EEB501 (Graduate core course)

UTK EEB requires new graduate students to take an intensive team-taught course covering ecology and evolution. I present the phylogenetics portion (tree creation, not tree use).

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

Potential students: Our lab needs motivated students. Deadline for grad students is Dec. 15, annually. See info here. Accepted students are guaranteed funding through TAships, though other funds may be sought, too. Though our lab is mostly about creating and applying tools in order to understand evolutionary questions, it's possible (and often a good idea) for a student to be jointly advised in a more empirical lab.

Everyone: Check NIMBios deadlines for funds for postdocs, visitors, working groups, etc.

Brian O'Meara Lab

Primary links