Integrative
Biology 200B
Spring
2009
"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION"
Syllabus [PDF]
Jan. 20: Introduction to aims of course / Phylogenetic reconstruction in a nutshell: homology & characters (BDM) [Handout]
LAB: tour of systematics collections & resources in VLSB
Jan. 22 Phylogenetic reconstruction in a nutshell: trees (BDM) [Handout]
LAB: Get acquainted roundtable
Lab Preparation for Week 1: Installing Mesquite, R and BEAST
Jan. 27: What can we do with trees once we have them? Classification dos and don'ts (BDM) [Handout]
LAB: Introduction to Statistical Thinking (all) [Handout]
Jan. 29: Dating in the 21st Century: putting dates on nodes, characters, and events (BDM, DRL, & B. Moore) [DRL Handout] [BDM Handout] [B. Moore Handout]
LAB: BEAST (B. Moore) [Lab Prep]
Feb. 3: Qualitative character evolution within a cladogram (discrete states; ancestral state reconstructions; single characters - DDA) [Handout]
LAB: Introduction to Mesquite; Discrete character reconstruction (Hallinan) [Lab Prep] [Handout]
Feb. 5: Qualitative character evolution (Maximum Likelihood; comparing two or more characters - DDA) [Handout]
LAB: Phylogenetic Conservatism and Correlation of Discrete Characters in Mesquite (Hallinan) [Lab Prep] [Signal Handout] [Correlation Handout]
Feb. 10: Quantitative character evolution within a cladogram (intro; ancestral trait reconstruction; conservatism) - (DDA) [Handout]
LAB: Introduction to R (Hallinan) [Lab Prep] [Handout]
Feb. 12: Independent contrasts and trait correlations (DDA) [Handout]
LAB: Intro to R continued: Phylogenies; Continuous characters (Hallinan) [Lab Prep] [Handout]
Feb. 17: Evolution and development - heterochrony (DRL) [Handout]
LAB: independent contrasts in R (Hallinan) [Lab Prep] [Handout] [Assignment Answers]
Feb. 19: Morphometrics (DRL) [Handout]
LAB: morphometrics applications (Hallinan) [Lab Prep] [Handout]
Feb. 24: Molecular evolution (BDM) [Handout]
Likelihood : Frequentis vs Bayesian Reasoning [Handout]
LAB: analysis of molecular evolution (Hallinan) [Lab Prep] [Handout]
Feb. 26: Gene family evolution; comparative genomics; evo-devo (BDM) [Handout]
LAB: tools for comparative genomics (Hallinan) [Lab Prep] [Handout]
March 3: Fossil data in phylogenetics (DRL)
LAB: discussion: the use of fossil data in phylogenetic reconstruction (all)
March 5: Tempo in macroevolution (DRL) [Handout]
LAB: PROJECT TOPIC DUE: discuss your potential project in class
March 10: Phylogenetics and adaptation (DDA, BDM, & DRL) [Handout]
LAB: discussion of adaptation (all)
March 12: Tree shape: phylogenies and macroevolution (Hallinan) [Handout]
LAB: generating random trees; testing cladogram imbalance (Hallinan) [Lab Prep] [Handout]
March 17: Adaptive radiations (DDA) [Handout1] [Handout2]
LAB: lineages through time; diversification analyses (Hallinan) [Lab Prep] [Handout]
March 19: Phylogenies and Community Ecology (DDA) [Handout]
LAB: phylocom (DDA, Hallinan) [Lab Prep] [Handout]
March 23 - 27: SPRING BREAK
March 31: Speciation and related issues: species revisited (BDM) [Handout]
LAB: discussion of species (all)
April 2: Phylogenetics and conservation biology (DDA) [Handout]
LAB: QUIZ 1
April 7: Reticulation and phylogenetics; "phylogeography" and population biology (BDM) [Handout]
LAB: coalescence theory; applications in population genetics (Hallinan; rm. 3056) [Lab Prep] [Handout]
April 9: Modes in macroevolution (DRL) [Handout]
LAB: Review old labs (Hallinan)
April 14: Comparing cladograms; supertrees (BDM) [Handout]
LAB: consensus methods; Brooks parsimony (Hallinan) [Lab Prep] [Handout]
April 16: Biogeography I -- basic principles; ecological vs. historical approaches (DRL) [Handout]
LAB: Biogeographic software; Treemap, Lagrange (Hallinan and Matzke) [Lab Prep] [Handout 1] [Lagrange Handout]
April 21: Biogeography II -- vicariance biogeography (DRL) [Handout]
LAB: discuss progress on projects in class
April 23: Interactions among clades in macroevolution (DRL) [Handout]
LAB: Help with projects (Hallinan)
April 28: Coevolution; symbiosis (DDA) [Handout] [Slides]
LAB: discussion of application papers (students to bring papers from their groups)
April 30: Assembly of regional biota (DDA) [Handout] [Slides]
LAB: Help with projects (Hallinan)
May 5: Macroevolution: putting it all together - patterns of diversification and extinction (DRL)
LAB: discussion on levels of selection (all)
May 7: Glimpses of the future - comparative and functional genomics; integrating genetics, physiology, ecology and evolution (DDA, BDM, & DRL)
LAB: QUIZ 2
May 13th: MiniSymposium 1PM - 8PM 2063 VLSB