Principles and Methods of Systematic Biology (EEB 5347)

From EEBedia
Revision as of 19:01, 14 October 2011 by ChrisOwen (Talk | contribs)

Jump to: navigation, search
2009 Class on top of the AMNH

Fall 2011

Lecture MW 9:00-10:30, Lab F 9:00-10:30

Instructor: Dr. David L. Wagner, TLS Rm 471
Phone: 486-2139
office hours as available
email: david.wagner'at'

Graduate Teaching Assistant: Chris Owen
Office hours: BioPharm 325 Wednesdays 10:30-11:30 or by appointment
Phone: 486-6650
email: christopher.l.owen'at'

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.


Supplementary Reading

Day Topics Reading/Assignment Lab
Aug 29 Class canceled due to Hurricane Irene
Lecture instead of lab this week
Aug 31 Organizational meeting, an introduction to biological systematics Pdficon small.gifHubbell.pdf (for Friday) (for Friday)
Pdficon small.gifMayr&Ashlock1991_pgs1-18.pdf (optional)
Sept 2 The many roles of biological systematics & collections tour Pdficon small.gifTempleton 1989.pdf
Pdficon small.gifDe Queiroz 2007.pdf
Pdficon small.gifFutuyma_spconcepts_445-451.pdf
Sept 5 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
Sept 7 Pdficon small.gifSpecies I 2011.pdf
Sept 9 Meet in library Meet in library
Sept 12 Pdficon small.gifSpecies II 2011.pdf Pdficon small.gifEhrlich&Raven1969.pdf Taxonomic resources: key websites, taxonomy exercise assigned (Meet in McCarthy Room, 4th floor TLS)
Sept 14 Pdficon small.gifSpecies III 2011.pdf
Sept 16 lab lab
Sept 19 Pdficon small.gifSubspecies 2011.pdf Intro to Mesquite and Morphological Matrices (Meet in McCarthy Room, 4th floor TLS)
Sept 21 Infrapopulation variation (lecture sent via email)
Sept 23 lab lab
Sept 26 Pdficon small.gifHigher Categories 2011.pdf Keys, species descriptions, and cybertaxonomy (Meet in McCarthy Room, 4th floor TLS)
Sept 28 Pdficon small.gifIntro to phylogenetic inference
Sept 30 lab lab
Oct 3 Pdficon small.gifForey et al 1992 Chap2&3.pdf
(only read chapter 2)
Pdficon small.gifPage & Holmes 1998.pdf
Manipulating molecular characters with Mesquite
and a BLAST tutorial (Meet in McCarthy Room, 4th floor TLS)
Oct 5 Pdficon small.gifCharacters_1 2011.pdf Pdficon small.gifKrell&Cranston.pdf
Pdficon small.gifFelsenstein2004.pdf
Oct 7 lab lab
Oct 10 Pdficon small.gifMultivariate Methods 2011.pdf Parsimony and distant methods with PAUP (Meet in McCarthy Room, 4th floor TLS)
Oct 12 Pdficon small.gifDistance Methods 2011.pdf
Pdficon small.gifParsimony 2011.pdf
Pdficon small.gifParsimonyLectureForMidTerm.ppt
Pdficon small.gifPage&Holmes_Chap6.pdf
Oct 14 lab lab
Topics Additional Reading
Species as ranked taxa and species concepts Pdficon small.gifApplication of Evolutionary Species concept.pdf Pdficon small.gifSpecies concept for prokaryotes.pdf Pdficon small.gifIs the BSC showing its age?.pdf
Pdficon small.gifImportance of stating species concept for conservation purposes.pdf Pdficon small.gifImpact of species concepts on biodiversity studies.pdf
Pdficon small.gifThe need for specifying species concepts.pdfPdficon small.gifOn the failure of modern species concepts.pdf Pdficon small.gifSpecies as ranked taxa.pdf

Pdficon small.gifDoes the choice of species concept result in an increase in bird species?.pdf Pdficon small.gifMethod for delimiting Cohesion speceis.pdf

DNA Barcodes Pdficon small.gifElias et al. 2007.pdf
Pdficon small.gifJanzen et al 2005.pdf
Pdficon small.gifTen Reasons For Barcoding.pdf
Pdficon small.gifWill & Rubinoff 2004.pdf
Pdficon small.gifHebert and Gregory 2005.pdf
Pdficon small.gifMoritz and Cicero 2004.pdf
Pdficon small.gifHebert et al.2003.pdf
Pdficon small.gifPLoS_Birds_Hebert et al. 2004.pdf


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 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.
Pdficon small.gifFunding for biodiversity and taxonomy 2010.pdf

Important dates

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