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Integrative Biology 200B "PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Syllabus • Spring 2011


David R. Lindberg -- phone: 2-3926; email:

Brent D. Mishler -- phone: 2-6810; e-mail:

Graduate Student Instructor:

Nicholas J. Matzke -- phone: 3-6299; email:


            Class meeting time: Tu-Th, 12:30 - 3:30 pm in 3083 VLSB. This year lab exercises will be done on personal computers -- you need to have access to one to bring to class, preferably a laptop!

            Our class web page is: -- please check this often as it will have class announcements and answers to questions about the course material.


Tentative Schedule of Topics:


Jan. 18:            Introduction to aims of course / Phylogenetic reconstruction in a nutshell: homology & characters (BDM)

                              LAB: Get acquainted roundtable (all)

Jan. 20             Phylogenetic reconstruction in a nutshell: trees (BDM)

                              LAB: tour of systematics collections & resources in VLSB


Jan. 25:            What can we do with trees once we have them? 1. Classification classical and modern (DRL)

                              LAB: Introduction to Statistical Thinking (all)

Jan. 27:            Qualitative character evolution within a cladogram (discrete states; ancestral state reconstructions; single

                                    characters - BDM)

                              LAB: Introduction to Mesquite; Discrete character reconstruction (Matzke)


Feb. 1:             Qualitative character evolution (comparing two or more characters - BDM)

                              LAB: Phylogenetic Conservatism and Correlation of Discrete Characters (Mesquite - Matzke)

Feb. 3:             Quantitative character evolution within a cladogram (intro; ancestral trait reconstruction; phylogenetic                                   conservatism - BDM)

                              LAB: Introduction to R (Matzke)


Feb. 8:             Evolution and development - heterochrony (DRL)                

                              LAB: Intro to R continued: Phylogenies; Continuous characters (Matzke)

Feb. 10:           Independent contrasts and trait correlations (Ginger Jui)

                              LAB: independent contrasts (R) (Matzke)


Feb. 15:           Morphometrics (DRL)

                              LAB: morphometrics applications (Matzke)

Feb. 17:           Fossil data in phylogenetics (DRL)

                              LAB: PROJECT TOPIC DUE: discuss your potential project in class


Feb. 22:           Tempo in macroevolution (DRL)

                              LAB: testing molecular clock, r8s, BEAST (Matzke)

Feb. 24:           Dating in the 21st Century: putting dates on nodes, characters, and events (DRL)

                        LAB: discussion: the use of fossil data in phylogenetic reconstruction (all)


March 1:          Molecular evolution (BDM)

                              LAB: analysis of molecular evolution; substitution models, Modeltest, etc (Matzke)

March 3:          Gene family evolution; comparative genomics (Matzke)

                              LAB: tools for comparative genomics; BLAST, etc. (Matzke)


March 8           Evolution and Development (DRL)

                              LAB: tools for evo-devo (Matzke)

March 10:        Phylogenetics and adaptation (BDM)

                             LAB: discussion of adaptation (all)



March 15:        Comparing sister clades within a cladogram: the shape of evolution (DRL)

                              LAB: generating random trees; testing cladogram imbalance (Matzke)

March 17:        Adaptive radiations (BDM)

                              LAB: lineages through time; diversification analyses (Matzke)


March 21 - 25:          SPRING BREAK                                                       


March 29:        Speciation and related issues: species revisited (BDM)

                              LAB: QUIZ 1

March 31         Reticulation and phylogenetics; "phylogeography" and population biology (BDM)

                              LAB: discussion of species (all) (your project data set should be complete)


April 5:            Phylogenetics and conservation biology (BDM)

                              LAB: coalescence theory; applications in population genetics and phylogeography (Matzke)

April 7:            Modes in macroevolution - patterns of diversification and extinction (DRL)

                              LAB: discussion on levels of selection (all)


April 12:          Comparing cladograms; supertrees; coevolution; symbiosis (BDM)

                              LAB: consensus methods; Brooks parsimony (Matzke)

April 14:          Biogeography I -- basic principles; ecological vs. historical approaches; vicariance

                                    biogeography (DRL)

                              LAB: Biogeographic software; DIVA, Lagrange (Matzke)


April 19:          Biogeography II -- New tools, databases, and research possibilities (Matzke)

                              LAB: discuss progress on projects in class (hand in outline of project April 18th, details TBA)

April 21:          Interactions among clades in macroevolution (DRL)

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


April 26:          Phylogenies and Community Ecology; Assembly of Regional Biota (Ginger Jui)

                              LAB: phylocom, picante (Matzke)

April 28:          Glimpses of the future - comparative and functional genomics; integrating genetics, physiology, ecology

                                    and evolution (all)

                              LAB: QUIZ 2


May 2 - 6:     Reading/Review Week -- work on projects with help from instructors                        


May 9-13:     FINALS WEEK -- student minisymposium -- projects due (dates to be determined)


Requirements & Grading:

(1/3) Participation. Do the reading, come to each class and lab, and participate in discussions. A few homework assignments will also be given.

(1/3) Quizzes. Two equally-weighted, one-hour quizzes will be given, that emphasize problem solving and conceptual understanding.

(1/3) Project. This will be a substantive, comparative analysis of data from a group of the student's choice (with approval of the instructors; we encourage the study of thesis or other study groups). Based on phylogenetic trees (whether self-generated or from the literature), the project should apply all appropriate comparative methods to evaluate several types of comparative questions. There should also be a rigorous critique of previous comparative literature on the organismal group of choice. A written report will be turned in during finals week, in the form of a professional journal publication, that is, with an introduction (containing the literature review and critique), materials and methods section, results (using summary figures -- no raw data), and a discussion (being sure to compare results from the different methodologies applied, and to reach some biological conclusions). We will schedule a minisymposium at the end of the term where students can give a short presentation of their results.