Grading: There will be weekly short homework assignments to make sure that you have some practice with the material. These will be due on the Wednesdays of the week following the assignment. I will average your grades on these assignments after dropping your lowest two grades and this average will be the basis for your grade in the course. You may talk to others about the homeworks but the work you turn in should be your own.
Tentative Syllabus | |||
|---|---|---|---|
| Date | Lecture | Reading | Homework |
| Monday, August 29 | Tree Types | Chapter 3 | Homework Assignment 1 |
| Wednesday, August 31 | Counting trees | Chapter 3 | |
| Friday, September 2 | Generating random trees | Chapter 3 | |
| Monday, September 5 | Parsimony for a given tree | Chapter 1 | Homework Assignment 2 |
| Wednesday, September 7 | Parsimony for a given tree | Chapter 2 | |
| Friday, September 9 | Searching tree space for the most parsimonious tree | Chapter 4 | |
| Monday, September 12 | Searching tree space for the most parsimonious tree | Chapter 5 | Homework Assignment 3 |
| Wednesday, September 14 | Branch and bound algorithms | Chapter 5 | |
| Friday, September 16 | Computer Demonstration | Chapter 5 | |
| Monday, September 19 | Ancestral States and Branch Lengths | Chapter 6 | Homework Assignment 4 |
| Wednesday, September 21 | Computer Demonstration | Chapter 6 | |
| Friday, September 23 | Compatibility and Computer Demonstration | Chapter 8 | |
| Monday, September 26 | Models for DNA evolution | Chapter 13 | Homework Assignment 5 |
| Wednesday, September 28 | Models for DNA evolution | Chapter 13 | |
| Friday, September 30 | Calculating the likelihood for a given tree | Chapter 13 | |
| Monday, October 3 | Finding the most likely tree | Chapter 16 | Homework Assignment 6 |
| Wednesday, October 5 | More algorithms for searching tree-space | Chapter 16 | |
| Friday, October 7 | Ancestral States, Branch Lengths, and Computer Demonstration | Chapter 16 | |
| Monday, October 10 | Is ML consistent? | Chapter 16 | Break in Homework - no HW 7 |
| Wednesday, October 12 | Is parsimony consistent? | Chapter 9 | |
| Friday, October 14 | Robustness and using likelihoods to compare trees | Chapter 19 | |
| Monday, October 17 | Computer demonstration using likelihoods to compare trees | Chapter 19 | Homework Assignment 8 |
| Wednesday, October 19 | Bootstrapping | Chapter 20 | |
| Friday, October 21 | Bootstrapping plus computer demonstration | Chapter 20 | |
| Monday, October 24 | The Bayesian philosophy | Chapter 18 | Homework Assignment 9 - No Homework |
| Wednesday, October 26 | Baysean Monte-Carlo Markov chains for phylogenies | Chapter 18 | |
| Friday, October 28 | Computer Demonstration | Chapter 18 | |
| Monday, October 31 | Distance Methods | Chapter 11 | Homework Assignment 10 - due Monday, November 14 |
| Wednesday, November 2 | Distance methods | Chapter 11 | |
| Friday, November 4 | Computer Demonstration | Chapter 11 | |
| Monday, November 7 | Consensus versus Total Evidence | Chapter 30 | Homework Assignment 11 |
| Wednesday, November 9 | Selection of Phylogenetic Reconstruction technique | Overview | |
| Friday, November 11 | Example 1 Example 2 | Overview | |
| Monday, November 14 | Overview | Second article for discussion | Homework Assignment 12 |
| Wednesday, November 16 | Phylogenetic Comparative Methods | Chapter 25 | |
| Friday, November 18 | Phylogenetic Comparative Methods | Chapter 25 | |
| Monday, November 21 | Computer demonstration of phylogenetic comparative methods | Chapter 26 | Homework Assignment 13 |
| Wednesday, November 23 | Thanksgiving Break | -- | |
| Friday, November 25 | Thanksgiving Break | -- | |
| Monday, November 28 | Evaluations and plan for the rest of the term | No reading | no Homework |
| Wednesday, November 30 | Ferns phylogeny | Ferns paper | |
| Friday, December 2 | Boundary of Phylogenetics with Population Genetics | Native American phylogeny and Asian phylogeny and | |
| Monday, December 5 | Incongruence Length Difference Test and Partition Homogeneity Test | Chapter 20 and Original Farris paper and The Utility of the ILD Test | No homework |
| Wednesday, December 7 | Software for fitting models | Chapter 19 and | |