PhyloMath is an experimental course being offered Spring 2004 under the course number 396 ("Investigation of Special Topics"). Although some of the material offered in PhyloMath will be incorporated into my Phylogenetics course (to be offered for the first time Spring 2005), the goals for the two courses are somewhat different. Phylogenetics will strive to present a well-rounded introduction to phylogeny reconstruction and applications of phylogenetics in ecology, evolution and systematics. PhyloMath attempts to cover the nitty-gritty details of model-based phylogenetics, and thus assumes that the student already has considerable experience with phylogeny estimation and wants to develop a much more thorough understanding of how the model-based methods work. The PhyloMath course does not assume that you remember your 8th grade algebra or your first semester of undergraduate calculus, but you should be prepared to put some time into these subjects if you are rusty.

I am experimenting with a new means of student participation this semester (which I learned about from Tanya Berger-Wolf). Students taking the course for credit are expected to sign up to prepare notes for one of the lectures. This has two advantages: 1) it makes the student aware of just how much (or little) they understood from the lecture; and 2) it makes me aware of just how much (or little) the students are understanding from the lecture! This allows me to correct my course if I start assuming too much background knowledge on the part of the participants. I predict this system will work really well. If you are a current student in the course reading this, I might add that I think you will get the most out of this course if you actually prepare notes for every lecture, not just the one for which you have signed up.

Date | Notes Preparer | Topics | Link to PDF |
---|---|---|---|

January 20, 2004 | Paul O. Lewis | Simulation of one sequence, likelihood of one sequence under JC and F81 models, logarithms | Paul's notes |

January 27, 2004 | NO CLASS - Paul convalescing | ||

February 3, 2004 | Jon Richmond | Simulation of two sequences, likelihood of two sequences under JC model, time reversibility, binomial "straw man" model | Jon's notes |

February 10, 2004 | Norm Wickett | Expected values, binomial to poisson, transition equations, joint and conditional probabilities | Norm's notes |

February 17, 2004 | Brigid O'Donnell | Expected number of substitutions, PDFs, CDFs, derivatives, integrals, sojourn times | Brigid's notes |

February 24, 2004 | Jessica Budke | Sojourn times, estimating JC distances, Method of Moments, Method of Maximum Likelihood, rate heterogeneity, proportion of invariable sites | Jessica's notes |

March 2, 2004 | Roberta Engel | Gamma distributed relative rates | Roberta's notes |

March 9, 2004 | NO CLASS - Spring Break | ||

March 16, 2004 | Maxi Polihronakis | Other substitution models: K2P, HKY, F84, GTR, amino acid models | Maxi's notes |

March 23, 2004 | Dan Vanderpool, Andreas Bernauer | Transition:transversion ratio vs. rate ratio, site likelihoods of a 4-taxon tree | Lecture 8: Dan's notes, Andreas' notes, Paul's handout |

March 30, 2004 | Carrie Fyler | Likelihood with rate heterogeneity, molecular clock constraint, introduction to Bayesian inference | Carrie's notes |

April 6, 2004 | Michael McAloon | Bayesian inference (cont.), phylogenetic Markov chain Monte Carlo | Michael's notes, BayesianDist.xls (warning: xls file is now up to 6.6 megabytes!) |

April 13, 2004 | Hilary McManus | MCMC continued, plus intro to codon models | Hilary's notes, Codon model rate matrix |

April 15, 2004 | Jeff Thorne visits and gives EEB Seminar | ||

April 20, 2004 | Jadranka Rota | MCMC continued: Hastings ratio, LOCAL move, sliding windows, etc. | Jadranka's notes |

April 27, 2004 | Nic Tippery | Bayes' factors, discrete morphology model, ... |

Paul O. Lewis, Instructor

Assistant Professor of Ecology and Evolutionary Biology

Office: Torrey Life Science Room 166a

Telephone: (860) 486-2069

E-mail: paul.lewis@uconn.edu