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

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(Schedule (Will be updated soon))
(Schedule (Will be updated soon))
Line 65: Line 65:
|Oct 4 || lab || lab
|Oct 4 || lab || lab
|Oct 7 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Multivariate%20Methods%202011.pdf}}Multivariate Methods 2011.pdf || || rowspan="3"| Parsimony and distant methods with PAUP '''(Meet in McCarthy Room, 4th floor TLS)'''
|Oct 7 || || || rowspan="3"| Parsimony and distant methods with PAUP '''(Meet in McCarthy Room, 4th floor TLS)'''
|Oct 9 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Distance%20Methods%202011.pdf}}Distance Methods 2011.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Parsimony%202011.pdf}}Parsimony 2011.pdf <br/> {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/ParsimonyLectureForMidTerm.ppt}}ParsimonyLectureForMidTerm.ppt ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes_Chap6.pdf}}Page&Holmes_Chap6.pdf
|Oct 9 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Distance%20Methods%202011.pdf}}Distance Methods 2011.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Parsimony%202011.pdf}}Parsimony 2011.pdf <br/> {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/ParsimonyLectureForMidTerm.ppt}}ParsimonyLectureForMidTerm.ppt ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes_Chap6.pdf}}Page&Holmes_Chap6.pdf

Revision as of 14:48, 22 August 2013

2009 Class on top of the AMNH
2011 Class on top of the AMNH

Fall 2013

Lecture MW 9:05-10:35, Lab F 9:05-10:35

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

Graduate Teaching Assistant: Russ Meister
Office hours: BioPharm 323 TBD
Phone: 486-3947
email: russell.meister'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. 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.

Schedule (Will be updated soon)

Day Topics Reading/Assignment Lab
Aug 26 Organizational meeting; an introduction to biological systematics
Lecture instead of lab this week
Aug 28 The many roles of biological systematics
Aug 30 Species definitions & species intermediacy & collections tour
Sept 2 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 (http://classguides.lib.uconn.edu/content.php?pid=238531&sid=1968055)
Sept 4 Species definitions & species intermediacy
Sept 6 Lab, Meet in library Room EC1 Meet in library
Sept 9 Species definitions & species intermediacy; variation within species Taxonomic resources: key websites, taxonomy exercise assigned (Meet in McCarthy Room, 4th floor TLS)
Sept 11 Subspecies and geographic variation
Sept 13 lab lab
Sept 16 Variation within a genotype: ontogeny & phenotypic plasticity Lab: Alpha taxonomy: finding taxonomic characters & keys; descriptions and diagnoses; introduction to Mesquite’s alpha taxonomic features (Meet in McCarthy Room, 4th floor TLS)
Sept 18 Supraspecific taxa
Sept 20 lab lab
Sept 23 Phylogenetic inference: mostly a historical overview Describing and diagnosing species; specimen/museumdatabases DELTA, MANTIS & other taxonomic computer tools Lab: NYC field trip (Meet in McCarthy Room, 4th floor TLS)
Sept 25 Phylogenetic inference: mostly a historical overview
Sept 27 lab lab
Sept 30 Trees and characters; types of dendrograms;
rooting and polarization
Lab: Mesquite II (Meet in McCarthy Room, 4th floor TLS)
Oct 2 Taxonomic characters: polarity, outgroups, order, weighting, and step matrices
Oct 4 lab lab
Oct 7 Parsimony and distant methods with PAUP (Meet in McCarthy Room, 4th floor TLS)
Oct 9 Pdficon small.gifDistance Methods 2011.pdf
Pdficon small.gifParsimony 2011.pdf
Pdficon small.gifParsimonyLectureForMidTerm.ppt
Pdficon small.gifPage&Holmes_Chap6.pdf
Oct 11 lab lab
Oct 14 Midterm exam Pdficon small.gifPageHolmesChptr5.pdf Parsimony with PAUP (Meet in McCarthy Room, 4th floor TLS)
Oct 16 Midterm Review
Oct 18 lab lab
Oct 21 lab lab PAUP*: tree searches and tree statistics
(Meet in McCarthy Room, 4th floor TLS)
Oct 23 Pdficon small.gifReliability 2011.pdf
Oct 25 No Lab/AMNH & Bronx Zoo Trip Pdficon small.gifLewis_2001_TREE.pdf
Pdficon small.gifHolder&Lewis2003_NatRevGen.pdf
Oct 28 lab lab Model comparison with Modeltest (Meet in McCarthy Room, 4th floor TLS)
Oct 30 Pdficon small.gifGuest Lecture Paul Lewis
Nov 1 Pdficon small.gifGuest Lecture Paul Lewis
Nov 4 Data partitions; consensus; comparing tree topologies
Pdficon small.gifConsensus 2011.pdf
Maximum likelihood and Bayesian inference (Meet in McCarthy Room, 4th floor TLS)
Nov 6 Guest lecture by Don Les:
Molecular systematics in plants(lecture too big, so I emailed it to you)
Nov 8 lab lab
Nov 11 Guest lecture by Chris Simon:
Molecular systematics in animals
Pdficon small.gifCSimon Lecture.pdf
COI Barcoding and analyzing your own data sets (Meet in McCarthy Room, 4th floor TLS)
Nov 13 lab lab
Nov 15 Procedural flow chart for phylogenetic analysis; DNA barcoding
Pdficon small.gifDNA Barcodes 18 Nov 2011.pdf
Nov 18 Thanksgiving recess Thanksgiving recess DO NOT Meet in McCarthy Room
Nov 20 Thanksgiving recess
Nov 22 Thanksgiving recess
Nov 25 Nomenclature
Pdficon small.gifNomenclature 2011 final.pdf
Mesquite and R: Ancestral states and character correlation (Meet in McCarthy Room, 4th floor TLS)
Nov 27 Nomenclature; phylocode
Nov 29 lab lab
Dec 2 Patterns and process
Pdficon small.gifPatterns and Processes 2011 One.pdf
Pdficon small.gifPatterns and Processes 2011 Two.pdf
No lab this week DO NOT Meet in McCarthy Room
Dec 4 Taxonomic collections
Pdficon small.gifImportance of Collections 2011.pdf
Dec 6 Biodiversity Crisis and Future of Systematics
Pdficon small.gifBiodiversity Crisis and Future of Systematics.pdf

Supplementary Reading

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

Grading (May change soon)

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

Important dates (To be updated soon)

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