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 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 Pdficon small.gif 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 Pdficon small.gif
Templeton (1989)Pdficon small.gif
Sep 4 Labor Day, No class Kevin away in Mexico
Babbidge Library resources; taxonomic literature
Sept 6 Species definitions & species intermediacy
Species 1 Lecture Pdficon small.gif
Finish reading/reread Templeton from Friday
DeQuieroz (2007)Pdficon small.gif
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 Pdficon small.gif
Erlich & Raven (1969)Pdficon small.gif
Mallet (2013) Pdficon small.gif
Meet in McCarthy Room
Taxonomic resources: key websites; taxonomy exercise Pdficon small.gif.
Online Resource List Pdficon small.gif
BioBlitz in Stamford.
Sept 13 Subspecies and geographic variation Pdficon small.gif 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 Pdficon small.gif
Notes Pdficon small.gif
Intro to Mesquite exercise Pdficon small.gif
(Wagner away on Friday)
Sept 20 Supraspecific taxa or Higher Categories Pdficon small.gif
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 Pdficon small.gif
A bit on descriptions and reading taxonomic literature Pdficon small.gif
External anatomy of tiger beetles Pdficon small.gif
(Wagner away)
Sept 27 Start Infraspecific variation or "packaging" of variation Pdficon small.gif Schuh and Brower 2009 (pp 131-140) Pdficon small.gif
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") Pdficon small.gif
Oct 4 Phylogenetic inference: mostly a historical overview Pdficon small.gif, Begin: Trees and Characters Pdficon small.gif Page and Holmes (1998)Pdficon small.gif
Krell and Cranston (2004)Pdficon small.gif
Tree View of Life Pdficon small.gif
Oct 6 lab
Oct 9 End: Trees and characters, Parsimony Pdficon small.gif 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") Pdficon small.gif
Oct 13 Head to NYC
NYC Trip Reference Pdficon small.gif
Oct 16 Tree reliability, sensitivity, and support measures IPdficon small.gif Lab: Finish last week's lab + phylogenetic inference
Oct 18 Tree reliability, sensitivity, and support measures II
Oct 20 lab
Oct 23 Maximum Likelihood (Lewis) Lab: Tree reliability and measures
(Meet in McCarthy Room, 4th floor TLS)
Oct 25 Bayesian Inference (Lewis)
Oct 27 lab
Oct 30 Multivariate and distance methods I Lab: neighbor-joining and correcting distance data (Meet in McCarthy Room, 4th floor TLS)
Nov 1 Multivariate and distance methods II
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
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 Thanksiving Thanksiving
Nov 22
Nov 24
Nov 27 Nomenclature Lab: Mesquite; character optimization; character correlation
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