Prerequisites, Course Schedule, and Grades

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Since the course will use  John Wakeley's forthcoming text Coalescent Theory: An Introduction as one of its two text-books, its prerequisites will be similar to that of the text-book:   "This book is a intended mainly for biologists. It assumes that the reader is familiar with the basic facts of biology, including population and evolutionary biology, as for example can be obtained by pursuing an undergraduate degree in the subject. It also assumes that the reader is motivated to understand variation in the biological world. The aim of the book is to bring to the reader the beginnings of a mathematical understanding of coalescent theory, which is a collection of stochastic models used to generate predictions about patterns of genetic variation and to make inferences from samples of genetic data. After a brief introductory chapter, the book dives right into the mathematics at a level which is hoped to facilitate learning. However, a certain amount of prior mathematical training is necessary. In addition to the usual college level general mathematics courses, including calculus, some exposure to probability theory and statistics is highly recommended.  Readers who find the material in Section 2.1.1 completely unfamiliar will struggle. However, anyone who one masters the material in this book will be able to read papers in the primary literature with some confidence, and also be in a position to carry out some independent research using coalescent theory."

Although the book is not quite available yet, its first three chapters are.  Since the course itself will be commence on September 18 (perhaps even September 25), please download the chapters and try to skim through them.

Course Schedule

  1. The Basic Coalescent.
  2. From Genealogies to Sequences: The Wright-Fisher Model.
  3. From Genealogies to Sequences: Infinite Sites Model.
  4. Trees and Topologies
  5. The Coalescent with Population Structure
  6. The Evolution of Marine Organisms I
  7. The Coalescent with Recombination
  8. Gene Trees with Recombination.
  9. Monte Carlo Integration and the Coalescent
  10. Software
  11. The Evolution of Marine Organisms II
  12. Genealogical Trees Around a Disease Mutation
  13. Linkage Disequilibrium
  14. Model Based Linkage Disequilibrium Mapping
  15. The Evolution of Marine Organisms III


Course work will consist of a total of eight home work assignments; in addition, a review paper on  literature or software will be due in the last week of the course.  The course grades will be based on:
  1. Homework: 40%
  2. Review paper on literature or software: 60%


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Last updated September 5, 2007
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