Phylogenetics Syllabus and Reading Assignments

Phylogenetics Syllabus and Reading Assignments - Fall, 2017

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

CLASS	DATE	TOPICS	ASSIGNED READING	ADDITIONAL TOPICS
1.	Aug. 29	Introduction to phylogenetics. Molecular phylogenetics Tree terminology Lecture notes	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.
2.	Aug. 31	Tree terminology and tree comparison Lecture notes Newick format, Newick mirror site	Tree terminology Understanding Evolutionary Trees Gregory, 2008. Page and Holmes Ch. 2.1.1 - 2.1.4, 2.4 2
3.	Sep. 5	Phylogenetic characters, reconstruction of ancestral characters and trait evolutionon a tree; species evolution, models of speciation. Lecture notes	Reconstructing the history of character change Page and Holmes Ch. 2.2
4.	Sep. 7	Gene family evolution Lecture notes	Organismal phylogeny, gene and species trees Page and Holmes Ch. 2.4 Genomes, 3rd Ed. T.A. Brown. Chapter 18: How Genomes Evolve, Sections 18.2, 18.2.1 Chapter 9.2: Mobile genetic elements , Sections 9.2, 9.2.1 New Genes as drivers of phenotypic evolution, Chen et al., NRG, 2013. Box 1: Mechanisms of New-Gene origination. New Gene Evolution: Little did we know, Long et al., Annu.Rev.Genet., 2013. pdf, pp. 307-314, only.	New Genes as drivers of phenotypic evolution, Chen et al., NRG, 2013. New Gene Evolution: Little did we know , Long et al., Annu.Rev.Genet., 2013.
5.	Sep. 12	Gene evolution, part 2 Lecture notes
6.	Sep. 14	Gene families, gene trees vs species trees Lecture notes	Homology a personal view on some of the problems. Fitch, Trends Gen., 2000.	Distinguishing homologous from analogous proteins. Fitch, Syst. Zool., 1970.
7.	Sep. 19	Gene families, gene trees vs species trees, part 2 Lecture notes
8.	Sep. 21	Lecture notes
9.	Sep. 26	Sequence databases Lecture notes
10.	Sep. 28	Introduction to the practica Lecture notes		Pyrrolysine review, Krzycki, 2011: pdf
11.	Oct. 3	Class is canceled.
12.	Oct. 5	Case study: The evolutionary history of the sporulation initiation pathway in Firmicutes. Philip's Spo0 lecture
13.	Oct. 10	Searching sequence databases PAM30, BLOSUM62 PAM250	BLAST resources on line: Using BLAST in practise: Blast tutorial Using NCBI's BLAST BLAST documentation BLAST statistics: The statistics of sequence similarity scores S. F. Altschul
14.	Oct. 12
15.	Oct. 17	Multiple Sequence Alignment	Multiple sequence alignment Pevsner, Ch. 6 Jalview documentation Jalview documentation page Editing sequences with Jalview.- Online Jalview tutorial youtube	Protein multiple sequence alignment Do and Katoh, 2008
16.	Oct. 19	Tree reconstruction: Maxiumum Parsimony	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
17.	Oct. 24	Maximum likelihood estimation, model selection
18.	Oct. 26	Phylogeny reconstruction with MLE	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
19.	Oct. 31	Projects, background for Practicum 2
20.	Nov. 2	Class Projects
21.	Nov. 7	Distance-based phylogeny reconstruction	Page and Holmes, Distance-based tree reconstruction Genetic distance (5.3) Distance based methods (6.2), pp. 179-186.
22.	Nov. 9	Distance-based phylogeny reconstruction, assessing tree accuracy	Page and Holmes, Comparing tree methods Bases for comparison (6..14), 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
23.	Nov. 14	Assessing tree accuracy: bootstrapping, splits trees, phylogeny reconstruction pitfalls.
24.	Nov. 16	Interpreting a gene trees in the context of a species trees
25.	Nov. 21	No class.
	Nov. 23
26.	Nov. 28	Gene tree reconciliation with duplications and losses Reconciliation guide: step-by-step. Notung 2.9, Example trees used in today's demo: zip
27.	Nov. 30	Applications of reconciliation, reconciliation with transfers.
28.	Dec. 5	Reconciliation with transfers, Dr. Maureen Stolzer
29.	Dec. 7	Guest lecture: Evolution of paralogous transcription factors Jimmy Khor, Ettensohn lab Final projects presentation guidelines
Final Exam	Dec 12, 5:30-- 8:30 MI 448	Final project presentations Guidelines

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Last modified: August 28, 2017.
Maintained by Dannie Durand (durand@cs.cmu.edu).