Principles and Methods of Systematic Biology (EEB 5347)
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Fall 2017
Lecture MW 9:05-10:45 In TLS 313
Lab F 9:05-10:45 McCarthy Room, 4th floor TLS
Instructor: Dr. David L. Wagner, TLS Rm 471
Phone: 486-2139
office hours open; best to call or email ahead
email: david.wagner'at'uconn.edu
Graduate Teaching Assistant: Kevin Keegan
Office hours: TLS 461 MWF 10:45-11:45 or by appointment
Phone: 617-272-5054
email: kevin.keegan'at'uconn.edu
Textbook and readings
There is no assigned text. Generally you can expect one or two readings to be assigned for each lecture. Most readings will be available as PDFs, downloadable from the course website.
Schedule
Day | Topics | Reading/Assignment | Lab |
---|---|---|---|
Aug 28 | Organizational meeting | Hubbell Reading | Dave away in Fort Collins Introduction to McCarthy Room; Collections tour with Dr. Jane O'Donnell; Species concept discussion and letter to yourself |
Aug 30 | An introduction to biological systematics; The many roles of biological systematics and collections |
||
Sep 1 | Species definitions & species intermediacy |
Templeton (1989) | |
Sep 4 | Labor Day, No class | Kevin away in Mexico Babbidge Library resources; taxonomic literature | |
Sept 6 | Species definitions & species intermediacy |
Finish reading/reread Templeton from Friday | |
Sept 8 | Lab, Meet in library Room EC1, walking in through the main entrance, go straight back and up to level 1, then see this map (http://www.lib.uconn.edu/maps/Level1EC12013.pdf), you will be coming out of the stairs in the center of the map | ||
Sept 11 | Species definitions & species intermediacy; start variation within species | Taxonomic resources: key websites; taxonomy exercise. BioBlitz in Stamford. Online Resource List | |
Sept 13 | Subspecies and geographic variation | ||
Sept 15 | lab | ||
Sept 18 | Variation within a genotype: ontogeny & phenotypic plasticity | Lab: Alpha taxonomy: finding taxonomic characters & keys; descriptions and diagnoses; taxonomic cybertools for alpha taxonomy and phylogenetics (Wagner away on Friday) | |
Sept 20 | Supraspecific taxa | ||
Sept 22 | lab | lab | |
Sept 25 | Supraspecific taxa | Lab: Describing and diagnosing species; specimen/museum databases; Taxonomic cybertools: DELTA, MANTIS, Mesquite & others (Wagner away)
Phylogenetic inference | |
Sept 27 | Phylogenetic inference: mostly a historical overview | ||
Sept 29 | lab | lab | |
Oct 2 | Trees and characters: types of dendrograms, rooting and polarization | Lab: Mesquite II, Parsimony??? | |
Oct 4 | Taxonomic characters: polarity, outgroups, order, weighting, and step matrices | ||
Oct 6 | lab | lab | |
Oct 9 | Parsimony; tree searches; tree statistics | Lab: Trip to American Museum of Natural History and Bronx Zoo in NYC!!! | |
Oct 11 | Midterm exam | ||
Oct 13 | Head to NYC | ||
Oct 16 | Maximum likelihood (lecture by Lewis; Wagner away) | Lab: likelihood (Garli and/or RAxML) and Bayesian analyses | |
Oct 18 | Bayesian inference (lecture by Lewis; Wagner away) | ||
Oct 20 | lab | lab | |
Oct 23 | Tree reliability, sensitivity, and support measures I | Lab: Tree reliability and measures (Meet in McCarthy Room, 4th floor TLS) | |
Oct 25 | Tree reliability, sensitivity, and support measures II | ||
Oct 27 | Lab | ||
Oct 30 | Multivariate and distance methods | Lab: neighbor-joining and correcting distance data (Meet in McCarthy Room, 4th floor TLS) | |
Nov 1 | Bayesian inference (Lewis Guest Lecture) | ||
Nov 3 | lab | ||
Nov 6 | Molecular systematics in animals (Simon) (Wagner in Denver) | Lab: PAUP*: ModelTest; molecular clocks; AIC et al. (Meet in McCarthy Room, 4th floor TLS) | |
Nov 8 | Molecular systematics in plants (Les) | ||
Nov 10 | lab | lab | |
Nov 13 | Data partitions; consensus; comparing trees | Lab: Find and analyze your own data set; COI problem (Meet in McCarthy Room, 4th floor TLS) | |
Nov 15 | DNA barcoding | ||
Nov 17 | Lab | ||
Nov 20 | Thanksiving | ||
Nov 22 | |||
Nov 24 | |||
Nov 27 | Thanksgiving Recess | Thanksgiving Recess, Do NOT meet in McCarthy Room | |
Nov 29 | Thanksgiving Recess | ||
Dec 1 | Thanksgiving Recess | ||
Dec 4 | Special topic: Nomenclature 2 | No lab this week DO NOT Meet in McCarthy Room | |
Dec 6 | Special topic: Taxonomic collections | Mares 2009 Thomson 2005 BioScience (http://www.actionbioscience.org/evolution/thomson.html) | |
Dec 8 | Special topic: Phylogenetic trees & evolutionary processes | ||
Dec circa 15 | Final: 8-11 AM (Bamford) |
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