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

Problem Set 1 (due Sept. 14)
Solutions
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

  Problem set 1 due in class

Problem set 2 (due Sept. 21st)
Solutions
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

    Problem set 2 due in class

   
9. Sep. 26 Sequence databases Lecture notes

 
 
10. Sep. 28 Introduction to the practica
Lecture notes

    Practical assignment 1a: Prac 1a
  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   Practical assignment 1b,
  worksheet,   solutions.
   
15. Oct. 17 Multiple Sequence Alignment

Jalview demo
fasta file: Mystery_Fasta.fa
Get to know Jalview Mini-assignment
Due Friday email pdavidso@andrew.cmu.edu by 4pm
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

Jalview practice exercise,
test data: Test_Fasta.fa
This exercise walks you through some basic Jalview functions. You are not required to hand it in. However, doing this exercise will help you with the next Practicum.
 
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

  Practical assignment 2,
  Prac 2 worksheet,   PylS.fasta,   PylB.fasta
solutions.
   
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.

  Practical assignment 3,
  Prac 3 worksheet,
Files you will need: MSA file ,   species tree
Solutions,   WAG tree,   WAG-I-G tree.
24. Nov. 16 Interpreting a gene trees in the context of a species trees

 
25. Nov. 21 No class.

Practicum 3 due
   
  Nov. 23    
26. Nov. 28 Gene tree reconciliation with duplications and losses
    Reconciliation guide: step-by-step.

Problem set 3 (due December 5th)
solutions.

Notung 2.9,  Example trees used in today's demo: zip
   
27. Nov. 30 Applications of reconciliation, reconciliation with transfers.

  Practical assignment 4,
  Prac 4 worksheet,
Files you will need: gene tree ,   species tree,   A.txt
Solutions
   
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).