Phylogenetics Syllabus and Reading Assignments - Fall, 2015

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.   Sep. 1
Introduction to phylogenetics.
Speciation
Lecture notes

  
2.  Sep. 3 Tree terminology and tree comparison Lecture notes
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.
 
3.  Sep. 8 Phylogenetic characters, reconstruction of ancestral characters and character state changes. Lecture notes

  
4.  Sep. 10 Genome plasticity
Lecture notes

    
5.   Sep. 15 Gene origination: Mechanisms and fates of duplicated genes.
Lecture notes
Genomes, 3rd Ed. T.A. Brown.
Chapter 18: How Genomes Evolve
Chapter 9.2: Mobile genetic elements
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.
6.   Sep. 17 Gene origination: Horizontal gene transfer, domain shuffling.
Lecture notes


    
7.  Sep. 22 Multigene families
Lecture notes
 Homology a personal view on some of the problems. Fitch, Trends Gen., 2000. Distinguishing homologous from analogous proteins. Fitch, Syst. Zool., 1970.
8.   Sep. 24   Gene families, cont'd
Lecture notes

    
9.   Sep. 29   Finding gene families in practice.
Lecture notes

    
10. Oct. 1 Finding gene families in practice, part 2
Lecture notes

    
11. Oct. 6
  • Review session for the first exam. Bring your questions to class!
  • Installing phylogenetic software (P. Spealman). Bring your laptop to class!
    		•    
    12. Oct. 8 In class Exam
    This exam is closed book. You may bring two pages (or one page, front and back) of your own notes.

    		   
    13. Oct. 13   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. 15 Introduction to the practica

    Introduction to Pyrrolysine: slides ,   handout (P. Spealman).

    Gene order browsers:   Genomicus,  YGOB     		&nbps; Pyrrolysine review, Krzycki, 2011: pdf
    15. Oct. 20 Sequence similarity searching, amino acid substitution matrices Lecture notes



    		    
    16. Oct. 22 Sequence similarity searching, using the BLAST program Lecture notes

    		    
    17. Oct. 27 Phylogeny reconstruction: maximum parsimony
    Lecture notes
    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
    Topology and length distributions
    Durbin, 3.4
    Multiple alignment using HMMs
    Ewens and Grant, pp. 337 - 339 Electronic reserves.
    18. Oct. 29 Multiple Sequence Alignment
    Lecture notes
    Multiple sequence alignment
    Pevsner, Ch. 6
    		 
    19. Nov. 3 Hands on exercise with Jalview
    fasta file for exercise.
    Jalview documentation
    Jalview documentation page
    Editing sequences with Jalview.-
    Online Jalview tutorial youtube
    		 
    20. Nov. 5 Maximum Likelihood Estimation
    Lecture notes

    21. Nov. 10 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
    		 
    22. Nov. 12 MLE summary.
    Topali demo

    Introduction to the Phylogenetics Projects, slides

    		   
    23. Nov. 17 Distance-based tree inference   assessing phylogenetic accuracy, Lecture notes
    Page and Holmes,
    Distance-based tree reconstruction
    Distance based methods (6.2), pp. 179-186.
    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
    		 
    24. Nov. 19 Projects:   Milestone 1
    Bring your blast searches and proposed sequence lists to class.

    		   
    25. Nov. 24      
      Nov. 26 No class. Thanksgiving holiday    
    25. Dec. 1    
    26. Dec. 3 Reconciling and interpreting gene trees
    Lecture notes



    		   
    27 Dec. 8 Project update    
    28. Dec. 10 Project presentations    
           
    Final exam Dec 18 1pm - 4pm, PHA120
    This exam is closed book. You may bring two pages (or one page, front and back) of your own notes.     		   


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    Last modified: June 15, 2015.
    Maintained by Dannie Durand (durand@cs.cmu.edu).