Schedule

Fall 2008 • STAT 298 Sec 30 • CCN 87680

Seminars in Statistical Phylogenetics

Mondays 11-12 AM, Evans 334. 1 credit S/U only.

http://fisher.berkeley.edu/~rasmus/STAT298.html

In this course we will mix lectures and student led discussions of current topics in statistical phylogenetics. The objective of phylogenetics is to estimate evolutionary trees, typically from DNA sequence data, or other genetic data. The course will start with a series of lectures aimed at introducing the field of phylogenetics for students of the mathematical sciences. We will thereafter move to student led discussions of current papers in the field. Topics will include model choice and hypothesis testing, MCMC methods, interpretations of the bootstrap in phylogenetics, the star-phylogeny paradox, and more. The course is open to all graduate students, and we will assume no prior knowledge regarding genetics. Familiarity with basic probability theory and theory of statistics will be assumed.

During each meeting, except for the first three weeks, one (or sometimes two) students give a presentation. These presentations should provide sufficient background on the subject being covered, review the current state of knowledge in the area, and then critically analyze, in detail, the assigned paper. All students in the class are expected to read the specific paper that will be presented at each session. All presentations should leave at least 20 minutes in the end of the class for discussion.

Regular attendance and active participation in discussions is required of all students in the seminar in order to receive a passing grade.

Schedule

(Please report dead links)

This is a preliminary schedule – we may choose to change it The first three session will be lectures aimed at providing all students with a suitable background in phylogenetics. We will then start student lead discussion on a number of topics. Many of the topics chosen focus on current controversies and open problems I statistical phylogenetics.

9/1/2008 Institutional holiday (Labor Day)

9/8/2008 Organizational meeting and introduction

9/15/2008 Lecture I: Trees, Models of Molecular Evolution and the Likelihood Function

9/22/2008 Lecture II: Parsimony and Optimization

9/29/2008 Lecture III: Neighbor-Joining and Related Methods

Readings for the three lectures here.

10/06/2008 Bayesian Phylogenetics and MCMC (Nick Matzke, Chris Nasrallah)

Mau, B., M. A. Newton, and B. Larget. 1999. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55:1–12.

Huelsenbeck JP et al. (2002) Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol 51:673-688

10/13/2008 MCMC on mixtures (David Hendrix, Wenjing)

Eric Vigoda and Elchanan Mossel. 2005. Phylogenetic MCMC algorithms are misleading on mixtures of trees. Science 309: 2207 – 2209.

See also this comment and this response. And see also this.