Difference between revisions of "Principles and Methods of Systematic Biology (EEB 5347)"
Line 19: | Line 19: | ||
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. | 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. | ||
<br/> | <br/> | ||
− | =='''Schedule'''== | + | =='''Schedule (Will be updated soon)'''== |
{| border="1" cellpadding="2" | {| border="1" cellpadding="2" | ||
!style="background:#99cccc;" width="90" align="center"|Day | !style="background:#99cccc;" width="90" align="center"|Day |
Revision as of 16:35, 19 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 Wednesdays 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 29 | Class canceled due to Hurricane Irene |
Lecture instead of lab this week | |
Aug 31 | Organizational meeting, an introduction to biological systematics | Hubbell.pdf (for Friday) http://www.nytimes.com/2009/08/11/science/11naming.html (for Friday) Mayr&Ashlock1991_pgs1-18.pdf (optional) | |
Sept 2 | The many roles of biological systematics & collections tour | Templeton 1989.pdf De Queiroz 2007.pdf http://en.wikipedia.org/wiki/Species#Definitions_of_species Futuyma_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 | Species I 2011.pdf | ||
Sept 9 | Meet in library | Meet in library | |
Sept 12 | Species II 2011.pdf | Ehrlich&Raven1969.pdf | Taxonomic resources: key websites, taxonomy exercise assigned (Meet in McCarthy Room, 4th floor TLS) |
Sept 14 | Species III 2011.pdf | ||
Sept 16 | lab | lab | |
Sept 19 | Subspecies 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 | Higher Categories 2011.pdf | Keys, species descriptions, and cybertaxonomy (Meet in McCarthy Room, 4th floor TLS) | |
Sept 28 | Intro to phylogenetic inference | ||
Sept 30 | lab | lab | |
Oct 3 | 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 5 | Characters_1 2011.pdf | Krell&Cranston.pdf Felsenstein2004.pdf | |
Oct 7 | lab | lab | |
Oct 10 | Multivariate Methods 2011.pdf | Parsimony and distant methods with PAUP (Meet in McCarthy Room, 4th floor TLS) | |
Oct 12 | Distance Methods 2011.pdf Parsimony 2011.pdf ParsimonyLectureForMidTerm.ppt |
Page&Holmes_Chap6.pdf | |
Oct 14 | lab | lab | |
Oct 17 | Midterm exam | PageHolmesChptr5.pdf | Parsimony with PAUP (Meet in McCarthy Room, 4th floor TLS) |
Oct 19 | Midterm Review | ||
Oct 21 | lab | lab | |
Oct 24 | lab | lab | PAUP*: tree searches and tree statistics (Meet in McCarthy Room, 4th floor TLS) |
Oct 26 | Reliability 2011.pdf | ||
Oct 28 | No Lab/AMNH & Bronx Zoo Trip | Lewis_2001_TREE.pdf Holder&Lewis2003_NatRevGen.pdf | |
Oct 31 | lab | lab | Model comparison with Modeltest (Meet in McCarthy Room, 4th floor TLS) |
Nov 2 | Guest Lecture Paul Lewis | ||
Nov 4 | Guest Lecture Paul Lewis | ||
Nov 7 | Data partitions; consensus; comparing tree topologies Consensus 2011.pdf |
Maximum likelihood and Bayesian inference (Meet in McCarthy Room, 4th floor TLS) | |
Nov 9 | Guest lecture by Don Les: Molecular systematics in plants(lecture too big, so I emailed it to you) |
||
Nov 11 | lab | lab | |
Nov 14 | 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 16 | lab | lab | |
Nov 18 | Procedural flow chart for phylogenetic analysis; DNA barcoding DNA Barcodes 18 Nov 2011.pdf |
||
Nov 21 | Thanksgiving recess | Thanksgiving recess DO NOT Meet in McCarthy Room | |
Nov 23 | Thanksgiving recess | ||
Nov 25 | Thanksgiving recess | ||
Nov 28 | Nomenclature Nomenclature 2011 final.pdf |
Mesquite and R: Ancestral states and character correlation (Meet in McCarthy Room, 4th floor TLS) | |
Nov 30 | Nomenclature; phylocode | ||
Dec 2 | lab | lab | |
Dec 5 | 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 7 | Taxonomic collections Importance of Collections 2011.pdf |
||
Dec 9 | 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