BISC 499 Special Topics: Population Genetics and Molecular Evolution

Description

This course is designed to introduce graduate students and advanced undergraduates to modern topics in population genetics, genomics, and molecular evolution. Like much of biology, this area is currently experiencing explosive growth (mostly driven by human genetics). Unlike most of biology, it has been quantitative (“computational” in modern parlance) since its inception about a hundred years ago. The combination of a deep and often mathematically sophisticated literature can make the field seem impenetrable. The aim of this course is to help students make the leap. The course will focus on understanding modern papers, by identifying the major questions and exploring them through a combination of lectures by the instructors and discussion of papers (modern as well as classical).

Logistics

The class will meet Tuesdays 3:30-6:20 in RRI 421 for lectures by the instructors and student-lead discussions of assigned papers. Each student will be responsible for reading and presenting a paper to the class. All students are expected to participate vigorously in discussions. Take-home quizzes will be given after each topic is completed. In addition, students will, either individually or as small groups, write a final paper that analyzes real data. Unpublished data will be provided by the instructors: published data requiring further analysis may present itself during the course. We hope (but will not require) that the final papers will be publishable in a scientific journal.

The course is intended for Biology/Biochemistry majors and graduate students in appropriate fields. Familiarity with basic genetics and molecular biology is assumed. Permission of instructors is required, but not hard to get.

In assigning grades for this course, presentations will count for 40%, participation and quizzes 20%, and the final paper 40%.

Required Materials

In addition to course notes and primary literature, the following are useful references:

• Schierup, Wiuf & Hein: Gene genalogy, Variation and Evolution: A Primer in Coalescent Theory
• Hartl & Clark: Principles of Population Genetics
• Lynch & Walsh: Genetics and Analysis of Quantitative Traits

Depending on your background, you may also need a good, general text on evolutionary biology (like Futuyma's Evolutionary Biology).

Access to a computer and coffee is probably essential (and can be provided).

Lessons

January 15 (MN)

A brief introduction to the history of the subject [Lecture][Paper][Assignment]

January 22 (SN)

Decomposing variance

January 29 (MN) 

The Coalescent, Part 1 [Lecture]

February 5 (MN)

The Coalescent, Part 2 [Lecture][Mathematica notebook][Paper][Assignment]

February 12 (SN)

Emergency stand-in for MN

February 19 (SN)

TBA

February 26 (SN)

TBA

March 4

TBA

March 11

The coalescent with structure and with recombination [Papers (for March 25): sweeps and Fst+XP-EHH]

March 25

Modeling selection [Papers: Drosophila population genomics and philosophical musings 1 and 2]

April 1

Discussion of backlogged papers from 3/11 and 3/25.

April 8

More discussion: we still have not gone through Begun et al (2007), and we should also discuss the comparative genomics of 12 Drosophila species.  Plus evidence that whites have more deleterious mutations than blacks!  And Sergey will introduce some papers for next time.

April 15 (SN)

Sergey's postdoc Ryan will present some of his stuff, and we will discuss the papers Sergey distributed last time.

April 22

Genome-Wide Association Day!  A sampler of papers can be found here.

April 29 (SN)

Various papers on evolutionary genomics, suggested by Sergey.

Final

By May 6, turn in an essay in which you review what has been published during the last several months on one of the topics of your choosing!