Phylogenetics Syllabus and Reading Assignments

Phylogenetics Syllabus and Reading Assignments - Fall, Mini-2 2012

The materials in the "Assigned Reading" column are directly related to the topics covered in class. Readings under "Additional Topics" are strictly optional and will not be covered on the exams.

Readings from:: Inferring Phylogenies Felsenstein, Sinauer Associates; 2 edition (September 4, 2003); Molecular Evolution: A Phylogenetic Approach. Page and Holmes, Wiley-Blackwell, 1st ed. (1998)

CLASS	DATE	TOPICS	ASSIGNED READING	ADDITIONAL TOPICS
1.	Oct. 23	Introduction to phylogenetics. Tree properties Lecture notes Concept review Problem set 1 , due Oct 30th.	Read: Page and Holmes Ch. 1 and 2 Understanding Evolutionary Trees Gregory, 2008. Review: You should already be familiar with the material on gene and genome organization in the first half of Ch. 3 of Page and Holmes. Look over pp 37-62 to make sure you know it. If not, read it carefully.	Felsenstein, Ch. 10: History and philosophy. Read: pp: 123-138.
2.	Oct. 25	Introduction to phylogenetics. Overview of tree reconstruction lecture notes Concept review Projects	Read: Page and Holmes Ch.3: pp. 63-77.	Page and Holmes Ch. 3: pp. 77-87. Non-coding repetitive DNA, transposable elements. Jody Hey on species concepts.
3.	Oct. 30	Character data. Reconstructing evolutionary change on a tree Lecture notes Concept review Problem set 1 due in class Problem set 2 due Nov. 6th.	Read: Page and Holmes 5.1: Sequence alignment, homology Page and Holmes 5.3: Evolutionary change on a tree
4.	Nov. 1	Multiple Sequence alignment Lecture notes Concept review	Multiple sequence alignment Pevsner, Ch. 6 Jalview reference card	Additional jalview info Jalview tutorial Screencast Other jalview documentation Additional jalview info Jalview tutorial Screencast Other jalview documentation
5.	Nov. 6	Phylogeny reconstruction. Parsimony methods. Lecture notes Problem set 2 due in class. Practicum 1; Worksheet to hand in.; phospholipase A2 sequences;	Page and Holmes, Introduction to tree methods (6.1.0 - 6.1.3), pp. 172-178. Discrete methods (6.3) and Parsimony (6.4.0 - 6.4.3), pp. 187-191
6.	Nov. 8	Phylogeny reconstruction. Maximum likelihood estimation. Lecture notes Project plans due by midnight; email to comp-bio@cs.cmu.edu
7.	Nov. 13	Substitution models and model selection Lecture notes	Read: Reading guide Kosiol et al. J. Biomed. Info., 2006. Page and Holmes 6.5: Maximum likelihood estimation Page and Holmes 5.3: Genetic distance
8.	Nov. 15	Substitution models and model selection Lecture notes		See pp. 454-458 of Sullivan and Joyce, 2005 for more information on the Akaike and Bayesian Information Criteria.
	Nov. 20	No lecture. Optional software demo and Q&A session. Practicum 1 due Practicum 2; due Nov 29 Worksheet to hand in.; Trimmed MSA of PA2 sequences. Or use your own. (This will be available after all Practicum 1 assignments have been turned in.) Species list
	Nov. 22	No class (Thanksgiving Holiday)
9.	Nov. 27	Distance based methods, Lecture notes	Page and Holmes, Distance based methods (6.2), pp. 179-186.
10.	Nov. 29	Assessing phylogenetic accuracy, potential pitfalls Lecture notes Practicum 3; due Dec 7 Worksheet to hand in.; Gene tree, Species tree, Species list.	Page and Holmes, Comparing tree methods Bases for comparison (6.1.4), pp. 178 - 179. Pbs with distance methods (6.2.4), pp. 185 - 187. Parsimony, Likelihood (6.5.3, 6.5.4), pp. 199 - 201 Assessing tree quality Splits, section 6.6, pp. 201-208, but skip Box 6.5 True tree, section 6.7, pp. 209-216 Bootstrapping, section 6.8, but skip 6.83; pp. 216-222,225-227
11.	Dec. 4	Gene family evolution, gene duplication Lecture notes	Page and Holmes, Comparing tree methods Gene trees and species trees, pp. 30, 31. The evolution of multigene families (3.3.2), pp. 73 - 77
12.	Dec. 6	Gene family evolution, horizontal transfer Lecture notes
	Dec. 17	Final Exam: 8:30am - 11:30am, Location TBA

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Last modified: April 25, 2013.
Maintained by Dannie Durand (durand@cs.cmu.edu).