The first  and  homework assignment  is  due Sept. 26. The second homework assignment is  due Oct. 3. The third homework assignment is due Oct. 17 The fourth homework assignment is due Oct.  31 The fifth homework assignment is due Nov. 7 The sixth homework assignment is due Nov.  16 The seventh  homework assignment is due  Nov. 30 Student projects and reading materials are posted on the syllabus. Coalescent Theory Slides Approximate Bayesian Computation

Homework 1 Homework 2 Homework 3 Homework 4 Homework 5 Homework 6 Homework 7

 

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  Departments of Mathematics and Statistics Initiative for Bioinformatics and Computational Biology (IBEST)  WSU Professor: Richard Gomulkiewicz  School of Biological Sciences       E-mail: joyce@uidaho.edu Office Brink Hall 413  Phone:  885-6338  Office Hours for Paul Joyce: By appointment E-mail:  gomulki@wsu.edu Office:  Eastlick 391 Phone: 335-2527 Office Hours for Richard Gomulkiewicz: By appointment. Class Meeting Wednesday 5:10- 6:25 pm  TLC 122 UI CAMPUS Class Meeting Monday 5:10:-6:25 pm TODD 307 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 Lamarc Genetree A recombination program List of phylogenetic software by Joe Felsenstein	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 [10%], (b) the contributions you make during discussions (including asking and answering questions, and making thoughtful comments) [10%], and (c) attempting and solving any assigned homework problems [30%].   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.     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. Parking information: You may park for free after 5:00 pm on most lots at both WSU and UI.  For more information about UI parking visit<>  http://www.uidaho.edu/parking/parkingenforcementschedule For information about WSU parking visit http://www.parking.wsu.edu/ WSU Academic Integrity Statement: Academic dishonesty will not be tolerated in this course. Any student who acts unethically will be given an F for the course and referred to the Office of Student Conduct.  For information, see:   http://www.conduct.wsu.edu/default.asp?PageID=343 http://www.wsulibs.wsu.edu/plagiarism/main.html   WSU Students with Disabilities: Reasonable accommodations are available for students with a documented disability. If you have a disability and may need accommodations to fully participate in this class, please visit the Disability Resource Center (DRC). All accommodations MUST be approved through the DRC (Washington Building, Room 217). Please stop by or call 509-335-3417 to make an appointment with a disability specialist. Campus Safety/Emergency Information:       In the interest of campus safety and emergency procedures, please become familiar with the information available on the WSU-provided websites. Also, please register your emergency contact information at myWSU.       • http://safetyplan.wsu.edu, Campus Safety Plan       • http://oem.wsu.edu/emergencies, Emergency management web site       • http://alert.wsu.edu, WSU Alert site.