Syllabus PDF


Jan. 17:  Introduction - contemporary issues in systematic biology - what is at stake? (BDM & NH);

            What is Systematic Biology?  History (BDM) [Handout]

            LAB:  discussion: student interests


Jan. 19: What is Systematic Biology? Philosophy  (BDM) [Handout]

            LAB: Tour of systematics collections, labs, and resources



Jan. 24: The Hennig Principle: synapomorphy; rooting issues (BDM) [Handout]

            LAB: A simple parsimony algorithm by hand  (BDM)


Jan. 26: Homology (BDM) [Handout]

            LAB: Compatibility methods by hand (BDM)



Jan. 31: Character analysis -- what is a data matrix? (BDM) [Handout]

            LAB: Introduction to PHYLIP [Handout]


Feb. 2:  Character coding [primary homology, polarity, additivity , etc.]; (KWW) [Handout]

            Character coding worksheet [Handout]

            LAB: Introduction to PAUP [Handout]



Feb. 7: Morphological data I -- the importance of incorporating fossils into phylogenetics  (BDM)            


            LAB: Introduction to WinClada, Nona, TNT [Handout]


Feb. 9: Morphological data II  -- ontogeny & structure of plants (BDM) [Handout]

            LAB: [PROJECT TOPIC DUE]



Feb. 14: Morphological data III  -- ontogeny & structure of animals (KWW) [Handout]

            LAB: Introduction to MacClade [Handout]


Feb. 16: Morphological data IV  -- morphometrics  (David Lindberg)



Feb. 21: Molecular data I -- General introduction; types of molecular data (immunological distance; DNA                hybridization; allozymes;  restriction sites, DNA sequences; genomics) (BDM) [Handout]

            LAB: GENBANK; sequence analysis [Handout]


Feb. 23:  Molecular data II -- Sequence alignment (KWW) [Handout]

            LAB: morphometrics [Handout]



Feb. 28:  Classification I -- basic principles (monophyly & information content) (BDM) [Handout]

            LAB: discussion of molecular application papers (students to bring papers from their groups)

            [Alignment assignment]


March 2: Classification II -- species concepts (BDM) [Handout]

            LAB: discussion of species concepts



March 7:  Classification III -- DNA barcoding and DNA taxonomy (KWW) [Handouts]

             LAB: discuss progress on projects in class


March 9: Classification IV -- nomenclature; Zoological and Botanical Codes; practical systematics  (KWW)


            LAB: The systematic monograph (students to bring papers from their groups)



March 14: Classification V - phylogenetic taxonomy; Phylocode  (BDM) [Handout]

            LAB: discussion of phylogenetic taxonomy (all)


March 16: Phylogenetic trees I:  reconstruction; models, algorithms & assumptions (BDM) [Handout]

            LAB: Introduction to POY, Clustal [Handout]



March 21:       Phylogenetic trees II: Phenetics; distance-based algorithms (KWW) [Handout]

            LAB: UPGMA and neighbor-joining using PAUP [Handout]


March 23:       Phylogenetic trees III: Parsimony (KWW) [Handout]

            LAB: QUIZ 1 (covers through March 14th)


March 27 - 31:           SPRING BREAK


April 4: Phylogenetic trees IV:  Maximum likelihood; molecular evolution and phylogenetics (KWW) 


            LAB: Maximum likelihood applications using PAUP and Modeltest [Handout]


April 6: Phylogenetic trees V: Bayesian methods (Jimmy McGuire)

            LAB: Mr Bayes [Handout]



April 11: Phylogenetic trees VI:  measures of support; methods of testing robustness and threshold values

                            (KWW) [Handout]

            LAB: discuss progress on projects in class


April 13: Phylogenetic trees VII:  Tree comparisons; consensus methods (KWW) [Handout]

            LAB: Tree comparisons [Handout] [MRP Trees]


April 18: Phylogenetic trees VIII: Below the "species level;" phylogeography; dealing with reticulation  

                            (BDM) [Handout]

            LAB: advanced PAUP [Handout]


April 20: Phylogenetic trees IX:  Summary -- what are they, really, and what can go wrong? (BDM)


            LAB: discussion on the nature of phylogenetic trees, and problem solving



April 25: Phylogenetics and conservations; biodiversity measures (KWW) [Handout]

            LAB: Phylogenetic biodiversity assessment applications


April 27: Historical Biogeography (KWW) [Handout]

            LAB: Biogeographic software; COMPONENT, TREEMAP, DIVA [Handout]



May 2: Introduction to macroevolution (diversification, extinction, coevolution)   (BDM)


            LAB: advanced MacClade [Handout]


May 4: Introduction to comparative methods for evolution, ecology & behavior  (BDM)


            LAB: QUIZ 2 (covers March 16th through May 2nd)



May 9: Mesquite



May 16: Student minisymposium @ 5:00PM until ?


May 19: Projects due @ 5:00pm