Principles and Methods of Systematic Biology (EEB 5347)
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 F 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 A Bit on Names |
Templeton (1989) | |
Sep 4 | Labor Day, No class | Kevin away in Mexico Babbidge Library resources; taxonomic literature | |
Sept 6 | Species definitions & species intermediacy Species 1 Lecture |
Finish reading/reread Templeton from Friday DeQuieroz (2007) | |
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 | Finish species definitions & species intermediacy; start variation within species Species II Lecture |
Erlich & Raven (1969) Mallet (2013) |
Meet in McCarthy Room Taxonomic resources: key websites; taxonomy exercise . Online Resource List BioBlitz in Stamford. |
Sept 13 | Subspecies and geographic variation | Send Wagner an example (~3 ppt slides) of intraspecific geographic variation before 11:59 PM Sunday | |
Sept 15 | lab | ||
Sept 18 | Variation within a genotype: ontogeny & phenotypic plasticity | Send Wagner an example (~3 ppt slides) of intraspecific non-geographic variation before 11:59 PM Tuesday | Lab: Alpha taxonomy: finding taxonomic characters & keys; descriptions and diagnoses; taxonomic cybertools for alpha taxonomy and phylogenetics Slides Notes Intro to Mesquite exercise (Wagner away on Friday) |
Sept 20 | Supraspecific taxa or Higher Categories | ||
Sept 22 | lab | ||
Sept 25 | Supraspecific taxa or Higher Categories | Lab: Describing and diagnosing species; Keys; Taxonomic cybertools: DELTA, Lucid, MANTIS A bit on keys A bit on descriptions and reading taxonomic literature | |
Sept 27 | Start Infraspecific variation or "packaging" of variation | Schuh and Brower 2009 (pp 131-140) | |
Sept 29 | Continue Infraspecific variation or "packaging" of variation | ||
Oct 2 | Finish Infraspecific variation or "packaging" of variation | Lab: GenBank and DNA Sequence Data (right-click "save as") | |
Oct 4 | Phylogenetic inference: mostly a historical overview , Begin: Trees and Characters | Page and Holmes Ch. 2 pp 11-36 Krell and Cranston (2004) Tree View of Life | |
Oct 6 | lab | ||
Oct 9 | End: Trees and characters, Parsimony | Lab: Trip to American Museum of Natural History and Bronx Zoo in NYC!!! Photo Album | |
Oct 11 | Midterm exam Sample questions (right click "save as") | ||
Oct 13 | Head to NYC NYC Trip Reference |
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Oct 16 | Tree reliability, sensitivity, and support measures I | Page and Holmes Ch.6 pp. 209-227 | Lab: Review midterm, Finish last week's lab, any extra time work on key/description/diagnoses |
Oct 18 | Tree reliability, sensitivity, and support measures II | Page and Holmes Ch. 6 pp 172-208 | |
Oct 20 | lab | ||
Oct 23 | Maximum Likelihood (Lewis) | Key, Description, and Diagnoses due!!! | Lab: Phylogenetic Inference using distance and parsimony with PAUP*: UPGMA, neighbor-joining, bootstrap, and jackknife Lab 5 (right-click "save-as") Primate COI data (right-click "save-as") |
Oct 25 | Bayesian Inference (Lewis) | ||
Oct 27 | lab | ||
Oct 30 | Midterm Q&A Multivariate and distance methods I Multivariate Methods Distance Methods |
Lab: Examining and correcting distance data in PAUP* Exercise (right click "save-as") Nexus File (right click "save-as") | |
Nov 1 | Multivariate and distance methods II | ||
Nov 3 | lab | ||
Nov 6 | Molecular systematics in animals (Simon) (Wagner in Denver) | Lab: Maximum Likelihood, Model Choice, and CIPRES | |
Nov 8 | Molecular systematics in plants (Les) | ||
Nov 10 | lab | ||
Nov 13 | Data partitions; consensus; comparing trees | Lab: Bayesian Inference | |
Nov 15 | DNA barcoding | ||
Nov 17 | lab | ||
Nov 20 | Thanksiving | Thanksiving | Thanksiving |
Nov 22 | |||
Nov 24 | |||
Nov 27 | Nomenclature | Lab: Spread Your Wings | |
Nov 29 | Nomenclature; Phylocode | ||
Dec 1 | lab | ||
Dec 4 | Phylogenetic trees & evolutionary processes | No lab this week | |
Dec 6 | Special topic: Taxonomic collections | ||
Dec 8 | Special topic: Systematics and conservation biology and the future of biological systematics | ||
Dec circa 15 | Final: 8-11 AM (Bamford) |
Grading
Item | Percentage | Points |
---|---|---|
Lab and take home exercises | 25 |
250
|
Midterm Exam | 20 |
200
|
Paper | 25 |
250
|
Nomenclature Exercise | 2 |
20
|
Class Participation | 3 |
30
|
Final Exam | 25 |
250
|
Total | 100 |
1000
|
Term Paper
Each student will be required to prepare a paper that will be due on December 2. Acceptable styles: (1) a literature review that is structured to be a thesis chapter; (2) grant proposal; (3) stand-alone review a subject relevant to systematic theory or methodology.
Important Dates
Date | Milestone |
---|---|
6 October 2017 | conference; topic selection |
20 October 2017 | outline with 5+ references |
17 November 2017 | first draft due |
1 December 2017 | paper due |