Principles of Systematics - Integrative Biology 467

Lecture Syllabus

# Date Lecture Topic Req. Readings Optional Readings
Documents posted in Moodle
1 August 27
(T)
Course Organization and Overview of Systematics: Nomenclature, Classification, and Schools of Phylogenetics

Overview of Systematics Outline

Systematics Terms

Nomenclature Outline

Nomenclature Terms

Baum & Smith, ch. 1 and 2; Quicke 1993, ch. 6 Felsenstein 2001; Winston chs. 2&7, and pp. 103-105, 346, 424; Hull 1988, ch. 5; Mayr 1982, pp 147-208; Felsentein 2004, ch. 10 (ref)
2 August 29
(Th)
Paper Discussion 1 - Future of Taxonomy Godfray 2002
Deans et al. 2012
3 September 3
(T)
Principles of Phylogenetics: Characters, Character States, and Polarity

Char State and Polarity Handout

Phylogenetic Terms Handout
Baum & Smith, ch. 4 and 5;
Quicke 1993, ch. 2, pp 11-31
4 September 5
(Th)
Principles of Phylogenetics: Tree Thinking, Hennigian Concepts, and Character Conflict

Notes on Hennig, Character Conflict & Cladistics
Baum & Smith, ch. 3;
Kitching et al. 1998, ch. 1
Hennig 1966; Farris 1970 (ref)
5 September 10
(T)
Inferring Trees with Maximum Parsimony

Parsimony Notes
Baum & Smith, ch. 7; Hillis et al. 1996, ch. 11, pp. 415-426 Kitching et al., ch. 3, pp 38-48; ch. 4, 70-79 Edwards 2009; Hennig 1966; Farris 1970 (ref)
6 September 12
(Th)
Paper Discussion 2 - Species Concepts Hausdorf 2011 Howard and Berlocher 1998, ch. 2 (ref)
7 September 17
(T)
Diversity of Systematic Data and Uses

Data Diversity Notes
Quicke 1993, ch 8, pp 32-41 Systematics and Biological Characteristics
8 September 19
(Th)
Molecular Markers

Markers Notes
Avise 2004, ch 3; Dowton 2003 Rokas 2000; Genetic marker (wiki)
9 September 24
(T)
Alignment of DNA Sequences

Alignment Notes
Lockhart ms ch.2; ch.3 jRNA website; MUSCLE website; SQUINT website
10 September 26
(Th)
Issues with Sequence Data

Sequence Data Notes
Page & Holmes 1998, ch. 2 Boussau et al. 2008; Boussau et al. 2009; Steel 2005; Penny et al. 2001
11 October 1
(T)
Paper Discussion 3 - Computer Alignment

Review Session 1 (Study Guide)
Morrison 2009 Edgar 2004; Martin et al. 2007; Kjer et al. 2009
12 October 3
(Th)
EXAM - Midterm 1
13 October 8
(T)
Inferring Trees with Maximum Likelihood and Models of Molecular Evolution

ML Handout
Baum & Smith ch. 8, pg 1-20; Page & Holmes 1998, ch. 6 pp.193-201 Hillis et al. 1996, ch. 11, pp.426-446; Felsenstein 2004, ch. 16 (ref)
14 October 10
(Th)
Inferring Trees by Distance Methods

Distance Notes

Distance Homework
Baum & Smith ch. 8, pg 1-15 Hillis et al. 1996, ch. 11. pp. 446-453; Steel and Penny 2000; Lockhart ms ch. 5
15 October 15
(T)
Inferring Trees with Bayesian Methods

Bayesian Notes
Baum & Smith, ch. 8, pg. 20-28; Huelsenbeck et al. 2002 Ronquist & Deans 2009
16 October 17
(Th)
Paper Discussion 4 - Challenges with Genomic Data TBA
17 October 22
(T)
Evaluating Results and Measures of Support

Support Measures notes
Baum & Smith, ch. 9; Page & Holmes, ch 6 pp. 209-214, 218-227 Sanderson & Schaffer 2002
18 October 24
(Th)
Assessing Phylogenetic Congruence (guest lec: Jim Whitfield) TBA McBreen & Lockhart 2006; Bininda-Emonds et al. 2002
19 October 29
(T)
Historical Biogeography and Divergence Times

Historical Biogeography and Divergence Times Notes
Baum & Smith, ch. 11 Hines 2008; Rutschmann 2006; Landis et al. 2013; Ree and Smith 2008; Ronquist and Sanmartín 2011; Tamura et al 2012
20 October 31
(Th)
Paper Discussion 5 - Bootstrap vs. Posterior Probability Alfaro et al. 2003; Douady et al. 2003  
21 November 5
(T)
Review Session 2 (Study Guide)    
22 November 7
(Th)
EXAM - Midterm 2    
23 November 12
(T)
Comparative Method: Testing Evolutionary Correlations Among Traits

Comparative Method Notes
Baum & Smith, ch. 10; Felsenstein 1985; Harvey & Pagel 1991 ch. 4, pp 78-100; Pagel 1999; Pagel, Atkinson & Meade 2007
24 November 14
(Th)
Host Parasite Coevolution

Host Parasite Coevolution Notes
Clayton et al. 2003; Johnson et al. 2003
25 November 19
(T)
Gene Trees/Species Trees and Phylogeography Rosenberg & Nordberg 2002 Cheviron & Brumfield 2009; Domingues et al. 2012
26 November 21
(Th)
Paper Discussion 6 - Issues with Gene Trees TBA
-- November 25-29 Thanksgiving Break
27 December 3
(T)
Rapid Radiations

Radiations Handout
Whitfield & Lockhart 2007 Philippe & Laurent 1998
28 December 5
(Th)
Paper Discussion 7 - Rapid Radiations Salichos & Rokas
29 December 10
(T)
Phylogenomics Boussau 2010; Boussau 2009 Philippe et al. 2005; Rokas&Carroll 2006
  Final Exam Review
December 13
(F)
10 am - 1 pm
FINAL EXAM

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