

(258 intermediate revisions by 3 users not shown) 
Line 1: 
Line 1: 
−  [[Image:AMNH2009.jpgright''2009 Class on top of the AMNH'']]
 +  <span style="fontsize: large">Fall 2017<br/> 
−  [[Image:AMNH2011_roof.jpgright''2011 Class on top of the AMNH'']]
 +  
   
−  <span style="fontsize: large">Fall 2011<br/>
 +  <span style="fontsize: large">Lecture MW 9:0510:45 In TLS 313<br/> 
−   +  Lab F 9:0510:45 McCarthy Room, 4th floor TLS<br/> 
−  <span style="fontsize: large">Lecture MW 9:0010:30, Lab F 9:0010:30<br/>  +  
 <br/>   <br/> 
 <span style="fontsize: large">'''Instructor''': Dr. David L. Wagner, TLS Rm 471<br/>   <span style="fontsize: large">'''Instructor''': Dr. David L. Wagner, TLS Rm 471<br/> 
 Phone: 4862139<br/>   Phone: 4862139<br/> 
−  office hours as available<br/>  +  office hours open; best to call or email ahead<br/> 
 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''': Chris Owen<br/>  +  
−  Office hours: BioPharm 325 Wednesdays 10:3011:30 or by appointment<br/>  +  '''Graduate Teaching Assistant''': Kevin Keegan<br/> 
−  Phone: 4866650<br/>  +  Office hours: TLS 461 F 10:4511:45 or by appointment<br/> 
−  email: [mailto:christopher.l.owen'at'uconn.edu christopher.l.owen'at'uconn.edu]<br/>  +  Phone: 6172725054<br/> 
 +  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.  +  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/> 
 +  
 =='''Schedule'''==   =='''Schedule'''== 
 { border="1" cellpadding="2"   { border="1" cellpadding="2" 
Line 25: 
Line 26: 
 !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 29 Class canceled due to Hurricane Irene<br/><!{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Introduction%202009%20class%20notes.pdf}}Introduction 2009 class notes.pdf {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Syllabus%202009.pdf}}Syllabus.pdf<br/>{{pdfhttp://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 31 Organizational meeting, an introduction to biological systematics{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hubbell.pdf}}Hubbell.pdf (for Friday)<br/>http://www.nytimes.com/2009/08/11/science/11naming.html (for Friday)<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mayr_Ashlock1991_pgs118.pdf}}Mayr&Ashlock1991_pgs118.pdf (optional)  +  Aug 28 Organizational meeting  Hubbell Reading {{pdfhttp://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 
     
−   Sept 2 The many roles of biological systematics & collections tour <!Species definitions & species intermediacy<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20Definitions.pdf}}Species Definitions.pdf {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20Level%20Terminology%202009.pdf}}Species Level Terminology 2009.pdf>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/A_Templeton%201989.pdf}}Templeton 1989.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/De%20Queiroz%202007.pdf}}De Queiroz 2007.pdf<br/>http://en.wikipedia.org/wiki/Species#Definitions_of_species<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Futuyma_spconcepts_445451.pdf}}Futuyma_spconcepts_445451.pdf  +  Aug 30 An introduction to biological systematics; The many roles of biological systematics and collections <br/>  
     
−   Sept 5 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 '''  +  Sep 1 Species definitions & species intermediacy<br/> A Bit on Names {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/A_bit_on_names_2017.pdf}} Templeton (1989){{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/A_Templeton%201989.pdf}} 
     
−  Sept 7  {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20I%202011.pdf}}Species I 2011.pdf   +  Sep 4 Labor Day, No class   rowspan="3" Kevin away in Mexico<br/>Babbidge Library resources; taxonomic literature 
     
−  Sept 9  Meet in library  Meet in library  +  Sept 6 Species definitions & species intermediacy <br/> Species 1 Lecture {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species_I_2017.pdf}} Finish reading/reread Templeton from Friday<br/> DeQuieroz (2007){{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/De%20Queiroz%202007.pdf}} 
     
−  Sept 12  {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20II%202011.pdf}}Species II 2011.pdf  {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Ehrlich%26Raven_1969.pdf}}Ehrlich&Raven1969.pdf  rowspan="3" Taxonomic resources: key websites, taxonomy exercise assigned '''(Meet in McCarthy Room, 4th floor TLS)'''  +  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 14  {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20III%202011.pdf}}Species III 2011.pdf   +  Sept 11  Finish species definitions & species intermediacy; start variation within species <br/> Species II Lecture {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species_II_2017.pdf}}  Erlich & Raven (1969){{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Ehrlich&Raven_1969.pdf}} <br/> Mallet (2013) {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mallett_2013.pdf}}  rowspan="3" '''Meet in McCarthy Room'''<br/>Taxonomic resources: key websites; taxonomy exercise {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab1_Literature_Search_2017_dlw.doc}}.<br/>Online Resource List {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab1_tax_resources_online_2017_dlw.pdf}}<br/> BioBlitz in Stamford. 
−  <!Individual variation(population variation){{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20II.pdf}}Species II.pdf  {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Futuyma_pg239to263master1.pdf}}Futuyma_pg239263.pdf (For 9/18) >
 +  
     
−  Sept 16  lab  lab  +  Sept 13  Subspecies and geographic variation  Send Wagner an example (~3 ppt slides) of intraspecific geographic variation '''before 11:59 PM Sunday''' 
     
−  Sept 19  {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Subspecies%202011.pdf}}Subspecies 2011.pdf   rowspan="3" Intro to Mesquite and Morphological Matrices '''(Meet in McCarthy Room, 4th floor TLS)'''  +  Sept 15  lab  
     
−  Sept 21  Infrapopulation variation (lecture sent via email)   +  Sept 18  Variation within a genotype: ontogeny & phenotypic plasticity  Send Wagner an example (~3 ppt slides) of intraspecific nongeographic 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 {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab2_Presentation_2017.pdf}} <br/> Notes {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab2_Presentation_2017_notes.pdf}} <br/>Intro to Mesquite exercise {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab2_mesquite_exercise_2017.pdf}} <br> (Wagner away on Friday) 
     
−  Sept 23  lab  lab  +  Sept 20  Supraspecific taxa  
     
−  Sept 26  {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Higher%20Categories%202011.pdf}}Higher Categories 2011.pdf   rowspan="3" Keys, species descriptions, and cybertaxonomy '''(Meet in McCarthy Room, 4th floor TLS)'''  +  Sept 22  lab  
     
−  Sept 28  {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Intro%20to%20Phylogenetic%20Inferencev2_2011.pdf}}Intro to phylogenetic inference   +  Sept 25  Supraspecific taxa   rowspan="3" Lab: Describing and diagnosing species; Keys; Taxonomic cybertools: DELTA, Lucid, MANTIS <br/> Example: Descriptions and Diagnoses {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Meister_Description_Diagnoses.pdf}}<br/>A bit on keys {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab3_Handout_Keys_2017.pdf}}<br/>(Wagner away) 
     
−  Sept 30  lab  lab  +  Sept 27  Phylogenetic inference: mostly a historical overview  
     
−  Oct 3  Trees and characters; types of dendrograms;<br/>rooting and polarization {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Forey%20et%20al%201992%20Chap2%263.pdf}}Forey et al 1992 Chap2&3.pdf<br/>(only read chapter 2)<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%20%26%20Holmes%201998.pdf}}Page & Holmes 1998.pdf  rowspan="3" Manipulating molecular characters with Mesquite<br/>and a BLAST tutorial '''(Meet in McCarthy Room, 4th floor TLS)'''  +  Sept 29  lab  
     
−  Oct 5  {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters_1%202011.pdf}}Characters_1 2011.pdf {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Krell%26Cranston.pdf}}Krell&Cranston.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Felsenstein2004.pdf}}Felsenstein2004.pdf  +  Oct 2  Trees and characters: types of dendrograms, rooting and polarization   rowspan="3" Lab: Mesquite II, Parsimony??? 
     
−  Oct 7  lab  lab  +  Oct 4  Taxonomic characters: polarity, outgroups, order, weighting, and step matrices  
     
−  Oct 10 {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Multivariate%20Methods%202011.pdf}}Multivariate Methods 2011.pdf   rowspan="3" Parsimony and distant methods with PAUP '''(Meet in McCarthy Room, 4th floor TLS)'''  +  Oct 6  lab  
     
−  Oct 12  {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Distance%20Methods%202011.pdf}}Distance Methods 2011.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Parsimony%202011.pdf}}Parsimony 2011.pdf <br/> {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/ParsimonyLectureForMidTerm.ppt}}ParsimonyLectureForMidTerm.ppt {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes_Chap6.pdf}}Page&Holmes_Chap6.pdf  +  Oct 9  Parsimony; tree searches; tree statistics   rowspan="3" Lab: Trip to American Museum of Natural History and Bronx Zoo in NYC!!! 
     
−  Oct 14  lab  lab  +  Oct 11 ''' Midterm exam'''  
     
−  Oct 17  Midterm exam {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/PageHolmesChptr5.pdf}}PageHolmesChptr5.pdf rowspan="3" Parsimony with PAUP '''(Meet in McCarthy Room, 4th floor TLS)'''  +  Oct 13  '''Head to NYC'''  
     
−  Oct 19 Midterm Review   +  Oct 16  Maximum likelihood (lecture by Lewis; Wagner away)   rowspan="3" Lab: likelihood (Garli and/or RAxML) and Bayesian analyses 
     
−  Oct 21  lab  lab  +  Oct 18  Bayesian inference (lecture by Lewis; Wagner away)  
     
−  Oct 24 lab lab  rowspan="3" PAUP*: tree searches and tree statistics<br/>'''(Meet in McCarthy Room, 4th floor TLS)'''  +  Oct 20  lab  
     
−  Oct 26  {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Reliability%202011.pdf}}Reliability 2011.pdf  +  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 28  No Lab/AMNH & Bronx Zoo Trip  {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lewis_2001TREE161.3037.pdf}}Lewis_2001_TREE.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Holder%26Lewis2003NatRevGen.pdf}}Holder&Lewis2003_NatRevGen.pdf  +  Oct 25  Tree reliability, sensitivity, and support measures II  
     
−  Oct 31 lab lab  rowspan="3" Model comparison with Modeltest '''(Meet in McCarthy Room, 4th floor TLS)'''  +  Oct 27  lab  
     
−  Nov 2  {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Likelihood_2Nov2011.pdf}}Guest Lecture Paul Lewis   +  Oct 30  Multivariate and distance methods   rowspan="3" Lab: neighborjoining and correcting distance data '''(Meet in McCarthy Room, 4th floor TLS)''' 
     
−  Nov 4  {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Bayesian_4Nov2011.pdf}}Guest Lecture Paul Lewis   +  Nov 1  Bayesian inference (Lewis Guest Lecture) {{pdfhttp://hydrodictyon.eeb.uconn.edu/people/plewis/downloads/Bayesian_30Oct2013.key.pdf}}  
     
−  Nov 7  Data partitions; consensus; comparing tree topologies<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Consensus%202011.pdf}}Consensus 2011.pdf   rowspan="3" Maximum likelihood and Bayesian inference '''(Meet in McCarthy Room, 4th floor TLS)'''  +  Nov 3  lab  
     
−  Nov 9  Guest lecture by Don Les:<br/>Molecular systematics in plants(lecture too big, so I emailed it to you)   +  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 11  lab  lab  +  Nov 8  Molecular systematics in plants (Les)  
     
−  Nov 14  Guest lecture by Chris Simon:<br/>Molecular systematics in animals<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/CSimon%20LectureHow%20Molecules%20Evolve.%20Parts%20I%20%26%20II.pdf}}CSimon Lecture.pdf  rowspan="3" COI Barcoding and analyzing your own data sets '''(Meet in McCarthy Room, 4th floor TLS)'''  +  Nov 10  lab  
     
−  Nov 16  lab  lab  +  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 18  Procedural flow chart for phylogenetic analysis; DNA barcoding<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/DNA%20Barcodes%2018%20Nov%20%5BCompatibility%20Mode%5D.pdf}}DNA Barcodes 18 Nov 2011.pdf  +  Nov 15  DNA barcoding  
−    +  
     
−  Nov 21  Thanksgiving recess   rowspan="3" Thanksgiving recess '''DO NOT Meet in McCarthy Room'''  +  Nov 17  lab  
     
−  Nov 23  Thanksgiving recess   +  Nov 20 rowspan="3" '''Thanksiving'''  rowspan="3" '''Thanksiving'''  rowspan="3" '''Thanksiving''' 
     
−  Nov 25  Thanksgiving recess  +  Nov 22 
     
−  Nov 28  Nomenclature<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Nomenclature%202011%20final.pdf}}Nomenclature 2011 final.pdf  rowspan="3" Mesquite and R: Ancestral states and character correlation '''(Meet in McCarthy Room, 4th floor TLS)'''  +  Nov 24 
     
−  Nov 30  Nomenclature; phylocode   +  Nov 27  Nomenclature   rowspan="3" Lab: Mesquite; character optimization; character correlation 
     
−  Dec 2  lab  lab  +  Nov 29  Nomenclature; Phylocode  
     
−  Dec 5 Patterns and process<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Patterns%20and%20Processes%202011%20One.pdf}}Patterns and Processes 2011 One.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Patterns%20and%20Processes%202011%20Two.pdf}}Patterns and Processes 2011 Two.pdf   rowspan="3" No lab this week '''DO NOT Meet in McCarthy Room'''  +  Dec 1  lab  
     
−  Dec 7  Taxonomic collections<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Importance%20of%20Collections%202011.pdf}}Importance of Collections 2011.pdf   +  Dec 4  Phylogenetic trees & evolutionary processes   rowspan="3" '''No lab this week''' 
     
−  Dec 9  Biodiversity Crisis and Future of Systematics<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Biodiversity%20Crisis%20and%20Future%20of%20Systematics.pdf}}Biodiversity Crisis and Future of Systematics.pdf   +  Dec 6  Special topic: Taxonomic collections  
     
−  <!Sept 21 Variation within a genotype: ontogeny & phenotypic plasticity{{pdfhttp://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/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Winston%201999.pdf}}Winston 1999.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mesquite%20morphological%20matrices.pdf}}Mesquite morphological tutorial.pdf
 +  Dec 8  Special topic: Systematics and conservation biology and the future of biological systematics  
     
−  Sept 23 Supraspecfic taxa {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Higher%20Categories%202009.pdf}}Higher Categories 2009.pdf{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%20%26%20Holmes%201998.pdf}}Page & Holmes 1998.pdf(For 09/28)  +  Dec circa 15  Final: 811 AM (Bamford)  
 +  } 
 +  
 +  =='''Grading'''== 
 +  { border="1" cellpadding="1" 
 +  !width="200"Item 
 +  !width="25"Percentage 
 +  !width="25"Points 
     
−  Sept 25 Lab {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Tiger%20Beetle%20Intro%202009.pdf}}Tiger Beetle Intro 2009.pdf   +  Lab and take home exercises <div style="textalign: center">25</div>  <div style="textalign: center">250</div> 
     
−  Sept 28 Phylogenetic inference: Mostly a historical overview<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Intro%20to%20Phylogenetic%20Inference.pdf}}Intro to Phylogenetic Inference.pdf{{pdfhttp://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/>{{pdfhttp://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  +  Midterm Exam  <div style="textalign: center">20</div>  <div style="textalign: center">200</div> 
     
−  Sept 30 Trees and characters: types of dendrograms, rooting and polarization<br/>weighting and step matrices {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters1.pdf}}Characters1.pdf   +  Paper  <div style="textalign: center">25</div>  <div style="textalign: center">250</div> 
     
−  Oct 2 Lab {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Krell%26Cranston.pdf}}Krell&Cranston.pdf(For 10/05)<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Forey%20et%20al%201992%20Chap2%263.pdf}}Forey et al 1992 Chap2&3.pdf (For 10/05)  +  Nomenclature Exercise  <div style="textalign: center">2</div>  <div style="textalign: center">20</div> 
     
−  Oct 5 Taxonomic characters: polarity, outgroups, order, weighting, and step matrices<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters%20II.pdf}}Characters II.pdf{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/CompleatCladist.pdf}}Cladistics Review I.pdf<br/>{{pdfhttp://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/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mesquite%20Lab%20II}}Mesquite Lab II<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/GenBank%20Tutorial%202009}}GenBank Tutorial  +  Class Participation  <div style="textalign: center">3</div>  <div style="textalign: center">30</div> 
     
−  Oct 7 More on trees<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/More%20on%20Trees.pdf}}Trees.pdf{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Cladistics.pdf}}Cladistics Review II.pdf  +  Final Exam  <div style="textalign: center">25</div>  <div style="textalign: center">250</div> 
     
−  Oct 9 Lab {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Felsenstein2004.pdf}}Felsenstein2004.pdf(For 10/16)  +  '''Total'''  <div style="textalign: center">'''100'''</div>  <div style="textalign: center">'''1000'''</div> 
−  
 +  } 
−  Oct 12 Distance methods, UPGMA, neighborjoining, correcting distance data, multivariate techniques<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Multivariate%20Methods%202009.pdf}}Multivariate Methods 2009.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Distance%20Methods%202009.pdf}}Distance Methods 2009.pdf{{pdfhttp://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/>neighborjoining<br/>corrected distances<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab%205_PAUP%20Intro%20revised1.doc}}Lab 5 PAUP Intro.doc
 +  
−  
 +  =='''Term Paper'''== 
−  Oct 14 Molecular systematics in animals (Simon guest lecture)<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Guest%20Lecture%20Wagner%27s%20Systematics%20How%20Molecules%20Evolve.%20Fall%2009.pdf}}How Molecules Evolve.pdf
 +  <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) standalone review a subject relevant to systematic theory or methodology. 
−  Oct 16 Lab 
 +  
−  
 +  
−  Oct 19 Exam{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Midterm%20Sample%20Questions%202009.pdf}}Midterm Sample Questions 2009.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Neighborjoining%20Exercise.pdf}}Neighborjoining Exercise.pdfrowspan="3"American Museum of Natural History
 +  
−  
 +  
−  Oct 21 Midterm Review<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Midterm%20PostExam%20Review.pdf}}Midterm PostExam Review.pdf
 +  
−  
 +  
−  Oct 23 AMNH Trip 
 +  
−  
 +  
−  Oct 26 Parsimony; search algorithms;<br/>algorithmic power, accuracy, and inconsistency<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Parsimony.pdf}}Parsimony.pdf{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes_Part2_1.pdf}}Page&Holmes_Rest_of_Ch6.pdfrowspan="3"Parsimony Lab<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab6_parsimony_2009.doc}}Lab6 Parsimony.doc
 +  
−  
 +  
−  Oct 28 Likelihood(Guest Lecture: Paul Lewis)<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Likelihood_28Oct2009_1perpage.pdf}}Likelihood.pdf
 +  
−  
 +  
−  Oct 30 Lab 
 +  
−  
 +  
−  Nov 2 Swine flu class cancelledrowspan="3"Modeltest, AIC & hLRT, Molecular clocks<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab7_2009_corrected.doc}}Lab7.doc
 +  
−  
 +  
−  Nov 4 Bayesian phylogenetics (Paul Lewis)<br/>{{pdfhttp://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/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Systematics_2009_Les.pdf}}Plant Systematics Les.pdf{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes280_285.pdf}}Page&Holmes280285.pdfrowspan="3"Garli and MrBayes Lab<br/>{{pdfhttp://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/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Reliability%202009.pdf}}Reliability 2009.pdf
 +  
−  
 +  
−  Nov 13 Lab 
 +  
−  
 +  
−  Nov 16 Data partitions; consensus; ILD<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Consensus%202009.pdf}}Consensus.pdf{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/ILD%202009.doc}}ILD 2009.docrowspan="3"COI data set analysis<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab9_barcoding_2009_corrected.doc}}Lab9 COI Barcodes.doc
 +  
−  
 +  
−  Nov 18 DNA Barcodes<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/DNA%20Barcodes.pdf}}DNA Barcodes.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/FunkOmlandARev.pdf}}Funk & Omland.pdf{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Astraptes%20fulgerator.pdf}}Hebert et al. 2004.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Meyer%20and%20Paulaypdf%20copy.pdf}}Meyer and Paulay.pdf
 +  
−  
 +  
−  Nov 20 Lab 
 +  
−  
 +  
−  Nov 2328 No classThanksgiving Break
 +  
−  
 +  
−  Nov 30 Nomenclature<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Nomenclature%202009.pdf}}Nomenclature 2009.pdf{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Berenbaum%20Article.pdf}}Berenbaum Article.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Conniff%20article.pdf}}Conniff article.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Gould_Bully%20for%20Bront.pdf}}Gould_Bully for Bront.pdfrowspan="3"Mesquite: Ancestral States Reconstruction
 +  
−  
 +  
−  Dec 2 Nomenclature; Phylocode{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mares2009.pdf}}Mares2009.pdf
 +  
−  
 +  
−  Dec 4 Lab 
 +  
−  
 +  
−  Dec 7 Special topic: Taxonomic collections<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Importance%20of%20Collections.pdf}}Importance of Collections.pdf{{pdfhttp://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/>:{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Patterns%20and%20Processes%202011%20One.pdf}}Patterns and Processes 2011 One.pdf{{pdfhttp://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/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Conservation_and_Systematics.pdf}}Conservation and Systematics.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Looking%20Ahead%202009.pdf}}
 +  
−  }>
 +  
 <br/>   <br/> 
−  =='''Supplementary Reading'''==
 +  
−  { border="1" cellpadding="2"
 +  '''Important Dates''' 
−  !style="background:#2A52BE;" width="275"Topics
 +  
−  !style="background:#008080;" width="975"Additional Reading
 +  
−  
 +  
−   Species as ranked taxa and species concepts  {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Application%20of%20Evol%20Spp%20concept.pdf}}Application of Evolutionary Species concept.pdf {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20concept%20for%20prokaryotes%202001.pdf}}Species concept for prokaryotes.pdf {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Noor%202002%20BSC%20showing%20age%3F.pdf}}Is the BSC showing its age?.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Sites%20and%20Crandall%20Con.Bio%201997.pdf}}Importance of stating species concept for conservation purposes.pdf {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/AgapowSpeciesQRB04.pdf}}Impact of species concepts on biodiversity studies.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Urge%20to%20state%20species%20concept.pdf}}The need for specifying species concepts.pdf{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hey%202007.pdf}}On the failure of modern species concepts.pdf {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20as%20Ranked%20Taxa%20Baum%202009.pdf}}Species as ranked taxa.pdf<br/>
 +  
−  {{pdfhttp://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 {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Bond%20and%20Stockman%202008.pdf}}Method for delimiting Cohesion speceis.pdf
 +  
−  
 +  
−  DNA Barcodes{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/elias%202007.pdf}}Elias et al. 2007.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Barcoding%20Leps%20of%20Costa%20Rica%20Guanacaste%20red.%20Janzen%20et%20al.pdf}}Janzen et al 2005.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/TenReasonsBarcoding.pdf}}Ten Reasons For Barcoding.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Will%20%26%20Rubinoff%202004.pdf}}Will & Rubinoff 2004.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hebert%20and%20Gregory%202005.pdf}}Hebert and Gregory 2005.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/PLoS_PromisesAndPitfalls.pdf}}Moritz and Cicero 2004.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hebert_et_al_2003_DNABarcodes.pdf}}Hebert et al.2003.pdf<br/>{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/PLoS_Birds_Hebert_et_al_2004.pdf}}PLoS_Birds_Hebert et al. 2004.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 4th. 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 20 November. 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/>
 
−  {{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Funding%20for%20biodiversity%20and%20taxonomy%202010.pdf}}Funding for biodiversity and taxonomy 2010.pdf
 
−  <br/>
 
−  =='''Important dates'''==
 
−  <span style="fontsize: large">
 
−  7 October, 2011: conference; topic selection<br/>
 
−  17 October, 2011: midterm<br/>
 
−  21 October, 2011: outline with 5+ references<br/>
 
−  18 November, 2011: first draft due<br/>
 
−  2 December, 2011: paper due<br/>
 
−  [[Category:EEB Courses]]
 