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'']]
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<span style="font-size: large">Fall 2017<br/>
  
<span style="font-size: large">Fall 2013<br/>
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<span style="font-size: large">Lecture MW 9:05-10:45 In TLS 313<br/>
 
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Lab F 9:05-10:45 McCarthy Room, 4th floor TLS<br/>
<span style="font-size: large">Lecture MW 9:05-10:35 In the Bamford Conference Room TLS 171B<br/>
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Lab F 9:05-10:35 Probably the McCarthy Room, 4th floor TLS<br/>
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<br/>
 
<br/>
 
<span style="font-size: large">'''Instructor''': Dr. David L. Wagner, TLS Rm 471<br/>
 
<span style="font-size: large">'''Instructor''': Dr. David L. Wagner, TLS Rm 471<br/>
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email: [mailto:david.wagner'at'uconn.edu david.wagner'at'uconn.edu]<br/>
 
email: [mailto:david.wagner'at'uconn.edu david.wagner'at'uconn.edu]<br/>
 
<br/>
 
<br/>
'''Graduate Teaching Assistant''': Russ Meister<br/>
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Office hours: BioPharm 323 Stop by or by appointment <br/>
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'''Graduate Teaching Assistant''': Kevin Keegan<br/>
Phone: 486-3947<br/>
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Office hours: TLS 461 F 10:45-11:45 or by appointment<br/>
email: [mailto:russell.meister'at'uconn.edu russell.meister'at'uconn.edu]<br/>
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Phone: 617-272-5054<br/>
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email: [mailto:kevin.keegan'at'uconn.edu kevin.keegan'at'uconn.edu]<br/>
 
<br/>
 
<br/>
 +
 
== '''Textbook and readings''' ==
 
== '''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.
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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.
 
<br/>
 
<br/>
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=='''Schedule'''==
 
=='''Schedule'''==
 
{| border="1" cellpadding="2"  
 
{| border="1" cellpadding="2"  
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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    Basic Definitions {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/f0/Basic_Definitions.pdf}} <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-->
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|Aug 28 ||Organizational meeting || Hubbell Reading {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/8/8e/Hubbell%2818Aug13%29.pdf}} || rowspan="3"| Dave away in Fort Collins<br/>Introduction to McCarthy Room;<br/>Collections tour with Dr. Jane O'Donnell;<br>Species concept discussion and letter to yourself
|| || rowspan="3"| Lecture instead of lab this week
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|-
 
|-
|Aug 28 ||The many roles of biological systematics <br/> Species Definitions {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/7/72/Species_Definitions_2013.pdf}}  Species Level Terminology {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/d/d4/Species_Level_Terminology_2013.pdf}} || Hubbell Reading {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/8/8e/Hubbell%2818Aug13%29.pdf}}
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|Aug 30 ||An introduction to biological systematics; The many roles of biological systematics and collections <br/> ||  
 
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|-
| Aug 30 ||Species definitions & species intermediacy & collections tour  <!--Species definitions & species intermediacy<br/>
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|Sep 1 ||Species definitions & species intermediacy<br/> A Bit on Names {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/A_bit_on_names_2017.pdf}}|| Templeton (1989){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/A_Templeton%201989.pdf}}
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20Level%20Terminology%202009.pdf}}Species Level Terminology 2009.pdf-->|| Templeton 1989 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/e8/A_Templeton_1989.pdf}}  De Queiroz 2007 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/5/51/De_Queiroz_2007.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 (http://classguides.lib.uconn.edu/content.php?pid=238531&sid=1968055) '''
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|Sep 4 ||Labor Day, No class || || rowspan="3"| Kevin away in Mexico<br/>Babbidge Library resources; taxonomic literature
 
|-
 
|-
|Sept 4 ||Species definitions & species intermediacy <br/> Species II and III Lecture {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/e8/Species_II_and_III_2013New.pdf}} ||  Finish reading/reread Templeton from Friday, Read Prosek's article (http://www.orionmagazine.org/index.php/articles/article/2868/)<br/>Optional Readings: Futuyama Section (via email),  Coyne and Orr's Species Concepts Overview (via email)
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|Sept 6 ||Species definitions & species intermediacy <br/> Species 1 Lecture {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species_I_2017.pdf}}||  Finish reading/reread Templeton from Friday<br/> DeQuieroz (2007){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/De%20Queiroz%202007.pdf}}
 
|-
 
|-
|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 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/7/7c/Ehrlich%26Raven_1969.pdf}} <br/>  Make a slide or two about geographic subspecific variation <br/>  Nichols Gene tree species tree discordance {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/3/37/Nichols_GeneSpecies_Tree.pdf}}
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|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 9 || Species definitions & species intermediacy; start variation within species || Mallet 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/a/a7/Mallet2013_Sub-semisp.pdf}}  Mallet 2013 Glossary if needed {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/d/d4/Mallet2013_SpeciesConcepts.pdf}} <br/> Wilson and Brown {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/File:WilsonBrown1953.pdf}} <br/>Winston Chapter (emailed)  || rowspan="3"| Taxonomic resources: key websites, taxonomy exercise assigned '''(Meet in McCarthy Room, 4th floor TLS)''' Literature Search Activity {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/2/2a/Lab1_Literature_Search_2013.pdf}} <br/> Online Resource List {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/e2/Lab1_tax_resources_online_2013.pdf}}
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|Sept 11 || Finish species definitions & species intermediacy; start variation within species <br/> Species II Lecture {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species_II_2017.pdf}}  || Erlich & Raven (1969){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Ehrlich&Raven_1969.pdf}} <br/> Mallet (2013)  {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mallett_2013.pdf}} || rowspan="3"| '''Meet in McCarthy Room'''<br/>Taxonomic resources: key websites; taxonomy exercise {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab1_Literature_Search_2017_dlw.doc}}.<br/>Online Resource List {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab1_tax_resources_online_2017_dlw.pdf}}<br/> BioBlitz in Stamford.
 
|-
 
|-
|Sept 11 || Subspecies and phylogeography {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/6/6c/Subspecies_2013.pdf}} ||  Read Futuyma's section on gene tree/species tree issues (from the Species chapter distributed earlier, pages 476-478) <br/> Mayr Chapter 4 (emailed) <br/> Send Dave or myself an example slide of infrasubspecific variation <br/>  Possibly read this too {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/ee/Agrawal_PhenotypicPlasticity.pdf}}
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|Sept 13 || Subspecies and geographic variation || Send Wagner an example (~3 ppt slides) of intraspecific geographic variation '''before 11:59 PM Sunday'''
<!--Individual variation(population variation){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20II.pdf}}Species II.pdf || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Futuyma_pg239to263master1.pdf}}Futuyma_pg239-263.pdf (For 9/18) -->
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|-
 
|-
|Sept 13 || lab || lab <br/> Dave's names lecture {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/c/c6/A_bit_on_names.pdf}}
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|Sept 15 || lab ||  
 
|-
 
|-
|Sept 16 || Subspecies (cont.) and Genes Trees versus Species Tress  {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/e7/SubspeciesII_GeneTrees.pdf}} || || rowspan="3"| Lab: Alpha taxonomy: finding taxonomic characters & keys; descriptions and diagnoses; introduction to Mesquite’s alpha taxonomic features  Mesquite I {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/d/de/MesquiteLabI.pdf}} '''(Meet in McCarthy Room, 4th floor TLS)''' <br/> Dave's Tiger Beetle Intro {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/6/64/TigerBeetleIntro.pdf}}
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|Sept 18 || Variation within a genotypeontogeny & phenotypic plasticity || Send Wagner an example (~3 ppt slides) of intraspecific non-geographic variation '''before 11:59 PM Tuesday''' || rowspan="3"| Lab: Alpha taxonomy: finding taxonomic characters & keys; descriptions and diagnoses; taxonomic cybertools for alpha taxonomy and phylogenetics <br/> Slides {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab2_Presentation_2017.pdf}} <br/> Notes {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab2_Presentation_2017_notes.pdf}} <br/>Intro to Mesquite exercise {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab2_mesquite_exercise_2017.pdf}} <br> (Wagner away on Friday)
 
|-
 
|-
|Sept 18 ||  Variation within a genotype:  ontogeny & phenotypic plasticity || Macrotaxonomy and plant systematics readings sent out by Dave
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|Sept 20 ||  Supraspecific taxa ||
 
|-
 
|-
|Sept 20 || lab || lab
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|Sept 22 || lab ||
 
|-
 
|-
|Sept 23 || Supraspecific taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/2/2a/HigherCatagories2013.pdf}} || || rowspan="3"|   NYC field trip '''(Do NOT meet in McCarthy Room, 4th floor TLS)'''
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|Sept 25 || Supraspecific taxa || || rowspan="3"| Lab: Describing and diagnosing species; specimen/museum databases; Taxonomic cybertools: DELTA, MANTIS, Mesquite & others (Wagner away)
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Phylogenetic inference
 
|-
 
|-
|Sept 25 || Phylogenetic inference:  mostly a historical overview {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/7/7a/Intro_Phylogenetic_Inference_2013.pdf}} ||
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|Sept 27 || Phylogenetic inference:  mostly a historical overview ||
 
|-
 
|-
|Sept 27 || lab || lab
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|Sept 29 || lab ||
 
|-
 
|-
|Sept 30 || Trees and characters: types of dendrograms, rooting and polarization;<br/>rooting and polarization || Page and Holmes:  Trees {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/6/67/Page%26Holmes_Trees.pdf}} <br/> Forey et al. Chapters 2 and 3 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/d/d0/Forey_etal_2%263.pdf}} <br/> Krell and Cranston 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/7/74/Krell%26Cranston2004.pdf}} <br/>  Possibly one more, by Felsenstein || rowspan="3"|  Describing and diagnosing species; specimen/museumdatabases DELTA, MANTIS & other taxonomic computer tools.  '''(Meet in McCarthy Room, 4th floor TLS)'''
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|Oct 2 || Trees and characters: types of dendrograms, rooting and polarization || || rowspan="3"|  Lab: Mesquite II, Parsimony???
 
|-
 
|-
|Oct 2 || Taxonomic characters: polarity, outgroups, order, and weighting  {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/8/8b/Characters_1_2013.pdf}} (Combined with Sept 30 lecture)  ||  
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|Oct 4 || Taxonomic characters: polarity, outgroups, order, weighting, and step matrices ||  
 
|-
 
|-
|Oct 4 || lab || lab
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|Oct 6 || lab ||
 
|-
 
|-
|Oct 7 || Distance methods, UPGMA, neighbor-joining, correcting distance data {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/6/60/Distance_Methods_2013.pdf}} ||  Page and Holmes Chapter 6 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/2/28/Page%26Holmes_Chap6.pdf}} <br/>Felsenstein 2004  {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/8/8c/Felsenstein2006.pdf}} <br/> Strimmer and Haeseler 2009 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/d/d3/Strimmer%26Haeseler2009.pdf}} || rowspan="3"| Lab: Neighbor-joining and corrected distances; PAUP* (introduction) '''(Meet in McCarthy Room, 4th floor TLS)'''
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|Oct 9 || Parsimony; tree searches; tree statistics || || rowspan="3"| Lab: Trip to American Museum of Natural History and Bronx Zoo in NYC!!!
 
|-
 
|-
|Oct 9 || Search algorithms; algorithmic power, accuracy, and inconsistency    {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/3/38/Parsimony2013.pdf}}  ||
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|Oct 11 ||''' Midterm exam''' ||
 
|-
 
|-
|Oct 11 || lab || lab
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|Oct 13 || '''Head to NYC''' ||
 
|-
 
|-
|Oct 14 || Midterm exam || || rowspan="3"| Manipulating molecular characters with Mesquite and a BLAST tutorial '''(Meet in McCarthy Room, 4th floor TLS)'''
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|Oct 16 || Maximum likelihood (lecture by Lewis; Wagner away) || || rowspan="3"| Lab: likelihood (Garli and/or RAxML) and Bayesian analyses
 
|-
 
|-
|Oct 16 ||Midterm Review ||
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|Oct 18 || Bayesian inference (lecture by Lewis; Wagner away) ||
 
|-
 
|-
|Oct 18 || lab || lab
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|Oct 20 || lab ||
 
|-
 
|-
|Oct 21 || Reliability and measures of tree support  {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/d/d5/Reliability2013.pdf}}  || Page and Holmes Chapter 6 (Part 2) {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/4/44/PageHolmes6Part2.pdf}} || rowspan="3"| Lab:  PAUP*:  parsimony; tree searches; tree statistics    <br/>'''(Meet in McCarthy Room, 4th floor TLS)'''
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|Oct 23 || Tree reliability, sensitivity, and support measures I ||  || rowspan="3"| Lab: Tree reliability and measures <br/>'''(Meet in McCarthy Room, 4th floor TLS)'''
 
|-
 
|-
|Oct 23 || Data partitions; consensus; comparing trees  {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/d/d8/Consensus_2013.pdf}} ||  Optional Readings:  Phylogenetics Handbook Chapters 10 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/d/de/PhyloHandbook10.pdf}} and 12  {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/a/a0/PhyloHandbook12.pdf}},  Felsenstein Chapter 20  {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/9/9d/FelsensteinChap20.pdf}}
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|Oct 25 || Tree reliability, sensitivity, and support measures II ||
 
|-
 
|-
|Oct 25 || Lab ||  
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|Oct 27 || lab ||  
 
|-
 
|-
|Oct 28 || Maximum likelihood (Lewis Guest Lecture)  {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/7/76/Lewis_Likelihood_2013.pdf}} ||  Optional Readings: Phylogenetics Handbook Chapter 6 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/06/PhyloMaxLike.pdf}} <br/> Phylogenetics Handbook Chapter 7 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/0b/BayesPhylo.pdf}}    || rowspan="3"| Lab: PAUP*: ModelTest; molecular clocks; AIC et al. '''(Meet in McCarthy Room, 4th floor TLS)'''
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|Oct 30 || Multivariate and distance methods || || rowspan="3"| Lab: neighbor-joining and correcting distance data '''(Meet in McCarthy Room, 4th floor TLS)'''
 
|-
 
|-
|Oct 30 || Bayesian inference (Lewis Guest Lecture) {{pdf|http://hydrodictyon.eeb.uconn.edu/people/plewis/downloads/Bayesian_30Oct2013.key.pdf}} ||  
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|Nov 1 || Bayesian inference (Lewis Guest Lecture) {{pdf|http://hydrodictyon.eeb.uconn.edu/people/plewis/downloads/Bayesian_30Oct2013.key.pdf}} ||  
 
|-
 
|-
|Nov 1 || lab  ||
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|Nov 3 || lab  ||
 
|-
 
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|Nov 4 || DNA Barcoding  {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/e1/DNA_Barcoding.pdf}} ||  Required:  A. fulgerator {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/c/c1/Astraptesfulgerator.pdf}} and Ratnasignham & Herbert 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/2/20/RatnasignhamHerbert2013.pdf}} <br/> Optional: Bergman et al. 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/b/bb/Bergmanetal2013.pdf}} and Morrales and Vences 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/3/3b/MirralesVences2013.pdf}}  || rowspan="3"| Lab:  Likelihood (Garli and/or RAxML) and Bayesian analyses '''(Meet in McCarthy Room, 4th floor TLS)'''
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|Nov 6 || Molecular systematics in animals (Simon) (Wagner in Denver) || || rowspan="3"| Lab:  PAUP*: ModelTest; molecular clocks; AIC et al. '''(Meet in McCarthy Room, 4th floor TLS)'''
 
|-
 
|-
|Nov 6 || Molecular systematics in plants (Les Guest Lecture) Emailed out to all of you. ||
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|Nov 8 || Molecular systematics in plants (Les) ||
 
|-
 
|-
|Nov 8 || lab || lab
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|Nov 10 || lab ||
 
|-
 
|-
|Nov 11 || Molecular systematics in animals (Simon Guest Lecture)  {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/10/EEB5347_SimonLecture.pdf}} || || rowspan="3"| Lab:  Find and analyze your own data set; COI problem, WEDNESDAY, not Friday '''(Meet in McCarthy Room, 4th floor TLS)'''
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|Nov 13 || Data partitions; consensus; comparing trees || || rowspan="3"| Lab:  Find and analyze your own data set; COI problem '''(Meet in McCarthy Room, 4th floor TLS)'''
 
|-
 
|-
|Nov 13 || Lab Today, not Friday! || lab
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|Nov 15 || DNA barcoding  ||
 
|-
 
|-
|Nov 15 || Nomenclature  {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/4/46/Nomenclature2013Reduced.pdf}} ||  See the many optional nomenclature readings below.
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|Nov 17 || lab ||
 
|-
 
|-
|Nov 18 || Nomenclature, James Prosek will join our discussion today, it should be quite a class || DeQueiroz Phylocode 2006 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/19/PhylocodeReading.pdf}} <br/> Vane-Wright Nomenclature Concern {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/8/8c/IncreasingConcernNomenclature.pdf}} <br/> Name Poems {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/5/59/NamePoems.pdf}} <br/> The Phylocode Reading 2009 (http://www.ohiou.edu/phylocode/preface.html) <br/> Linnaean naming system challenges 2004 (http://www.newscientist.com/article.ns?id=dn6369) <br>/ ADDITIONALLY, choose one phylocode reading from the optional ones loaded below || rowspan="3"| Lab:  Mesquite; character optimization; character correlation '''(Meet in McCarthy Room, 4th floor TLS)'''
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|Nov 20 ||rowspan="3"| '''Thanksiving''' || rowspan="3"| '''Thanksiving''' || rowspan="3"| '''Thanksiving'''
 
|-
 
|-
|Nov 20 || Nomenclature; Phylocode ||
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|Nov 22
 
|-
 
|-
|Nov 22 || Lab || Lab
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|Nov 24
 
|-
 
|-
|Nov 25 ||Thanksgiving Recess || || rowspan="3"| Thanksgiving Recess, Do NOT meet in McCarthy Room
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|Nov 27 || Nomenclature || || rowspan="3"| Lab:  Mesquite; character optimization; character correlation
 
|-
 
|-
|Nov 27 || Thanksgiving Recess ||  
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|Nov 29 || Nomenclature; Phylocode ||
 
|-
 
|-
|Nov 29 || Thanksgiving Recess ||  
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|Dec 1 || lab ||
 
|-
 
|-
|Dec 2 ||Special topic:  Phylogenetic trees & evolutionary processes || || rowspan="3"| No lab this week '''DO NOT Meet in McCarthy Room'''
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|Dec 4 || Phylogenetic trees & evolutionary processes || || rowspan="3"| '''No lab this week'''
 
|-
 
|-
|Dec 4 || Special topic: Taxonomic collections ||  
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|Dec 6 || Special topic: Taxonomic collections ||
 
|-
 
|-
|Dec 6 || Special topic: Systematics and conservation biology and the future of biological systematics||  
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|Dec 8 || Special topic: Systematics and conservation biology and the future of biological systematics ||
 
|-
 
|-
|Dec 11 || Final: 8-11 AM || ||
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|Dec circa 15 || Final: 8-11 AM (Bamford) ||
 +
|}
 +
 
 +
=='''Grading'''==
 +
{| border="1" cellpadding="1"
 +
!width="200"|Item
 +
!width="25"|Percentage
 +
!width="25"|Points
 
|-
 
|-
<!--|Sept 21 ||Variation within a genotype: ontogeny & phenotypic plasticity{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Infrasubspecific%20Variation%202009.pdf}}Infrasubspecific Variation 2009.pdf || || rowspan="3"| Alpha Taxonomy<br/>Tiger Beetle Exercise<br/>Mesquite Morphological Matrices<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Winston%201999.pdf}}Winston 1999.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mesquite%20morphological%20matrices.pdf}}Mesquite morphological tutorial.pdf
+
|Lab and take home exercises|| <div style="text-align: center">25</div> || <div style="text-align: center">250</div>
 
|-
 
|-
|Sept 23 ||Supraspecfic taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Higher%20Categories%202009.pdf}}Higher Categories 2009.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%20%26%20Holmes%201998.pdf}}Page & Holmes 1998.pdf(For 09/28)
+
|Midterm Exam || <div style="text-align: center">20</div> || <div style="text-align: center">200</div>
 
|-
 
|-
|Sept 25 ||Lab {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Tiger%20Beetle%20Intro%202009.pdf}}Tiger Beetle Intro 2009.pdf ||
+
|Paper || <div style="text-align: center">25</div> || <div style="text-align: center">250</div>
 
|-
 
|-
|Sept 28 ||Phylogenetic inference: Mostly a historical overview<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Intro%20to%20Phylogenetic%20Inference.pdf}}Intro to Phylogenetic Inference.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Chart%20the%20evol%20history%20of%20life.pdf}}Chart the evol history of life.pdf(For 09/30)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Modernizing%20the%20tree%20of%20life.pdf}}Modernizing the tree of life.pdf(For 09/30) || rowspan="3"| Alpha Taxonomy: taxonomic keys,<br/>specimen/museum databases DELTA,<br/> MANTIS & other taxonomic computer tools
+
|Nomenclature Exercise || <div style="text-align: center">2</div> || <div style="text-align: center">20</div>
 
|-
 
|-
|Sept 30 ||Trees and characters: types of dendrograms, rooting and polarization<br/>weighting and step matrices {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters1.pdf}}Characters1.pdf ||
+
|Class Participation || <div style="text-align: center">3</div> || <div style="text-align: center">30</div>
 
|-
 
|-
|Oct 2 ||Lab ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Krell%26Cranston.pdf}}Krell&Cranston.pdf(For 10/05)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Forey%20et%20al%201992%20Chap2%263.pdf}}Forey et al 1992 Chap2&3.pdf (For 10/05)
+
|Final Exam || <div style="text-align: center">25</div> || <div style="text-align: center">250</div>
 
|-
 
|-
|Oct 5 ||Taxonomic characters: polarity, outgroups, order, weighting, and step matrices<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters%20II.pdf}}Characters II.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/CompleatCladist.pdf}}Cladistics Review I.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Collin%26Miglietta%202008%20Dollo%20Law.pdf}}Collin&Miglietta 2008 Dollo's Law.pdf|| rowspan="3"| Mesquite II: manipulating DNA/amino acid sequences<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mesquite%20Lab%20II}}Mesquite Lab II<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/GenBank%20Tutorial%202009}}GenBank Tutorial
+
|'''Total''' || <div style="text-align: center">'''100'''</div> || <div style="text-align: center">'''1000'''</div>
|-
+
|}
|Oct 7 ||More on trees<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/More%20on%20Trees.pdf}}Trees.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Cladistics.pdf}}Cladistics Review II.pdf
+
 
|-
+
=='''Term Paper'''==
|Oct 9 ||Lab ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Felsenstein2004.pdf}}Felsenstein2004.pdf(For 10/16)
+
<br/>
|-
+
Each student will be required to prepare a paper that will be due on December 2. Acceptable styles: (1) a literature review that is structured to be a thesis chapter; (2) grant proposal; (3) stand-alone review a subject relevant to systematic theory or methodology.
|Oct 12 ||Distance methods, UPGMA, neighbor-joining, correcting distance data, multivariate techniques<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Multivariate%20Methods%202009.pdf}}Multivariate Methods 2009.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Distance%20Methods%202009.pdf}}Distance Methods 2009.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes_Chap6.pdf}}Page&Holmes_Chap6.pdf (For 10/14&16)|| rowspan="3"|Intro to PAUP*:<br/>neighbor-joining<br/>corrected distances<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab%205_PAUP%20Intro%20revised-1.doc}}Lab 5 PAUP Intro.doc
+
|-
+
|Oct 14 ||Molecular systematics in animals (Simon guest lecture)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Guest%20Lecture%20Wagner%27s%20Systematics-%20How%20Molecules%20Evolve.%20Fall%2009.pdf}}How Molecules Evolve.pdf||
+
|-
+
|Oct 16 ||Lab ||
+
|-
+
|Oct 19 ||Exam||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Midterm%20Sample%20Questions%202009.pdf}}Midterm Sample Questions 2009.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Neighbor-joining%20Exercise.pdf}}Neighbor-joining Exercise.pdf||rowspan="3"|American Museum of Natural History
+
|-
+
|Oct 21 ||Midterm Review<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Midterm%20Post-Exam%20Review.pdf}}Midterm Post-Exam Review.pdf||
+
|-
+
|Oct 23 ||AMNH Trip ||
+
|-
+
|Oct 26 ||Parsimony; search algorithms;<br/>algorithmic power, accuracy, and inconsistency<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Parsimony.pdf}}Parsimony.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes_Part2_1.pdf}}Page&Holmes_Rest_of_Ch6.pdf||rowspan="3"|Parsimony Lab<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab6_parsimony_2009.doc}}Lab6 Parsimony.doc
+
|-
+
|Oct 28 ||Likelihood(Guest Lecture: Paul Lewis)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Likelihood_28Oct2009_1perpage.pdf}}Likelihood.pdf||
+
|-
+
|Oct 30 ||Lab ||
+
|-
+
|Nov 2 ||Swine flu class cancelled||||rowspan="3"|Modeltest, AIC & hLRT, Molecular clocks<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab7_2009_corrected.doc}}Lab7.doc
+
|-
+
|Nov 4 ||Bayesian phylogenetics (Paul Lewis)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Bayesian_2Nov2009_1perpage.pdf}}Bayesian phylogenetics.pdf||
+
|-
+
|Nov 6 ||Lab ||
+
|-
+
|Nov 9 ||Molecular systematics in plants (Don Les)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Systematics_2009_Les.pdf}}Plant Systematics Les.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes280_285.pdf}}Page&Holmes280-285.pdf||rowspan="3"|Garli and MrBayes Lab<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab8_2009.doc}}Lab8.doc
+
|-
+
|Nov 11 ||Reliability and measures of tree support:  c.i., r.i.,<br/>decay indices, bootstraps ; jackknifes; and sensitivity analyses;<br/>bootstraps, randomization tests<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Reliability%202009.pdf}}Reliability 2009.pdf||
+
|-
+
|Nov 13 ||Lab ||
+
|-
+
|Nov 16 ||Data partitions; consensus; ILD<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Consensus%202009.pdf}}Consensus.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/ILD%202009.doc}}ILD 2009.doc||rowspan="3"|COI data set analysis<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab9_barcoding_2009_corrected.doc}}Lab9 COI Barcodes.doc
+
|-
+
|Nov 18 ||DNA Barcodes<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/DNA%20Barcodes.pdf}}DNA Barcodes.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/FunkOmlandARev.pdf}}Funk & Omland.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Astraptes%20fulgerator.pdf}}Hebert et al. 2004.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Meyer%20and%20Paulaypdf%20copy.pdf}}Meyer and Paulay.pdf
+
|-
+
|Nov 20 ||Lab ||
+
|-
+
|Nov 23-28 ||No class-Thanksgiving Break||
+
|-
+
|Nov 30 ||Nomenclature<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Nomenclature%202009.pdf}}Nomenclature 2009.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Berenbaum%20Article.pdf}}Berenbaum Article.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Conniff%20article.pdf}}Conniff article.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Gould_Bully%20for%20Bront.pdf}}Gould_Bully for Bront.pdf||rowspan="3"|Mesquite: Ancestral States Reconstruction
+
|-
+
|Dec 2 ||Nomenclature; Phylocode||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mares2009.pdf}}Mares2009.pdf
+
|-
+
|Dec 4 ||Lab ||
+
|-
+
|Dec 7 ||Special topic: Taxonomic collections<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Importance%20of%20Collections.pdf}}Importance of Collections.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Nomenclature%20Exercise.doc}}Nomenclature Exercise.doc (due Dec 11)||rowspan="3"|No Lab
+
|-
+
|Dec 9 ||Special topic:  Phylogenetic trees & evolutionary processes;<br/>the comparative method<br/>:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Patterns%20and%20Processes%202011%20One.pdf}}Patterns and Processes 2011 One.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Patterns%20and%20Processes%202011%20Two.pdf}}Patterns and Processes 2011 Two.pdf||
+
|-
+
|Dec 11 ||Special topic: Biodiversity crisis and future of systematics<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Conservation_and_Systematics.pdf}}Conservation and Systematics.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Looking%20Ahead%202009.pdf}}||
+
|}-->
+
 
<br/>
 
<br/>
{| border="1" cellpadding="2"
 
  
=='''Supplementary Reading'''==
+
'''Important Dates'''
!style="background:#2A52BE;" width="275"|Topics
+
!style="background:#008080;" width="975"|Additional Reading
+
|-
+
| Species as ranked taxa and species concepts || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Application%20of%20Evol%20Spp%20concept.pdf}}Application of Evolutionary Species concept.pdf    {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20concept%20for%20prokaryotes%202001.pdf}}Species concept for prokaryotes.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Noor%202002%20BSC%20showing%20age%3F.pdf}}Is the BSC showing its age?.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Sites%20and%20Crandall%20Con.Bio%201997.pdf}}Importance of stating species concept for conservation purposes.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/AgapowSpeciesQRB04.pdf}}Impact of species concepts on biodiversity studies.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Urge%20to%20state%20species%20concept.pdf}}The need for specifying species concepts.pdf{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hey%202007.pdf}}On the failure of modern species concepts.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20as%20Ranked%20Taxa%20Baum%202009.pdf}}Species as ranked taxa.pdf<br/>
+
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Increase%20in%20bird%20species.pdf}}Does the choice of species concept result in an increase in bird species?.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Bond%20and%20Stockman%202008.pdf}}Method for delimiting Cohesion speceis.pdf
+
|-
+
|DNA Barcodes||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/elias%202007.pdf}}Elias et al. 2007.pdf  {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Barcoding%20Leps%20of%20Costa%20Rica%20Guanacaste%20red.%20Janzen%20et%20al.pdf}}Janzen et al 2005.pdf  {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/TenReasonsBarcoding.pdf}}Ten Reasons For Barcoding.pdf  {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Will%20%26%20Rubinoff%202004.pdf}}Will & Rubinoff 2004.pdf  {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hebert%20and%20Gregory%202005.pdf}}Hebert and Gregory 2005.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/PLoS_PromisesAndPitfalls.pdf}}Moritz and Cicero 2004.pdf  {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hebert_et_al_2003_DNABarcodes.pdf}}Hebert et al.2003.pdf  {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/PLoS_Birds_Hebert_et_al_2004.pdf}}PLoS_Birds_Hebert et al. 2004.pdf
+
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
+
<br/>Janzen and Hallwachs 2011  http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018123
+
<br/>Joly et al. 2013, Ecology in the age of DNA barcoding: the resource, the promise, and the challenges ahead {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fe/Jolyetal.2013.pdf}}
+
|-
+
|Optional Nomenclature Readings|| Schuh & Brower 2009 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/2/24/Schuh%26Brower2009.pdf}}    Jones and Luchsinger {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/6/6b/Jones%26Luchsinger.pdf}}    Conniff 1996 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/7/77/Conniff1996.pdf}}  Gould 1990 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/ec/Gould1990.pdf}} <br/>
+
|-
+
|Optional Phylocode Readings|| Benton 2007 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/e0/Benton2007.pdf}} Donoghue and Gauthier {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/b/b8/Donoghue%26Gauthier.pdf}}  Lee and Skinner 2007 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/e8/Lee%26Skinner2007.pdf}} Nixon et al. 2003 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/6/66/Nixonetal2003.pdf}}  Rieppel 2006  {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/d/d1/Rieppel2006.pdf}} <br/> Platnick 2012 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/a/af/Platnick2012.pdf}}  DeQueiroz 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/4/47/DeQueiroz2013.pdf}}  DeQueiroz and Donoghue 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/c/ca/DeQueiroz%26Don2011.pdf}}  DeQueiroz and Donoghue 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/07/DeQueiroz%26Don2013.pdf}} <br/>  DeQueiroz 2012 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/5/55/2012DeQueiroz.pdf}}
+
|}
+
 
+
=='''Grading'''==
+
 
{| border="1" cellpadding="1"
 
{| border="1" cellpadding="1"
| Lab and take home exercises || 20% || 200 pts
+
!width="150"|Date
 +
!width="200"|Milestone
 
|-
 
|-
| Midterm || 20% || 200 pts
+
|6 October 2017 || conference; topic selection
 
|-
 
|-
| Term paper || 22% || 220 pts
+
|20 October 2017 || outline with 5+ references
 
|-
 
|-
| Nomenclature exercise || 1% || 10 pts
+
|17 November 2017 || first draft due
 
|-
 
|-
| Participation || 2% || 20 pts
+
|1 December 2017 || paper due
 
|-
 
|-
| Final || 35% || 350 pts
 
|-
 
| '''Total''' || '''100%''' || '''1000 pts'''
 
 
|}
 
|}
<br/>
 
 
=='''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
 
<br/>
 
 
=='''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.<br/>
 
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Funding%20for%20biodiversity%20and%20taxonomy%202010.pdf}}Funding for biodiversity and taxonomy 2010.pdf
 
<br/>
 
=='''Important dates (May change a bit)'''==
 
<span style="font-size: large">
 
7 October, 2013: Paper Topic Due<br/>
 
14 October, 2013: Brief Outline with 5 references<br/>
 
14 October, 2013: Midterm<br/>
 
11 November, 2013: First draft due (May change)<br/>
 
2 December, 2013: Paper due (May change)<br/>
 
[[Category:EEB Courses]]
 
<br/>
 
EEB5347 website from 2011 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/EEB5347_2011)
 

Latest revision as of 15:27, 22 September 2017

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 F 10:45-11:45 or by appointment
Phone: 617-272-5054
email: kevin.keegan'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. Most readings will be available as PDFs, downloadable from the course website.

Schedule

Day Topics Reading/Assignment Lab
Aug 28 Organizational meeting Hubbell Reading Pdficon small.gif 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
Sep 1 Species definitions & species intermediacy
A Bit on Names Pdficon small.gif
Templeton (1989)Pdficon small.gif
Sep 4 Labor Day, No class Kevin away in Mexico
Babbidge Library resources; taxonomic literature
Sept 6 Species definitions & species intermediacy
Species 1 Lecture Pdficon small.gif
Finish reading/reread Templeton from Friday
DeQuieroz (2007)Pdficon small.gif
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 Finish species definitions & species intermediacy; start variation within species
Species II Lecture Pdficon small.gif
Erlich & Raven (1969)Pdficon small.gif
Mallet (2013) Pdficon small.gif
Meet in McCarthy Room
Taxonomic resources: key websites; taxonomy exercise Pdficon small.gif.
Online Resource List Pdficon small.gif
BioBlitz in Stamford.
Sept 13 Subspecies and geographic variation Send Wagner an example (~3 ppt slides) of intraspecific geographic variation before 11:59 PM Sunday
Sept 15 lab
Sept 18 Variation within a genotype: ontogeny & phenotypic plasticity Send Wagner an example (~3 ppt slides) of intraspecific non-geographic variation before 11:59 PM Tuesday Lab: Alpha taxonomy: finding taxonomic characters & keys; descriptions and diagnoses; taxonomic cybertools for alpha taxonomy and phylogenetics
Slides Pdficon small.gif
Notes Pdficon small.gif
Intro to Mesquite exercise Pdficon small.gif
(Wagner away on Friday)
Sept 20 Supraspecific taxa
Sept 22 lab
Sept 25 Supraspecific taxa Lab: Describing and diagnosing species; specimen/museum databases; Taxonomic cybertools: DELTA, MANTIS, Mesquite & others (Wagner away)

Phylogenetic inference

Sept 27 Phylogenetic inference: mostly a historical overview
Sept 29 lab
Oct 2 Trees and characters: types of dendrograms, rooting and polarization Lab: Mesquite II, Parsimony???
Oct 4 Taxonomic characters: polarity, outgroups, order, weighting, and step matrices
Oct 6 lab
Oct 9 Parsimony; tree searches; tree statistics Lab: Trip to American Museum of Natural History and Bronx Zoo in NYC!!!
Oct 11 Midterm exam
Oct 13 Head to NYC
Oct 16 Maximum likelihood (lecture by Lewis; Wagner away) Lab: likelihood (Garli and/or RAxML) and Bayesian analyses
Oct 18 Bayesian inference (lecture by Lewis; Wagner away)
Oct 20 lab
Oct 23 Tree reliability, sensitivity, and support measures I Lab: Tree reliability and measures
(Meet in McCarthy Room, 4th floor TLS)
Oct 25 Tree reliability, sensitivity, and support measures II
Oct 27 lab
Oct 30 Multivariate and distance methods Lab: neighbor-joining and correcting distance data (Meet in McCarthy Room, 4th floor TLS)
Nov 1 Bayesian inference (Lewis Guest Lecture) Pdficon small.gif
Nov 3 lab
Nov 6 Molecular systematics in animals (Simon) (Wagner in Denver) Lab: PAUP*: ModelTest; molecular clocks; AIC et al. (Meet in McCarthy Room, 4th floor TLS)
Nov 8 Molecular systematics in plants (Les)
Nov 10 lab
Nov 13 Data partitions; consensus; comparing trees Lab: Find and analyze your own data set; COI problem (Meet in McCarthy Room, 4th floor TLS)
Nov 15 DNA barcoding
Nov 17 lab
Nov 20 Thanksiving Thanksiving Thanksiving
Nov 22
Nov 24
Nov 27 Nomenclature Lab: Mesquite; character optimization; character correlation
Nov 29 Nomenclature; Phylocode
Dec 1 lab
Dec 4 Phylogenetic trees & evolutionary processes No lab this week
Dec 6 Special topic: Taxonomic collections
Dec 8 Special topic: Systematics and conservation biology and the future of biological systematics
Dec circa 15 Final: 8-11 AM (Bamford)

Grading

Item Percentage Points
Lab and take home exercises
25
250
Midterm Exam
20
200
Paper
25
250
Nomenclature Exercise
2
20
Class Participation
3
30
Final Exam
25
250
Total
100
1000

Term Paper


Each student will be required to prepare a paper that will be due on December 2. Acceptable styles: (1) a literature review that is structured to be a thesis chapter; (2) grant proposal; (3) stand-alone review a subject relevant to systematic theory or methodology.

Important Dates

Date Milestone
6 October 2017 conference; topic selection
20 October 2017 outline with 5+ references
17 November 2017 first draft due
1 December 2017 paper due