Syllabus [PDF]
Jan. 16: Introduction
to aims of course / Phylogenetic reconstruction in a nutshell: homology (BDM) [Handout]
LAB: Get acquainted roundtable
Jan. 18: Phylogenetic
reconstruction in a nutshell: characters (BDM) [Handout]
LAB:
tour of systematics collections & resources in VLSB
Jan. 23: Phylogenetic
reconstruction in a nutshell: trees (BDM)
[Handout]
LAB:
Introduction to MacClade (Hallinan; library comp. room) [Handout]
Jan. 25: Phylogenetic
reconstruction in a nutshell: classification, traditional and modern (BDM) [Handout]
LAB:
MacClade continued (Hallinan; library comp. room) [Handout] [Examples]
Jan. 30: What
can we do with trees once we have them?
Discussion of "tree-thinking" (BDM & DDA)
LAB:
Introduction to PAUP (Hallinan; library
comp. room) [Handout]
Feb. 1: Qualitative
character evolution within a cladogram (discrete states; ancestral state
reconstructions; single characters and comparing two or more characters - DDA) [Handout]
LAB:
Introduction to
Feb. 6: Maximum
likelihood reconstruction of discrete states (DDA) [Handout]
LAB:
Correlation of Discrete Characters
(Hallinan; library comp. room) [Handout]
Feb.
8: Quantitative character
evolution within a cladogram (intro; ancestral trait reconstruction - DDA) [Handout]
LAB:
Feb. 13 What
is phylogenetic conservatism and how do you measure it? (DDA) [Handout]
LAB:
Testing for conservatism in one character (DDA) [Handout]
Feb. 15: Independent
contrasts and trait correlations (DDA) [Handout1] [Handout2]
LAB:
PROJECT TOPIC DUE: discuss your
potential project in class
Feb. 20: Evolution
and development - heterochrony (BDM) [Handout]
LAB:
Intro. to morphometrics (Hallinan; rm. 3056) [Handout]
Feb. 22: Molecular
evolution (BDM) [Handout]
LAB:
analysis of molecular evolution (Hallinan; rm. 3056) [Handout] [Examples]
Feb. 27: Brownian
motion and evolutionary modes (DDA) [Handout1]
[Handout2]
LAB:
Independent Contrasts Using Mesquite
(Hallinan; library comp. room) [Handout] [Examples]
March 1: More
on continuous character evolution (DDA)
[Handout1] [Handout2]
LAB:
Contrasts on unresolved trees (Hallinan; library comp. room) [Handout] [Examples]
March 6: Phylogenetics
and adaptation (BDM & DDA) [Handout]
LAB:
discussion of adaptation (all)
March 8: Comparing
sister clades within a cladogram: the shape of evolution (BDM) [Handout]
LAB:
generating random trees; testing cladogram imbalance (Hallinan; library comp.
room) [Handout] [Examples]
March 13: Adaptive
radiations (DDA) [Handout]
LAB:
discuss progress on projects in class
March 15: Reticulation
and phylogenetics; "phylogeography" and population biology (BDM) [Handout]
LAB: coalescence theory; applications in
population genetics (Hallinan; rm. 3056)
[Handout] [Examples]
March 20: Maximum
likelihood and Bayesian approaches to hypothesis testing (J. Huelsenbeck)
LAB:
practice in quantitative hypothesis testing (J. Huelsenbeck)
March 22: Speciation and related issues: species revisited (BDM) [Handout]
LAB: QUIZ 1 (through March 15th)
March 26 - 30: SPRING
BREAK
April 3: Comparing
cladograms (BDM) [Handout]
LAB:
consensus methods; Brooks parsimony (Hallinan) [Handout] [Examples]
April 5: Phylogenies
and Community Ecology (DDA) [Handout]
LAB:
Community Ecology (rm. 3056) [Handout]
April 10: Biogeography I -- basic principles; ecological vs.
historical approaches (BDM) [Handout]
LAB:
biogeography algorithms (rm. 3056) (Hallinan) [Handout] [Examples]
April 12: Biogeography II -- vicariance biogeography (BDM) [Handout]
LAB:
discuss progress on projects in class
April
17: Coevolution; symbiosis (DDA)
[Handout1] [Handout2]
LAB:
discussion of application papers (students to bring papers from their groups)
April 19: Phylogenetics and conservation biology (DDA) [Handout1] [Handout2]
LAB:
discussion of application papers (students to bring papers from their groups)
April 24: Paleontology
and phylogenetic systematics (D. Lindberg) [Handout]
LAB:
discussion: the use of fossil data in phylogenetic reconstruction (all)
April 26: Dating
in the 21st Centrury: putting dates on nodes, characters, and events (BDM) [Handout]
LAB:
Practice dating; relative rate tests; the molecular clock? (Hallinan) (rm. 3056) [Handout] [Examples]
May 1: Macroevolution:
putting it all together - patterns of diversification and extinction (BDM) [Handout]
LAB: discussion on levels of selection (all)
May 3: Glimpses
of the future (comparative and functional genomics; integrating genetics,
physiology, ecology
and
evolution - BDM & DDA) [Handout1]
[Handout2] [Handout3]
LAB:
discuss progress on projects in class
May 8: Conclusions:
the central role of phylogenetic systematics in comparative biology (BDM &
DDA)
LAB:
QUIZ 2
May 11-18: FINALS WEEK -- student minisymposium -- projects due