Grad Core Phylogenetics 2009

Syllabus Fall 2009:

Day 1 (W. Sept. 30, 50 minutes)

Lecture1.pdf

Readings: Gregory 2008, Crisp and Cook 2005

Topics:

What trees are used for

history of life + cool discoveries about topology

Tree terminology

clades (dinos birds, reptiles, fish)

sister groups, crown/stem, etc.

rank and its importance

homology

Day 2 (F. Oct. 2, 50 minutes)

Lecture2.pdf

Readings: Felsenstein 1978.

Topics:

Treespace/NP-nasty

History

Distance

Parsimony

Long branch attraction

Day 3 (M. Oct. 5, 2 hr)

Lecture3.pdf

Readings: Huelsenbeck et al. 2002

Topics:

Models

Model selection

Bayes/Likelihood

Sample analysis walkthrough (genbank, alignment, tree search, sketch of posttree analysis)

Day 4 (W. Oct. 7, 50 minutes)

Lecture4.pdf

Readings: none.

Topics:

Bootstrap

Clocking

Day 5 (F. Oct. 9, 50 minutes)

Lecture5.pdf

Readings: Edwards 2009, Hugall et al. 2007

Topics:

Supertrees

Supermatrices

Gene tree species tree