Difference between revisions of "Principles and Methods of Systematic Biology (EEB 5347)"
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− | [[Image: | + | [[Image:AMNH_2013.jpg|right|''2013 Class on top of the AMNH'']] |
− | + | ||
− | <span style="font-size: large">Lecture MW 9: | + | <span style="font-size: large">Fall 2013<br/> |
+ | |||
+ | <span style="font-size: large">Lecture MW 9:05-10:35 In the Bamford Conference Room TLS 171B<br/> | ||
+ | Lab F 9:05-10:35 Probably the McCarthy Room, 4th floor TLS<br/> | ||
<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/> | ||
Phone: 486-2139<br/> | Phone: 486-2139<br/> | ||
− | office hours | + | office hours open; best to call or email ahead<br/> |
− | email: [mailto:david.wagner | + | email: [mailto:david.wagner'at'uconn.edu david.wagner'at'uconn.edu]<br/> |
<br/> | <br/> | ||
− | '''Graduate Teaching Assistant''': | + | '''Graduate Teaching Assistant''': Russ Meister<br/> |
− | Office hours: | + | Office hours: BioPharm 323 Stop by or by appointment <br/> |
− | Phone: 486- | + | Phone: 486-3947<br/> |
− | email: [mailto: | + | email: [mailto:russell.meister'at'uconn.edu russell.meister'at'uconn.edu]<br/> |
<br/> | <br/> | ||
== '''Textbook and readings''' == | == '''Textbook and readings''' == | ||
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!style="background:#008080;" width="315"|Reading/Assignment | !style="background:#008080;" width="315"|Reading/Assignment | ||
!style="background:#00B7EB;" width="275"|Lab | !style="background:#00B7EB;" width="275"|Lab | ||
− | |||
− | |||
− | |||
|- | |- | ||
− | | | + | |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 | ||
|- | |- | ||
− | | | + | |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}} |
|- | |- | ||
− | | | + | | Aug 30 ||Species definitions & species intermediacy & collections tour <!--Species definitions & species intermediacy<br/> |
+ | {{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}} | ||
|- | |- | ||
− | |Sept | + | |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) ''' |
|- | |- | ||
− | |Sept | + | |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) |
|- | |- | ||
− | |Sept | + | |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 | + | |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}} |
− | || {{pdf|http://hydrodictyon.eeb.uconn.edu/ | + | |
|- | |- | ||
− | |Sept | + | |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) --> | ||
|- | |- | ||
− | |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 13 || lab || lab <br/> Dave's names lecture {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/c/c6/A_bit_on_names.pdf}} |
+ | |- | ||
+ | |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}} | ||
+ | |- | ||
+ | |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 {{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)''' | ||
+ | |- | ||
+ | |Sept 25 || Phylogenetic inference: mostly a historical overview {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/7/7a/Intro_Phylogenetic_Inference_2013.pdf}} || | ||
+ | |- | ||
+ | |Sept 27 || lab || 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)''' | ||
+ | |- | ||
+ | |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) || | ||
+ | |- | ||
+ | |Oct 4 || lab || 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)''' | ||
+ | |- | ||
+ | |Oct 9 || Search algorithms; algorithmic power, accuracy, and inconsistency {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/3/38/Parsimony2013.pdf}} || | ||
+ | |- | ||
+ | |Oct 11 || lab || lab | ||
+ | |- | ||
+ | |Oct 14 || Midterm exam || || rowspan="3"| 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 {{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 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}} | ||
+ | |- | ||
+ | |Oct 25 || 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)''' | ||
+ | |- | ||
+ | |Oct 30 || Bayesian inference (Lewis Guest Lecture) {{pdf|http://hydrodictyon.eeb.uconn.edu/people/plewis/downloads/Bayesian_30Oct2013.key.pdf}} || | ||
+ | |- | ||
+ | |Nov 1 || lab || | ||
+ | |- | ||
+ | |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)''' | ||
+ | |- | ||
+ | |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) {{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)''' | ||
+ | |- | ||
+ | |Nov 13 || Lab Today, not Friday! || lab | ||
+ | |- | ||
+ | |Nov 15 || Nomenclature {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/4/46/Nomenclature2013Reduced.pdf}} || 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 {{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)''' | ||
+ | |- | ||
+ | |Nov 20 || Nomenclature; Phylocode || | ||
+ | |- | ||
+ | |Nov 22 || Lab || Lab | ||
+ | |- | ||
+ | |Nov 25 ||Thanksgiving Recess || || rowspan="3"| Thanksgiving Recess, Do NOT meet in McCarthy Room | ||
+ | |- | ||
+ | |Nov 27 || Thanksgiving Recess || | ||
+ | |- | ||
+ | |Nov 29 || Thanksgiving Recess || | ||
+ | |- | ||
+ | |Dec 2 ||Special topic: Nomenclature 2 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/3/35/Nomenclature2_2013.pdf}} || || rowspan="3"| No lab this week '''DO NOT Meet in McCarthy Room''' | ||
+ | |- | ||
+ | |Dec 4 || Special topic: Taxonomic collections {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/4/42/Collections2013.pdf}} || Mares 2009 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/8/8c/Mares2009.pdf}} Thomson 2005 BioScience (http://www.actionbioscience.org/evolution/thomson.html) | ||
+ | |- | ||
+ | |Dec 6 || Special topic: Phylogenetic trees & evolutionary processes|| | ||
+ | |- | ||
+ | |Dec 11 || Final: 8-11 AM || || | ||
+ | |- | ||
+ | <!--|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 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) | |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) | ||
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|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 | |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 | ||
|- | |- | ||
− | |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|| | + | |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 || |
|- | |- | ||
|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) | |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) | ||
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|Oct 9 ||Lab ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Felsenstein2004.pdf}}Felsenstein2004.pdf(For 10/16) | |Oct 9 ||Lab ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Felsenstein2004.pdf}}Felsenstein2004.pdf(For 10/16) | ||
|- | |- | ||
− | |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 | + | |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 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|| | ||
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|Oct 23 ||AMNH Trip || | |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 | + | |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 28 ||Likelihood(Guest Lecture: Paul Lewis)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Likelihood_28Oct2009_1perpage.pdf}}Likelihood.pdf|| | ||
Line 80: | Line 157: | ||
|Oct 30 ||Lab || | |Oct 30 ||Lab || | ||
|- | |- | ||
− | |Nov 2 ||Swine flu class cancelled||||rowspan="3"|Modeltest, AIC & hLRT, Molecular clocks | + | |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 4 ||Bayesian phylogenetics (Paul Lewis)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Bayesian_2Nov2009_1perpage.pdf}}Bayesian phylogenetics.pdf|| | ||
Line 86: | Line 163: | ||
|Nov 6 ||Lab || | |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 | + | |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 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|| | ||
Line 92: | Line 169: | ||
|Nov 13 ||Lab || | |Nov 13 ||Lab || | ||
|- | |- | ||
− | |Nov 16 ||Data partitions; consensus; ILD<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Consensus%202009.pdf}}Consensus | + | |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 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 | ||
Line 99: | Line 176: | ||
|- | |- | ||
|Nov 23-28 ||No class-Thanksgiving Break|| | |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'''== | =='''Supplementary Reading'''== | ||
− | |||
!style="background:#2A52BE;" width="275"|Topics | !style="background:#2A52BE;" width="275"|Topics | ||
!style="background:#008080;" width="975"|Additional Reading | !style="background:#008080;" width="975"|Additional Reading | ||
Line 109: | Line 199: | ||
{{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 | ||
|- | |- | ||
− | |DNA Barcodes||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/elias%202007.pdf}}Elias et al. 2007.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'''== | =='''Grading'''== | ||
{| border="1" cellpadding="1" | {| border="1" cellpadding="1" | ||
− | | Lab and take home exercises || 20% || | + | | Lab and take home exercises || 20% || 200 pts |
|- | |- | ||
− | | Midterm || 20% || | + | | Midterm || 20% || 200 pts |
|- | |- | ||
− | | Term paper || | + | | Term paper || 22% || 220 pts |
|- | |- | ||
− | | Nomenclature exercise || | + | | Nomenclature exercise || 1% || 10 pts |
|- | |- | ||
− | | | + | | Participation || 2% || 20 pts |
|- | |- | ||
− | | '''Total''' || '''100%''' || ''' | + | | Final || 35% || 350 pts |
+ | |- | ||
+ | | '''Total''' || '''100%''' || '''1000 pts''' | ||
|} | |} | ||
<br/> | <br/> | ||
+ | |||
=='''Term paper'''== | =='''Term paper'''== | ||
− | Each student will be required to prepare a paper that will be due on December | + | 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 | + | 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/> | <br/> | ||
− | =='''Important dates'''== | + | |
+ | =='''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"> | <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/> | |
+ | 7 December, 2013: Paper due (May change)<br/> | ||
[[Category:EEB Courses]] | [[Category:EEB Courses]] | ||
+ | <br/> | ||
+ | EEB5347 website from 2011 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/EEB5347_2011) |
Revision as of 14:45, 5 December 2013
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 |
Lecture instead of lab this week | |
Aug 28 | The many roles of biological systematics Species Definitions Species Level Terminology |
Hubbell Reading | |
Aug 30 | Species definitions & species intermediacy & collections tour | Templeton 1989 De Queiroz 2007 | |
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 |
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 Make a slide or two about geographic subspecific variation Nichols Gene tree species tree discordance | |
Sept 9 | Species definitions & species intermediacy; start variation within species | Mallet 2013 Mallet 2013 Glossary if needed Wilson and Brown Winston Chapter (emailed) |
Taxonomic resources: key websites, taxonomy exercise assigned (Meet in McCarthy Room, 4th floor TLS) Literature Search Activity Online Resource List |
Sept 11 | Subspecies and phylogeography | Read Futuyma's section on gene tree/species tree issues (from the Species chapter distributed earlier, pages 476-478) Mayr Chapter 4 (emailed) Send Dave or myself an example slide of infrasubspecific variation Possibly read this too | |
Sept 13 | lab | lab Dave's names lecture | |
Sept 16 | Subspecies (cont.) and Genes Trees versus Species Tress | Lab: Alpha taxonomy: finding taxonomic characters & keys; descriptions and diagnoses; introduction to Mesquite’s alpha taxonomic features Mesquite I (Meet in McCarthy Room, 4th floor TLS) Dave's Tiger Beetle Intro | |
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 | NYC field trip (Do NOT meet in McCarthy Room, 4th floor TLS) | |
Sept 25 | Phylogenetic inference: mostly a historical overview | ||
Sept 27 | lab | lab | |
Sept 30 | Trees and characters: types of dendrograms, rooting and polarization; rooting and polarization |
Page and Holmes: Trees Forey et al. Chapters 2 and 3 Krell and Cranston 2004 Possibly one more, by Felsenstein |
Describing and diagnosing species; specimen/museumdatabases DELTA, MANTIS & other taxonomic computer tools. (Meet in McCarthy Room, 4th floor TLS) |
Oct 2 | Taxonomic characters: polarity, outgroups, order, and weighting (Combined with Sept 30 lecture) | ||
Oct 4 | lab | lab | |
Oct 7 | Distance methods, UPGMA, neighbor-joining, correcting distance data | Page and Holmes Chapter 6 Felsenstein 2004 Strimmer and Haeseler 2009 |
Lab: Neighbor-joining and corrected distances; PAUP* (introduction) (Meet in McCarthy Room, 4th floor TLS) |
Oct 9 | Search algorithms; algorithmic power, accuracy, and inconsistency | ||
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 | Page and Holmes Chapter 6 (Part 2) | Lab: PAUP*: parsimony; tree searches; tree statistics (Meet in McCarthy Room, 4th floor TLS) |
Oct 23 | Data partitions; consensus; comparing trees | Optional Readings: Phylogenetics Handbook Chapters 10 and 12 , Felsenstein Chapter 20 | |
Oct 25 | Lab | ||
Oct 28 | Maximum likelihood (Lewis Guest Lecture) | Optional Readings: Phylogenetics Handbook Chapter 6 Phylogenetics Handbook Chapter 7 |
Lab: PAUP*: ModelTest; molecular clocks; AIC et al. (Meet in McCarthy Room, 4th floor TLS) |
Oct 30 | Bayesian inference (Lewis Guest Lecture) | ||
Nov 1 | lab | ||
Nov 4 | DNA Barcoding | Required: A. fulgerator and Ratnasignham & Herbert 2013 Optional: Bergman et al. 2013 and Morrales and Vences 2013 |
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) | 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 | 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 Vane-Wright Nomenclature Concern Name Poems The Phylocode Reading 2009 (http://www.ohiou.edu/phylocode/preface.html) Linnaean naming system challenges 2004 (http://www.newscientist.com/article.ns?id=dn6369) / ADDITIONALLY, choose one phylocode reading from the optional ones loaded below |
Lab: Mesquite; character optimization; character correlation (Meet in McCarthy Room, 4th floor TLS) |
Nov 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: Nomenclature 2 | No lab this week DO NOT Meet in McCarthy Room | |
Dec 4 | Special topic: Taxonomic collections | Mares 2009 Thomson 2005 BioScience (http://www.actionbioscience.org/evolution/thomson.html) | |
Dec 6 | Special topic: Phylogenetic trees & evolutionary processes | ||
Dec 11 | Final: 8-11 AM |
Topics | Additional Reading |
---|---|
Species as ranked taxa and species concepts | Application of Evolutionary Species concept.pdf Species concept for prokaryotes.pdf Is the BSC showing its age?.pdf Importance of stating species concept for conservation purposes.pdf Impact of species concepts on biodiversity studies.pdf The need for specifying species concepts.pdfOn the failure of modern species concepts.pdf Species as ranked taxa.pdf Does the choice of species concept result in an increase in bird species?.pdf Method for delimiting Cohesion speceis.pdf |
DNA Barcodes | Elias et al. 2007.pdf Janzen et al 2005.pdf Ten Reasons For Barcoding.pdf Will & Rubinoff 2004.pdf Hebert and Gregory 2005.pdf Moritz and Cicero 2004.pdf Hebert et al.2003.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
|
Optional Nomenclature Readings | Schuh & Brower 2009 Jones and Luchsinger Conniff 1996 Gould 1990 |
Optional Phylocode Readings | Benton 2007 Donoghue and Gauthier Lee and Skinner 2007 Nixon et al. 2003 Rieppel 2006 Platnick 2012 DeQueiroz 2013 DeQueiroz and Donoghue 2011 DeQueiroz and Donoghue 2013 DeQueiroz 2012 |
Grading
Lab and take home exercises | 20% | 200 pts |
Midterm | 20% | 200 pts |
Term paper | 22% | 220 pts |
Nomenclature exercise | 1% | 10 pts |
Participation | 2% | 20 pts |
Final | 35% | 350 pts |
Total | 100% | 1000 pts |
Term paper
Each student will be required to prepare a paper that will be due on December 2nd. Styles that have been adopted in the past include (1) a literature review
that could be incorporated into a thesis chapter or (2) an NSF Doctoral Dissertation Improvement Grant proposal. Another angle would be to (3) review a subject relevant to systematic theory or methodology. If you are considering the DDIG option this year's Dissertation Improvement Grants will be due on October 10th, 2013. Visit http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5234 htm
Funding sources for taxonomy and biodiversity
Here is a comprehensive guide to potential funding sources for taxonomy and biodiversity studies. It was created in 2010, so most sources are up to date.
Funding for biodiversity and taxonomy 2010.pdf
Important dates (May change a bit)
7 October, 2013: Paper Topic Due
14 October, 2013: Brief Outline with 5 references
14 October, 2013: Midterm
11 November, 2013: First draft due (May change)
7 December, 2013: Paper due (May change)
EEB5347 website from 2011 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/EEB5347_2011)