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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) 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: May 16: Student minisymposium @ May 19: Projects due @ |
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