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

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[[Image:AMNH_2013.jpg|right|''2013 Class on top of the AMNH'']]
[[Image:AMNH_2013.jpg|right|''2013 Class on top of the AMNH'']]
[[Image:AMNH2011_roof.jpg|right|''2011 Class on top of the AMNH'']]
[[Image:AMNH2009.jpg|right|''2009 Class on top of the AMNH'']]
<span style="font-size: large">Fall 2013<br/>
<span style="font-size: large">Fall 2013<br/>

Revision as of 00:25, 31 October 2013

2013 Class on top of the AMNH

Fall 2013

Lecture MW 9:05-10:35 In the Bamford Conference Room TLS 171B
Lab F 9:05-10:35 Probably the 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: Russ Meister
Office hours: BioPharm 323 Stop by or by appointment
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.


Day Topics Reading/Assignment Lab
Aug 26 Organizational meeting; an introduction to biological systematics Basic Definitions Pdficon small.gif
Lecture instead of lab this week
Aug 28 The many roles of biological systematics
Species Definitions Pdficon small.gif Species Level Terminology Pdficon small.gif
Hubbell Reading Pdficon small.gif
Aug 30 Species definitions & species intermediacy & collections tour Templeton 1989 Pdficon small.gif De Queiroz 2007 Pdficon small.gif
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
Species II and III Lecture Pdficon small.gif
Finish reading/reread Templeton from Friday, Read Prosek's article (http://www.orionmagazine.org/index.php/articles/article/2868/)
Optional Readings: Futuyama Section (via email), Coyne and Orr's Species Concepts Overview (via email)
Sept 6 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 Ehrlic & Raven 1969 Pdficon small.gif
Make a slide or two about geographic subspecific variation
Nichols Gene tree species tree discordance Pdficon small.gif
Sept 9 Species definitions & species intermediacy; variation within species Mallet 2013 Pdficon small.gif Mallet 2013 Glossary if needed Pdficon small.gif
Wilson and Brown Pdficon small.gif
Winston Chapter (emailed)
Taxonomic resources: key websites, taxonomy exercise assigned (Meet in McCarthy Room, 4th floor TLS) Literature Search Activity Pdficon small.gif
Online Resource List Pdficon small.gif
Sept 11 Subspecies and geographic variation Pdficon small.gif 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 Pdficon small.gif
Sept 13 lab lab
Dave's names lecture Pdficon small.gif
Sept 16 Variation within a genotype: ontogeny & phenotypic plasticity Pdficon small.gif Lab: Alpha taxonomy: finding taxonomic characters & keys; descriptions and diagnoses; introduction to Mesquite’s alpha taxonomic features Mesquite I Pdficon small.gif (Meet in McCarthy Room, 4th floor TLS)
Dave's Tiger Beetle Intro Pdficon small.gif
Sept 18 Variation within a genotype Macrotaxonomy and plant systematics readings sent out by Dave
Sept 20 lab lab
Sept 23 Supraspecific taxa Pdficon small.gif NYC field trip (Do NOT meet in McCarthy Room, 4th floor TLS)
Sept 25 Phylogenetic inference: mostly a historical overview Pdficon small.gif
Sept 27 lab lab
Sept 30 Trees and characters; types of dendrograms;
rooting and polarization
Page and Holmes: Trees Pdficon small.gif
Forey et al. Chapters 2 and 3 Pdficon small.gif
Krell and Cranston 2004 Pdficon small.gif
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 2 Taxonomic characters: polarity, outgroups, order, weighting, and step matrices Pdficon small.gif (Combined with Sept 30 lecture)
Oct 4 lab lab
Oct 7 Distance methods, UPGMA, neighbor-joining, correcting distance data, multivariate methods Pdficon small.gif Page and Holmes Chapter 6 Pdficon small.gif
Felsenstein 2004 Pdficon small.gif
Strimmer and Haeseler 2009 Pdficon small.gif
Lab: Neighbor-joining and corrected distances; PAUP* (introduction) (Meet in McCarthy Room, 4th floor TLS)
Oct 9 Parsimony; search algorithms; algorithmic power, accuracy, and inconsistency Pdficon small.gif
Oct 11 lab lab
Oct 14 Midterm exam Manipulating molecular characters with Mesquite and a BLAST tutorial (Meet in McCarthy Room, 4th floor TLS)
Oct 16 Midterm Review
Oct 18 lab lab
Oct 21 Reliability and measures of tree support Pdficon small.gif Page and Holmes Chapter 6 (Part 2) Pdficon small.gif Lab: PAUP*: parsimony; tree searches; tree statistics
(Meet in McCarthy Room, 4th floor TLS)
Oct 23 Reliability and measures of tree support , Consensus Pdficon small.gif Optional Readings: Phylogenetics Handbook Chapters 10 Pdficon small.gif and 12 Pdficon small.gif, Felsenstein Chapter 20 Pdficon small.gif
Oct 25 Lab
Oct 28 Maximum likelihood (Lewis Guest Lecture) Pdficon small.gif Optional Readings: Phylogenetics Handbook Chapter 6 Pdficon small.gif
Phylogenetics Handbook Chapter 7 Pdficon small.gif (I have a better copy if this does not please you, email me)
Lab: Likelihood (Garli and/or RAxML) and Bayesian analyses (Meet in McCarthy Room, 4th floor TLS)
Oct 30 Bayesian inference (Lewis Guest Lecture) Pdficon small.gif
Nov 1 lab
Nov 4 Data partitions; consensus; comparing trees Lab: PAUP*: ModelTest; molecular clocks; AIC et al. (Meet in McCarthy Room, 4th floor TLS)
Nov 6 Molecular systematics in plants (Les Guest Lecture)
Nov 8 lab lab
Nov 11 Molecular systematics in animals (Simon Guest Lecture) COI Barcoding and analyzing your own data sets (Meet in McCarthy Room, 4th floor TLS)
Nov 13 lab lab
Nov 15 DNA barcoding
Nov 18 Nomenclature Lab: Mesquite; character optimization; character correlation (Meet in McCarthy Room, 4th floor TLS)
Nov 20 Nomenclature; Phylocode
Nov 22 Lab Lab
Nov 25 Thanksgiving Recess Thanksgiving Recess, Do NOT meet in McCarthy Room
Nov 27 Thanksgiving Recess
Nov 29 Thanksgiving Recess
Dec 2 Special topic: Phylogenetic trees & evolutionary processes No lab this week DO NOT Meet in McCarthy Room
Dec 4 Special topic: Taxonomic collections
Dec 6 Special topic: Systematics and conservation biology and the future of biological systematics
Dec 14 Final: 8-11 AM

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


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.
Pdficon small.gifFunding 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)
2 December, 2013: Paper due (May change)

EEB5347 website from 2011 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/EEB5347_2011)