| WEEK | TOPICS |
| Aug 27-31 | Organizational meeting; an introduction to biological systematics,
lecture notes The many roles of biological systematics & collections tour Species definitions & species intermediacy Lecture handouts: Basic Definitions, Species Level Terminology, Species Definitions | Sept 3 | Labor Day, no lecture | Sept 5-7 | Species definitions & species intermediacy cont.,
lecture slides Lab 1: Taxonomic literature (visit to the library and lecture by Carolyn Mills in Level 1 Classroom) Taxonomic resources: some key websites, Taxonomic reference material, Search for Zoological Names, Intro to pronunciation of scientific names, Lab 1 Exercise |
Sept 10-14 | Subspecies and geographic variation,
lecture slides;
individual variation (population variation),
lecture slides Reading: Ehrlich and Raven 1969 Lab 2: Tiger beetle exercise: finding taxonomic characters & building keys; descriptions and diagnoses; introduction to MacClade's alpha taxonomic features , A Beetle's Last Stand |
Sept 17-21 | Variation within a genotype: ontogeny & phenotypic plasticity Supraspecific taxa, lecture slides Lab 3: Tiger beetle exercise: introduction to keys; specimen/museum databases and online keys: DELTA, MANTIS, Linnaeus II, Lucid, BioLink |
Sept 24-28 | Phylogenetic inference: an overview,
lecture slides;
readings from Science: Charting the Evolutionary History
of Life,
modernizing the tree of life,
Page & Holmes Taxonomic characters: types, polarity and order, weighting and step matrices, lecture slides 1, lecture slides 2 Lab 4: character coding, Wagner algorithm, rooting and polarization |
Oct 1-5 | Continuous characters and multivariate techniques,
lecture slides Phenetics, evolutionary taxonomy, and cladistics, lecture slides Lab 5: Introduction to PAUP* and MacClade: working with a molecular data set, data set, lab exercise Term paper: conference; topic selection |
Oct 8-12 | Midterm - sample questions Molecular systematics in animals (Simon) Lab 6: Parsimony, lab exercise |
Oct 15-19 | Maximum likelihood (Lewis),
lecture slides Bayesian inference (Lewis), lecture slides Lab 7: Maximum Likelihood, Modeltest, Garli, lab exercise, Modeltest PAUP block, ML bootstrap trees Term paper: outline with 5+ references |
Oct 22-26 | Molecular systematics in plants (Les) Distance methods: correcting distance data, neighbor-joining, etc., lecture slides Lab 8: Bayesian Inference, MrBayes, MrBayes_analyses |
Oct 29-Nov 2 |
Reliability and measures of tree support: c.i., r.i., decay indices,
lecture slides Consensus, data partitions, and total evidence, Bootstraps, randomization tests, lecture slides Lab 9: Partition Homogeneity Test, Bayes factors, and tests of phylogenetic hypotheses |
Nov 5-9 |
Comparing trees, lecture slides Taxonomic collections, Natural History Museum Collections in the 21st Century Lab 10: Morphological databases and virtual taxonomic collections, Brooke 2000, reply I, reply II |
Nov 10-11 | American Museum Field Trip | Nov 12-16 | Biological classification; nomenclature,
lecture slides; handouts: type definitions, funny or curious zoological names readings: Lee and Skinner, Benton, Donoghue and Gauthier, Nixon et al., Sereno, Berenbaum Lab 11: character evolution, MacClade folder, Mesquite folder, Mesquite web site |
Nov 19-23 | Thanksgiving break, no classes | Nov 26-30 | Term paper: first draft due on Nov 26 Special topic: Phylogenetic trees & evolutionary processes, lecture slides |
Dec 3-7 | Special topic: Systematics and conservation biology,
lecture slides Special topic: The future of biological systematics, lecture slides Readings: Preserving the Tree of Life, DNA Barcoding - Intro, DNA Barcoding - Perils, DNA Barcoding - Promises |
Dec 13 | Term paper due |
© 2007 Department of Ecology and Evolutionary Biology,
The University of Connecticut.
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Last modified: 27 August 2007
