Principles and Methods of Systematic Biology (EEB 5347)
Fall 2013
Lecture MW 9:05-10:35, Lab F 9:05-10:35
Instructor: Dr. David L. Wagner, TLS Rm 471
Phone: 486-2139
office hours as available
email: david.wagner'at'uconn.edu
Graduate Teaching Assistant: Russ Meister
Office hours: BioPharm 323 TBD
Phone: 486-3947
email: russell.meister'at'uconn.edu
Contents
Textbook and readings
There is no assigned text. Generally you can expect one or two readings to be assigned for each lecture. Many readings will be available as pdfs, downloadable from the course website. Others, available in hard copy only, will be on reserve in the departmental office (TLS 312) in the filing cabinet next to the window. You are free to check out copy #2 for 3 hours; copy #1 should stay in the office, i.e., so one is always there for others to photocopy.
Schedule (Will be updated soon)
Day | Topics | Reading/Assignment | Lab |
---|---|---|---|
Aug 26 | Organizational meeting; an introduction to biological systematics |
Lecture instead of lab this week | |
Aug 28 | The many roles of biological systematics | ||
Aug 30 | Species definitions & species intermediacy & collections tour | ||
Sept 2 | Labor Day, No class | Babbidge Library resources; taxonomic literature Meet in Babbidge library electronic classroom 1 (EC1) on level 1, to the left and behind Info Cafe 1 (http://classguides.lib.uconn.edu/content.php?pid=238531&sid=1968055) | |
Sept 4 | Species definitions & species intermediacy | ||
Sept 6 | Lab, Meet in library Room EC1 | Meet in library | |
Sept 9 | Species definitions & species intermediacy; variation within species | Taxonomic resources: key websites, taxonomy exercise assigned (Meet in McCarthy Room, 4th floor TLS) | |
Sept 11 | Subspecies and geographic variation | ||
Sept 13 | lab | lab | |
Sept 16 | Variation within a genotype: ontogeny & phenotypic plasticity | Lab: Alpha taxonomy: finding taxonomic characters & keys; descriptions and diagnoses; introduction to Mesquite’s alpha taxonomic features (Meet in McCarthy Room, 4th floor TLS) | |
Sept 18 | Supraspecific taxa | ||
Sept 20 | lab | lab | |
Sept 23 | Phylogenetic inference: mostly a historical overview | Describing and diagnosing species; specimen/museumdatabases DELTA, MANTIS & other taxonomic computer tools Lab: NYC field trip (Meet in McCarthy Room, 4th floor TLS) | |
Sept 25 | Phylogenetic inference: mostly a historical overview | ||
Sept 27 | lab | lab | |
Sept 30 | Trees and characters; types of dendrograms; rooting and polarization |
Lab: Mesquite II (Meet in McCarthy Room, 4th floor TLS) | |
Oct 2 | Taxonomic characters: polarity, outgroups, order, weighting, and step matrices | ||
Oct 4 | lab | lab | |
Oct 7 | Distance methods, UPGMA, neighbor-joining, correcting distance data, multivariate methods | Lab: Neighbor-joining and corrected distances; PAUP* (introduction) (Meet in McCarthy Room, 4th floor TLS) | |
Oct 9 | Parsimony; search algorithms; algorithmic power, accuracy, and inconsistency | ||
Oct 11 | lab | lab | |
Oct 14 | Midterm exam | Parsimony with PAUP (Meet in McCarthy Room, 4th floor TLS) | |
Oct 16 | Midterm Review | ||
Oct 18 | lab | lab | |
Oct 21 | lab | lab | Lab: PAUP*: tree searches; tree statistics (Meet in McCarthy Room, 4th floor TLS) |
Oct 23 | Reliability and measures of tree support | ||
Oct 25 | No Lab/AMNH & Bronx Zoo Trip | ||
Oct 28 | lab | lab | Lab: Likelihood (Garli and/or RAxML) and Bayesian analyses (Meet in McCarthy Room, 4th floor TLS) |
Oct 30 | Maximum likelihood (Lewis Guest Lecture) | ||
Nov 1 | Bayesian inference (Lewis Guest Lecture) | ||
Nov 4 | Data partitions; consensus; comparing trees | Lab: PAUP*: ModelTest; molecular clocks; AIC et al. (Meet in McCarthy Room, 4th floor TLS) | |
Nov 6 | Molecular systematics in plants (Les Guest Lecture) | ||
Nov 8 | lab | lab | |
Nov 11 | Molecular systematics in animals (Simon Guest Lecture) | COI Barcoding and analyzing your own data sets (Meet in McCarthy Room, 4th floor TLS) | |
Nov 13 | lab | lab | |
Nov 15 | DNA barcoding | ||
Nov 18 | Nomenclature | Lab: Mesquite; character optimization; character correlation (Meet in McCarthy Room, 4th floor TLS) | |
Nov 20 | Nomenclature; Phylocode | ||
Nov 22 | Lab | Lab | |
Nov 25 | Nomenclature![]() |
Mesquite and R: Ancestral states and character correlation (Meet in McCarthy Room, 4th floor TLS) | |
Nov 27 | Nomenclature; phylocode | ||
Nov 29 | lab | lab | |
Dec 2 | Patterns and process![]() ![]() |
No lab this week DO NOT Meet in McCarthy Room | |
Dec 4 | Taxonomic collections![]() |
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Dec 6 | Biodiversity Crisis and Future of Systematics![]() |
Lab and take home exercises | 20% | 200 pts |
Midterm | 20% | 200 pts |
Term paper | 22% | 220 pts |
Nomenclature exercise | 1% | 10 pts |
Participation | 2% | 20 pts |
Final | 35% | 350 pts |
Total | 100% | 1000 pts |
Term paper
Each student will be required to prepare a paper that will be due on December 4th. Styles that have been adopted in the past include (1) a literature review
that could be incorporated into a thesis chapter or (2) an NSF Doctoral Dissertation Improvement Grant proposal. Another angle would be to (3) review a subject relevant to systematic theory or methodology. If you are considering the DDIG option this year's Dissertation Improvement Grants will be due on 20 November. Visit http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5234 htm
Funding sources for taxonomy and biodiversity
Here is a comprehensive guide to potential funding sources for taxonomy and biodiversity studies. It was created in 2010, so most sources are up to date.
Funding for biodiversity and taxonomy 2010.pdf
Important dates (To be updated soon)
7 October, 2011: conference; topic selection
17 October, 2011: midterm
21 October, 2011: outline with 5+ references
18 November, 2011: first draft due
2 December, 2011: paper due