Difference between revisions of "Principles and Methods of Systematic Biology (EEB 5347)"
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!style="background:#00B7EB;" width="275"|Lab | !style="background:#00B7EB;" width="275"|Lab | ||
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− | + | |Aug 26 ||Organizational meeting; an introduction to biological systematics <br/><!--{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Introduction%202009%20class%20notes.pdf}}Introduction 2009 class notes.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Syllabus%202009.pdf}}Syllabus.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Rules%20of%20Pronunciation%20Sci.%20Name.PDF}}Rules of Pronunciation Sci.Name.pdf--> | |
|| || rowspan="3"| Lecture instead of lab this week | || || rowspan="3"| Lecture instead of lab this week | ||
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− | |Aug 28 || | + | |Aug 28 ||The many roles of biological systematics ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hubbell.pdf}}Hubbell.pdf (for Friday)<br/>http://www.nytimes.com/2009/08/11/science/11naming.html (for Friday)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mayr_Ashlock1991_pgs1-18.pdf}}Mayr&Ashlock1991_pgs1-18.pdf (optional) |
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− | | Aug 30 || | + | | Aug 30 ||Species definitions & species intermediacy & collections tour <!--Species definitions & species intermediacy<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20Definitions.pdf}}Species Definitions.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20Level%20Terminology%202009.pdf}}Species Level Terminology 2009.pdf-->||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/A_Templeton%201989.pdf}}Templeton 1989.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/De%20Queiroz%202007.pdf}}De Queiroz 2007.pdf<br/>http://en.wikipedia.org/wiki/Species#Definitions_of_species<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Futuyma_spconcepts_445-451.pdf}}Futuyma_spconcepts_445-451.pdf |
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|Sept 2 ||Labor Day No class || || rowspan="3"| 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 2 ||Labor Day No class || || rowspan="3"| Babbidge Library resources; taxonomic literature''' Meet in Babbidge library electronic classroom 1 (EC1) on level 1, to the left and behind Info Cafe 1 ''' |
Revision as of 12:51, 20 August 2013
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
Contents
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 | Hubbell.pdf (for Friday) http://www.nytimes.com/2009/08/11/science/11naming.html (for Friday) Mayr&Ashlock1991_pgs1-18.pdf (optional) | |
Aug 30 | Species definitions & species intermediacy & collections tour | Templeton 1989.pdf De Queiroz 2007.pdf http://en.wikipedia.org/wiki/Species#Definitions_of_species Futuyma_spconcepts_445-451.pdf | |
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 | |
Sept 4 | Species I 2011.pdf | ||
Sept 6 | Meet in library | Meet in library | |
Sept 9 | Species II 2011.pdf | Ehrlich&Raven1969.pdf | Taxonomic resources: key websites, taxonomy exercise assigned (Meet in McCarthy Room, 4th floor TLS) |
Sept 11 | Species III 2011.pdf | ||
Sept 13 | lab | lab | |
Sept 16 | Subspecies 2011.pdf | Intro to Mesquite and Morphological Matrices (Meet in McCarthy Room, 4th floor TLS) | |
Sept 18 | Infrapopulation variation (lecture sent via email) | ||
Sept 20 | lab | lab | |
Sept 23 | Higher Categories 2011.pdf | Keys, species descriptions, and cybertaxonomy (Meet in McCarthy Room, 4th floor TLS) | |
Sept 25 | Intro to phylogenetic inference | ||
Sept 27 | lab | lab | |
Sept 30 | Trees and characters; types of dendrograms; rooting and polarization |
Forey et al 1992 Chap2&3.pdf (only read chapter 2) Page & Holmes 1998.pdf |
Manipulating molecular characters with Mesquite and a BLAST tutorial (Meet in McCarthy Room, 4th floor TLS) |
Oct 2 | Characters_1 2011.pdf | Krell&Cranston.pdf Felsenstein2004.pdf | |
Oct 4 | lab | lab | |
Oct 7 | Multivariate Methods 2011.pdf | Parsimony and distant methods with PAUP (Meet in McCarthy Room, 4th floor TLS) | |
Oct 9 | Distance Methods 2011.pdf Parsimony 2011.pdf ParsimonyLectureForMidTerm.ppt |
Page&Holmes_Chap6.pdf | |
Oct 11 | lab | lab | |
Oct 14 | Midterm exam | PageHolmesChptr5.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 | Reliability 2011.pdf | ||
Oct 25 | No Lab/AMNH & Bronx Zoo Trip | Lewis_2001_TREE.pdf Holder&Lewis2003_NatRevGen.pdf | |
Oct 28 | lab | lab | Model comparison with Modeltest (Meet in McCarthy Room, 4th floor TLS) |
Oct 30 | Guest Lecture Paul Lewis | ||
Nov 1 | Guest Lecture Paul Lewis | ||
Nov 4 | Data partitions; consensus; comparing tree topologies Consensus 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) |
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Nov 8 | lab | lab | |
Nov 11 | Guest lecture by Chris Simon: Molecular systematics in animals CSimon 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 DNA Barcodes 18 Nov 2011.pdf |
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Nov 18 | Thanksgiving recess | Thanksgiving recess DO NOT Meet in McCarthy Room | |
Nov 20 | Thanksgiving recess | ||
Nov 22 | Thanksgiving recess | ||
Nov 25 | Nomenclature Nomenclature 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 Patterns and Processes 2011 One.pdf Patterns and Processes 2011 Two.pdf |
No lab this week DO NOT Meet in McCarthy Room | |
Dec 4 | Taxonomic collections Importance of Collections 2011.pdf |
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Dec 6 | Biodiversity Crisis and Future of Systematics Biodiversity Crisis and Future of Systematics.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 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 (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