Dates 11/05/09

Homework 6 ,  Homework 7 and Homework 8  are now posted.  See syllabus for due dates.           Students should be contacting us soon regarding their presentations! Click (here) to read Steven A. Frank's paper highlighting Price's contribution to Evolutionary Genetics

 For information on commuting to and from the campuses click (here)

Syllabus, Reading Assignments and Homework Handouts Textbooks REQUIRED Evolutionary Theory Mathematical and Conceptual Foundations by Sean Rice A list of typos for Rice Suggested reference books Gene Genealogies, Variation and Evolution by Hein, Schierup and Wiuf Coalescent Theory, An Introduction by John Wakeley	UI Professor: Paul Joyce  Dept. of Mathematics Initiative for Bioinformatics and Computational Biology (IBEST)  WSU Professor: Richard Gomulkiewicz  Department of Mathematics, School of Biological Sciences       E-mail: joyce@uidaho.edu Office Brink Hall 413  Phone:  885-6338  Office Hours for Paul Joyce: Monday and Tueday 3:30-4:30 pm or by appointment E-mail:  gomulki@wsu.edu Office: Biology Office: Eastlick 391 Math Office:     Neill 227 Phone: 335-2527 Office Hours for Richard Gomulkiewicz: Mondays from 2:30-3:30 in Eastlick 391 Wednesdays from 2:00-3:00 in  Neill 227, and by appointment. Class Meeting Tuesday 5:00- 6:15 pm  TLC 223 UI CAMPUS Class Meeting Monday 5:10:-6:25 pm TODD 204 WSU CAMPUS
	Course Goals (1) Gain exposure to, and experience with, major topics and methods in mathematical genetics;  (2) Survey classical and contemporary literature in mathematical genetics.     Course format: We plan to achieve the goals of the course through a series of instructor led “workshops” topics in mathematical genetics during the first part of the course and student led group discussions during the second part of the course.  One or two readings will usually be assigned per topic: one for background and a second for discussion.   For workshops, an instructor will briefly motivate the topic, outline the analyses, and summarize the main results.  The class will then work through the reading(s) as a group, stopping to clarify steps, methods, or concepts that are ambiguous.  Ideally, students who understand a step/method/concept will do the clarifying.  Of course, the instructors will help regulate the flow of discussion and contribute lucid explanations as necessary!  The instructors will also suggest homework problems which all students will be expected to attempt.  For this workshop format to succeed, it is critical that every student works to understand the readings prior to class.  If, in the course of reading the material, you don’t understand something (e..g., a term, concept, manipulation, or technique) make a note of it and go through the remaining material as best you can.  Be sure to bring your notes to class. Student-led group discussions will cover topics chosen by students (topics—which may involve original research—must be pre-approved by the instructors).  Leaders should prepare handouts and readings that their fellow students will read prior to the discussion.
Internet Resources Java Demonstrations of the coalescent Process	Grading Criteria Half of the grade in this course will based on the quality of a  student planned and executed group discussion during the second part of the course.  The other half of your grade will be based on in-class participation.  Your participation grade will be based on  (a) attendance, (b) the contributions you make during discussions (including asking and answering questions, and making thoughtful comments), and (c) attempting and solving any assigned homework problems.      Reading  Assignments: Readings will be assigned from current and classical literature.  You will be expected to  have read the assigned paper and participate in discussing the material.  You will be assigned four or five questions about the reading.  You will be required to answer each of the questions.
Computer Programs for Coalescent Models Lamarc Genetree A recombination program   Some Computer Programs  used in  Phylogenetic Analysis List of phylogenetic software by Joe Felsenstein	Web Resources To your left are a number of interesting web sites with information and computer software.   If you find any  web sites that you feel would be of interest to your instructors and/or fellow students, let me know (joyce@uidaho.edu).  I would be happy to post them.