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/>
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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 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-->
 
|| || rowspan="3"| Lecture instead of lab this week
 
|| || rowspan="3"| Lecture instead of lab this week
 
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|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}}
 
|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 9  || Species definitions & species intermediacy; 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 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 || Subspecies and geographic variation {{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 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}}
 
<!--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) -->
 
<!--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}}
 
|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 16 || Variation within a genotype:  ontogeny & phenotypic plasticity {{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 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 genotype || Macrotaxonomy and plant systematics readings sent out by Dave
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|Sept 18 ||  Variation within a genotype:  ontogeny & phenotypic plasticity || Macrotaxonomy and plant systematics readings sent out by Dave
 
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|Sept 20 || lab || lab
 
|Sept 20 || lab || lab
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|Sept 27 || lab || lab
 
|Sept 27 || lab || lab
 
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|Sept 30 || Trees and characters; types of dendrograms;<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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|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 || Taxonomic characters: polarity, outgroups, order, weighting, and step matrices {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/8/8b/Characters_1_2013.pdf}} (Combined with Sept 30 lecture)  ||  
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|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 || lab || lab
 
|Oct 4 || lab || lab
 
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|Oct 7 || Distance methods, UPGMA, neighbor-joining, correcting distance data, multivariate methods {{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 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; search algorithms; algorithmic power, accuracy, and inconsistency {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/3/38/Parsimony2013.pdf}}  ||
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|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 || lab || lab
 
|Oct 11 || lab || lab
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|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)'''
 
|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 || Reliability and measures of tree support , Consensus {{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 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 || Lab ||  
 
|Oct 25 || Lab ||  
 
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|Oct 28 || Maximum likelihood (Lewis Guest Lecture)  {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/7/76/Lewis_Likelihood_2013.pdf}} ||   || rowspan="3"| Lab:  Likelihood (Garli and/or RAxML) and Bayesian analyses '''(Meet in McCarthy Room, 4th floor TLS)'''
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|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 || Bayesian inference (Lewis Guest Lecture) ||  
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|Oct 30 || Bayesian inference (Lewis Guest Lecture) {{pdf|http://www.eeb.uconn.edu/people/plewis/downloads/Bayesian_30Oct2013.key.pdf}} ||  
 
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|Nov 1 || lab  ||
 
|Nov 1 || lab  ||
 
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|Nov 4 || Data partitions; consensus; comparing trees|| || rowspan="3"| Lab:  PAUP*: ModelTest; molecular clocks; AIC et al. '''(Meet in McCarthy Room, 4th floor TLS)'''
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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 plants (Les Guest Lecture) ||
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|Nov 6 || Molecular systematics in plants (Les Guest Lecture) Emailed out to all of you. ||
 
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|Nov 8 || lab || lab
 
|Nov 8 || lab || lab
 
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|Nov 11 || Molecular systematics in animals (Simon Guest Lecture) || || rowspan="3"| COI Barcoding and analyzing your own data sets '''(Meet in McCarthy Room, 4th floor TLS)'''
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|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 || lab || lab
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|Nov 13 || Lab Today, not Friday! || lab
 
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|Nov 15 || DNA barcoding ||
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|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 18 || Nomenclature || || rowspan="3"| Lab:  Mesquite; character optimization; character correlation '''(Meet in McCarthy Room, 4th floor TLS)'''
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|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 || Nomenclature; Phylocode ||  
 
|Nov 20 || Nomenclature; Phylocode ||  
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|Dec 6 || Special topic:  Systematics and conservation biology and the future of biological systematics||  
 
|Dec 6 || Special topic:  Systematics and conservation biology and the future of biological systematics||  
 
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|Dec 14 || Final: 8-11 AM  || ||
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|Dec 11 || Final: 8-11 AM  || ||
 
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<!--|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
 
<!--|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
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{{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
 
{{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
 
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|DNA Barcodes||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/elias%202007.pdf}}Elias et al. 2007.pdf<br/>{{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<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/TenReasonsBarcoding.pdf}}Ten Reasons For Barcoding.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Will%20%26%20Rubinoff%202004.pdf}}Will & Rubinoff 2004.pdf<br/>{{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<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hebert_et_al_2003_DNABarcodes.pdf}}Hebert et al.2003.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/PLoS_Birds_Hebert_et_al_2004.pdf}}PLoS_Birds_Hebert et al. 2004.pdf
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|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
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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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<br/>Janzen and Hallwachs 2011  http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018123
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<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}}
 
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Revision as of 11:20, 22 November 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

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


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; start 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 phylogeography 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 Subspecies (cont.) and Genes Trees versus Species Tress 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: ontogeny & phenotypic plasticity 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;
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, and weighting Pdficon small.gif (Combined with Sept 30 lecture)
Oct 4 lab lab
Oct 7 Distance methods, UPGMA, neighbor-joining, correcting distance data 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 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 Data partitions; consensus; comparing trees 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
Lab: PAUP*: ModelTest; molecular clocks; AIC et al. (Meet in McCarthy Room, 4th floor TLS)
Oct 30 Bayesian inference (Lewis Guest Lecture) Pdficon small.gif
Nov 1 lab
Nov 4 DNA Barcoding Pdficon small.gif Required: A. fulgerator Pdficon small.gif and Ratnasignham & Herbert 2013 Pdficon small.gif
Optional: Bergman et al. 2013 Pdficon small.gif and Morrales and Vences 2013 Pdficon small.gif
Lab: Likelihood (Garli and/or RAxML) and Bayesian analyses (Meet in McCarthy Room, 4th floor TLS)
Nov 6 Molecular systematics in plants (Les Guest Lecture) Emailed out to all of you.
Nov 8 lab lab
Nov 11 Molecular systematics in animals (Simon Guest Lecture) Pdficon small.gif Lab: Find and analyze your own data set; COI problem, WEDNESDAY, not Friday (Meet in McCarthy Room, 4th floor TLS)
Nov 13 Lab Today, not Friday! lab
Nov 15 Nomenclature Pdficon small.gif See the many optional nomenclature readings below.
Nov 18 Nomenclature, James Prosek will join our discussion today, it should be quite a class DeQueiroz Phylocode 2006 Pdficon small.gif
Vane-Wright Nomenclature Concern Pdficon small.gif
Name Poems Pdficon small.gif
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 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 11 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

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
Janzen and Hallwachs 2011 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018123
Joly et al. 2013, Ecology in the age of DNA barcoding: the resource, the promise, and the challenges ahead Pdficon small.gif

Optional Nomenclature Readings Schuh & Brower 2009 Pdficon small.gif Jones and Luchsinger Pdficon small.gif Conniff 1996 Pdficon small.gif Gould 1990 Pdficon small.gif
Optional Phylocode Readings Benton 2007 Pdficon small.gif Donoghue and Gauthier Pdficon small.gif Lee and Skinner 2007 Pdficon small.gif Nixon et al. 2003 Pdficon small.gif Rieppel 2006 Pdficon small.gif
Platnick 2012 Pdficon small.gif DeQueiroz 2013 Pdficon small.gif DeQueiroz and Donoghue 2011 Pdficon small.gif DeQueiroz and Donoghue 2013 Pdficon small.gif
DeQueiroz 2012 Pdficon small.gif

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.
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)

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