Difference between revisions of "Principles and Methods of Systematic Biology (EEB 5347)"

Revision as of 15:30, 11 September 2017

This article is still under construction. Expect it to change frequently until this notice is removed.

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	Molecular systematics in animals (Simon Guest Lecture)		Lab: Find and analyze your own data set; COI problem, WEDNESDAY, not Friday (Meet in McCarthy Room, 4th floor TLS)
Nov 15	Lab Today, not Friday!	lab
Nov 17	Nomenclature	See the many optional nomenclature readings below.
Nov 20	Nomenclature, James Prosek will join our discussion today, it should be quite a class	DeQueiroz Phylocode 2006 Vane-Wright Nomenclature Concern Name Poems The Phylocode Reading 2009 (http://www.ohiou.edu/phylocode/preface.html) Linnaean naming system challenges 2004 (http://www.newscientist.com/article.ns?id=dn6369) / ADDITIONALLY, choose one phylocode reading from the optional ones loaded below	Lab: Mesquite; character optimization; character correlation (Meet in McCarthy Room, 4th floor TLS)
Nov 22	Nomenclature; Phylocode
Nov 24	Lab	Lab
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)

Supplementary Reading

Topics	Additional Reading
Species as ranked taxa and species concepts	Application of Evolutionary Species concept.pdf Species concept for prokaryotes.pdf Is the BSC showing its age?.pdf Importance of stating species concept for conservation purposes.pdf Impact of species concepts on biodiversity studies.pdf The need for specifying species concepts.pdfOn the failure of modern species concepts.pdf Species as ranked taxa.pdf Does the choice of species concept result in an increase in bird species?.pdf Method for delimiting Cohesion speceis.pdf
DNA Barcodes	Elias et al. 2007.pdf Janzen et al 2005.pdf Ten Reasons For Barcoding.pdf Will & Rubinoff 2004.pdf Hebert and Gregory 2005.pdf Moritz and Cicero 2004.pdf Hebert et al.2003.pdf PLoS_Birds_Hebert et al. 2004.pdf Janzen et al., 2009. Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity. Molecular Ecology Resources 9(supplement 1):1-26. http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2009.02628.x/abstract Janzen and Hallwachs 2011 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018123 Joly et al. 2013, Ecology in the age of DNA barcoding: the resource, the promise, and the challenges ahead
Optional Nomenclature Readings	Schuh & Brower 2009 Jones and Luchsinger Conniff 1996 Gould 1990
Optional Phylocode Readings	Benton 2007 Donoghue and Gauthier Lee and Skinner 2007 Nixon et al. 2003 Rieppel 2006 Platnick 2012 DeQueiroz 2013 DeQueiroz and Donoghue 2011 DeQueiroz and Donoghue 2013 DeQueiroz 2012

Grading

Term paper

Each student will be required to prepare a paper that will be due on December 2nd. 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 October 10th, 2013. 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 (May change a bit)

7 October, 2013: Paper Topic Due
14 October, 2013: Brief Outline with 5 references
14 October, 2013: Midterm
11 November, 2013: First draft due (May change)
7 December, 2013: Paper due (May change)

EEB5347 website from 2011 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/EEB5347_2011)