Principles and Methods of Systematic Biology (EEB 5347)
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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
Contents
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 |
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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 |
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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 | Lab: Taxonomic resources: key websites; taxonomy exercise. BioBlitz in Stamford. Online Resource List ![]() | |
Sept 13 | Subspecies and phylogeography ![]() |
Read Futuyma's section on gene tree/species tree issues (from the Species chapter distributed earlier, pages 476-478) Mayr Chapter 4 (emailed) Send Dave or myself an example slide of infrasubspecific variation Possibly read this too ![]() | |
Sept 15 | lab | lab Dave's names lecture ![]() | |
Sept 18 | Subspecies (cont.) and Genes Trees versus Species Tress ![]() |
Lab: Alpha taxonomy: finding taxonomic characters & keys; descriptions and diagnoses; introduction to Mesquite’s alpha taxonomic features Mesquite I ![]() Dave's Tiger Beetle Intro ![]() | |
Sept 20 | Variation within a genotype: ontogeny & phenotypic plasticity | Macrotaxonomy and plant systematics readings sent out by Dave | |
Sept 22 | lab | lab | |
Sept 25 | Supraspecific taxa ![]() |
NYC field trip (Do NOT meet in McCarthy Room, 4th floor TLS) | |
Sept 27 | Phylogenetic inference: mostly a historical overview ![]() |
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Sept 29 | lab | lab | |
Oct 2 | Trees and characters: types of dendrograms, rooting and polarization; rooting and polarization |
Page and Holmes: Trees ![]() Forey et al. Chapters 2 and 3 ![]() Krell and Cranston 2004 ![]() Possibly one more, by Felsenstein |
Describing and diagnosing species; specimen/museumdatabases DELTA, MANTIS & other taxonomic computer tools. (Meet in McCarthy Room, 4th floor TLS) |
Oct 4 | Taxonomic characters: polarity, outgroups, order, and weighting ![]() |
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Oct 6 | lab | lab | |
Oct 9 | Distance methods, UPGMA, neighbor-joining, correcting distance data ![]() |
Page and Holmes Chapter 6 ![]() Felsenstein 2004 ![]() Strimmer and Haeseler 2009 ![]() |
Lab: Neighbor-joining and corrected distances; PAUP* (introduction) (Meet in McCarthy Room, 4th floor TLS) |
Oct 11 | Search algorithms; algorithmic power, accuracy, and inconsistency ![]() |
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Oct 13 | lab | lab | |
Oct 16 | Midterm exam | Manipulating molecular characters with Mesquite and a BLAST tutorial (Meet in McCarthy Room, 4th floor TLS) | |
Oct 18 | Midterm Review | ||
Oct 20 | lab | lab | |
Oct 23 | Reliability and measures of tree support ![]() |
Page and Holmes Chapter 6 (Part 2) ![]() |
Lab: PAUP*: parsimony; tree searches; tree statistics (Meet in McCarthy Room, 4th floor TLS) |
Oct 25 | Data partitions; consensus; comparing trees ![]() |
Optional Readings: Phylogenetics Handbook Chapters 10 ![]() ![]() ![]() | |
Oct 27 | Lab | ||
Oct 30 | Maximum likelihood (Lewis Guest Lecture) ![]() |
Optional Readings: Phylogenetics Handbook Chapter 6 ![]() Phylogenetics Handbook Chapter 7 ![]() |
Lab: PAUP*: ModelTest; molecular clocks; AIC et al. (Meet in McCarthy Room, 4th floor TLS) |
Nov 1 | Bayesian inference (Lewis Guest Lecture) ![]() |
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Nov 3 | lab | ||
Nov 6 | DNA Barcoding ![]() |
Required: A. fulgerator ![]() ![]() Optional: Bergman et al. 2013 ![]() ![]() |
Lab: Likelihood (Garli and/or RAxML) and Bayesian analyses (Meet in McCarthy Room, 4th floor TLS) |
Nov 8 | Molecular systematics in plants (Les Guest Lecture) Emailed out to all of you. | ||
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 ![]() | |
Dec 8 | Special topic: Phylogenetic trees & evolutionary processes | ||
Dec circa 15 | Final: 8-11 AM (Bamford) |
Topics | Additional Reading |
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Species as ranked taxa and species concepts | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]()
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DNA Barcodes | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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
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Optional Nomenclature Readings | Schuh & Brower 2009 ![]() ![]() ![]() ![]() |
Optional Phylocode Readings | Benton 2007 ![]() ![]() ![]() ![]() ![]() Platnick 2012 ![]() ![]() ![]() ![]() DeQueiroz 2012 ![]() |
Grading
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 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)