| # |
Date |
Lecture Topic |
Req. Readings |
Optional Readings |
| 1 |
August 23
(T) |
Course Organization and Overview of Systematics: Nomenclature, Classification, and Schools of Phylogenetics (2)
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 25
(Th) |
Paper Discussion 1 - Future of Taxonomy |
Godfray 2002;
Polaszek et al. 2005
Mallet&Willmott 2003 |
|
| 3 |
August 30
(T) |
Principles of Phylogenetics: Characters, Character States, and Polarity
Char State and Polarity Handout
Phylogenetic Terms Handout |
Quicke 1993, ch. 2, pp 11-31 |
Baum & Smith, ch. 4 and 5; Schuh 2000, ch. 5, 89-101; ch. 4, 77-86 (ref) |
| 4 |
September 1
(Th) |
Principles of Phylogenetics: Tree Thinking, Hennigian Concepts, and Character Conflict
Notes on Hennig, Character Conflict & Cladistics |
Kitching et al. 1998, ch. 1 |
Baum & Smith, ch. 3; Hennig 1966; Farris 1970 (ref) |
| 5 |
September 6
(T) |
Inferring Trees with Maximum Parsimony
Parsimony Notes |
Baum & Smith, ch. 7; Hillis et al. 1996, ch. 11, pp. 415-426 |
Lockhart ms ch.5.4; Kitching et al., ch. 3, pp 38-48; ch. 4, 70-79
Edwards 2009; Hennig 1966; Farris 1970 (ref) |
| 6 |
September 8
(Th) |
Paper Discussion 2 - Species Concepts |
Hey 2001; Hey, Fitch, & Ayala 2005; Hey 2006 |
Howard and Berlocher 1998, ch. 2; Avise 2004, ch. 7 (ref) |
| 7 |
September 13
(T) |
Diversity of Systematic Data and Uses
Data Diversity Notes |
Quicke 1993, ch 8, pp 32-41 |
Systematics and Biological Characteristics |
| 8 |
September 15
(Th) |
Molecular Markers
Markers Notes |
Avise 2004, ch 3; Dowton 2003 |
Rokas 2000; Genetic marker (wiki) |
| 9 |
September 20
(T) |
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 |
| 10 |
September 22
(Th) |
Alignment of DNA Sequences
Alignment Notes |
Lockhart ms ch.2; ch.3 |
jRNA website; MUSCLE website; SQUINT website |
| 11 |
September 27
(T) |
Paper Discussion 3 - Computer Alignment
Review Session 1 (Study Guide) |
Morrison 2009 |
Edgar 2004; Martin et al. 2007; Kjer et al. 2009
|
| 12 |
September 29
(Th) |
EXAM - Midterm 1 |
|
|
| 13 |
October 4
(T) |
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 |
| 14 |
October 6
(Th) |
Inferring Trees with Maximum Likelihood and Models of Molecular Evolution
ML Handout |
Baum & Smith ch. 8, pg 1-20; Hillis et al. 1996, ch. 11, pp.426-446; Page & Holmes 1998, ch. 6 pp.193-201 |
Lockhart ms ch. 5; Felsenstein 2004, ch. 16 (ref) |
| 15 |
October 11
(T) |
Paper Discussion 4 - Parsimony vs. Likelihood |
Sober 2004 |
|
| 16 |
October 13
(Th) |
Inferring Trees with Bayesian Methods
Bayesian Notes |
Baum & Smith, ch. 8, pg. 20-28; Huelsenbeck et al. 2002;
Lockhart ms ch. 4.2.3 |
Ronquist & Deans 2009
|
| 17 |
October 18
(T) |
Evaluating Results and Measures of Support
Support Measures notes |
Baum & Smith, ch. 9; Hillis et al. 1996, ch. 11, pp. 507-509; Page & Holmes, ch 6 pp. 209-214, 218-227 |
Sanderson & Schaffer 2002 |
| 18 |
October 20
(Th) |
Assessing Phylogenetic Congruence (guest lec: Jim Whitfield) |
Huson & Bryant 2006;
Kitching et al. 1998 ch. 7;
Sanderson et al. 1998 |
McBreen & Lockhart 2006;
Bininda-Emonds et al. 2002 |
| 19 |
October 25
(T) |
Historical Biogeography and Divergence Times
Historical Biogeography and Divergence Times Notes |
Magallón 2004; Sanderson 1998; Hines 2008 |
Rutschmann 2006; Whitfield 2002 |
| 20 |
October 27
(Th) |
Paper Discussion 5 - Bootstrap vs. Posterior Probability |
Alfaro et al. 2003; Douady et al. 2003 |
|
| 21 |
November 1
(T) |
Review Session 2 (Study Guide) |
|
|
| 22 |
November 3
(Th) |
EXAM - Midterm 2 |
|
|
| 23 |
November 8
(T) |
Comparative Method: Testing Evolutionary Correlations Among Traits
Comparative Method Notes |
Felsenstein 1985;
Harvey & Pagel 1991 ch. 4, pp 78-100;
Pagel 1999 |
Pagel, Atkinson & Meade 2007 |
| 24 |
November 10
(Th) |
Host Parasite Coevolution
Host Parasite Coevolution Notes |
|
|
| 25 |
November 15
(T) |
Gene Trees/Species Trees and Phylogeography (guest lec: Haw Chuan Lim) |
|
|
| 26 |
November 17
(Th) |
Paper Discussion 6 - Coevolution |
Clayton et al. 2003; Johnson et al. 2003 |
|
| -- |
November 21-25 |
Thanksgiving Break |
|
|
| 27 |
November 29
(T) |
Rapid Radiations
Radiations Handout |
Whitfield & Lockhart 2007 |
Philippe & Laurent 1998 |
| 28 |
December 1
(Th) |
Paper Discussion 7 - Rapid Radiations |
Whitfield & Kjer 2008 |
|
| 29 |
December 6
(T) |
Phylogenomics |
Boussau 2010; Boussau 2009 |
Philippe et al. 2005; Rokas&Carroll 2006 |
|
|
Final Exam Review |
|
|
|
December 14
(W)
8am - 11am |
Final Exam |
|
|