. These two aspects are intimately
related and insights from each drive the advancement of the other. The study of molecular evolution itself
fundamentally relies on ideas from population genetics (providing the theoretical basis for evolutionary
studies), phylogenetics (providing the tools for creating and evaluating evolutionary trees), and molecular
biology (providing the data whose patterns are the subject of analysis). Thus, studying molecular
evolution requires a basic understanding of concepts from each of these areas.
     This course provides a survey of the diverse field of molecular evolution and can be roughly divided
into four parts. Part I will review aspects of molecular and population genetics and phylogenetics required
to think about issues in molecular evolution. Part II will explore patterns of variation at the nucleotide
level and the evolutionary roles played by natural selection and genetic drift. Part III will describe
approaches to creating, comparing, and interpreting phylogenetic trees and introduce some of the
fascinating findings provided by a phylogenetic perspective. Part IV will consider major evolutionary
patterns and mechanisms helping us to understand large-scale patterns in the evolution of genes and entire
genomes. Each section of the course relies on concepts introduced in earlier sections. Thus, student
success will require consistently keeping up with material presented in each class period.

Class Structure:
     Because this course surveys many aspects of a broad field, lecture will be the primary format for
instruction. At the beginning of each lecture, students will receive a handout based on that day’s
PowerPoint presentation. This handout will begin with an outline of the lecture’s topics and will
otherwise include tables, figures, and other illustrations, as well as some text. Most of the text from the
presentation, however, will not be provided on the handouts. Because exams derive from the material
presented on the PowerPoint slides during class, students are strongly encouraged to write down the
additional information provided during the presentation onto the appropriate pages of the handouts. Text
that is not on the handouts will appear in yellow font in the presentation to assist students with their note-
taking. Also, definitions will be presented in red italics and are a likely focus of exam questions. I do not
provide handouts with complete class information for a specific reason. I have experimented with
distributing complete handouts in the past and have found that this reduces student engagement with the
class, and sometimes induces sleep (!) along the way. I have also found that most students find that
taking notes helps them in following the reasoning being developed in class and thus in their learning.
During class I will verbally supplement the information on the slides with supporting observations and
associated anecdotes. I provide this added information to further facilitate understanding of class
concepts while also making the material more accessible by connecting it with the human aspects of
science. You are NOT responsible for this additional spoken information for your exams – so do not feel
compelled to write down every word that comes out of my mouth! Also, please feel free to make use of
your own mouths during class: Specifically, students are strongly encouraged to ask questions, seek
clarification, and make requests (e.g., for me to go back to the previous slide for a bit longer) at any time
during the lecture.

     Remarkably, given the rapid growth and importance of this field, there is no single current textbook
that adequately covers the breadth of Molecular Evolution as a discipline. For this reason, I have not
assigned a text for this course. Nonetheless, I have put a number of books on reserve at the Science
Library for our class. These comprise volumes that cumulatively cover the suite of topics treated in this
course. These include two (somewhat dated, but still useful) textbooks that I have used for this course in
the past: Page and Holmes’ Molecular Evolution: a Phylogenetic Approach, and Li’s Molecular
Evolution. If you are interested in additional reading on any topic, please let me know and I will help you
locate appropriate literature.

    Over the course of the semester, students will be provided with sets of questions on the topics that
have recently been covered in class. These ‘homework’ assignments will not be graded and students are
not required to do them. They will be provided simply as an opportunity to practice the application of the
concepts you are learning. This will help you to really learn these ideas at a deeper level and may provide
good practice for answering/solving exam questions. An answer key for each question set will be
provided one week after it has been distributed.

    Grades for this course will be based on three in-class exams, a final exam, and class
attendance/participation. I hold ‘review sessions’ for each exam in the 7th floor lounge area of the
Biological Sciences Building. These sessions are typically held two evenings before the test. At these
sessions, I will answer any questions about class material that students have, for as long as students
continue to ask questions. Each exam will include questions of the following types: multiple choice,
matching and/or true/false, problems, definitions, and essays. Exams from previous years will be made
available, but these may differ in content due to the changing nature of the field and this course. Due to
the nature of course material, later exams will require knowledge of the subjects presented in earlier
lectures but should not, in the strict sense, be considered cumulative. Answer keys will be provided after
exams have been graded. One half of the final exam will be dedicated to material covered in the last
section of the course; the remainder will be wholly cumulative, covering material from throughout the
course. Students will be tested only on information that appears in print (and illustrations) in the
PowerPoint presentations.

In-class exams:                  20% each = 60% total
Final Exam:                      30%
Attendance/Participation:        10%
Total:                           100%
On-line information:
  All course information, handouts, past exams, and answer keys will be made available via Oak.

Attendance Policy:
    Classroom attendance should be viewed as mandatory. The cumulative nature of the material
presented over the course of the semester will make it difficult to understand later concepts if earlier
classes have been missed. Lecture handouts will be made available to those who have missed class, but
detailed lecture notes will not be distributed under any circumstances. Should a student miss an
exam, a formal written excuse from a doctor must be presented or the student will receive a zero. Personal
emergencies (such as a car accident) must similarly be certified with written documentation. When a
legitimate excuse is presented for a missed exam, the student will be allowed to take an essay-based
make-up exam.

Academic Honesty:
   The Vanderbilt University Honor Code applies to all graded work in this course. If you have any
questions about the Honor Code, please consult the Student Handbook. Uncertainty concerning the Honor
Code does not excuse a violation. Cheating is unfair to your classmates and disrespectful to them and to
me and will not be tolerated.
L#      Date                          Topic
Part I                          FUNDAMENTALS
 1     Jan. 11    Introduction to the course

 2    Jan. 16     Molecular Genetics: Structure and Variation I
 3    Jan. 18     Molecular Genetics: Structure and Variation II

 4    Jan. 23     Natural Selection and Genetic Drift
 5    Jan. 25     Phylogenetics: the Language of Trees.
       Jan. 30        ---Exam #1 (Lectures 1-5)---
 6    Feb. 1      Patterns of Nucleotide Substitution and the Neutral Theory

 7    Feb. 6      Codon Bias
 8    Feb. 8      Genetic Distances and Evolutionary Models

 9    Feb. 13     Molecular Clocks
10    Feb. 15     Molecular Evidence for Natural Selection I

11    Feb. 20     Molecular Evidence for Natural Selection II
12    Feb. 22     The Coalescent
      Feb. 27           ---Exam #2 (Lectures 6-12)---
 13 Mar. 1        Selecting, Preparing Data for Phylogenetic Analysis

      Mar. 6      —SPRING BREAK—
      Mar. 8      —SPRING BREAK—

14    Mar. 13     Methods of Phylogenetic Inference I
15    Mar. 15     Methods of Phylogenetic Inference II

16    Mar. 20     Evaluating the Reliability of Inferred Phylogenies
17    Mar. 22     Character Reconstruction and Other Uses for Phylogenies

18    Mar. 27     Gene Trees and Species Trees
19    Mar. 29     ---TO BE DETERMINED; DR. FUNK OUT OF TOWN---
 20 Apr. 3            ---Exam #3 (Lectures 13-19)---
      Apr. 5      Evolution of Gene Families and Gene Function I

21    Apr. 10     Evolution of Gene Families and Gene Function II
22    Apr. 12     Concerted Evolution

23    Apr. 17     Genome Organization and Evolution I
24    Apr. 19     Genome Organization and Evolution II

25    Apr. 24     Emerging fields: Genomics and Beyond

      Apr. 28     FINAL EXAM: Saturday, 9:00 AM (Lectures 20-25 + Cumulative)

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