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

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[[Image:AMNH2009.jpg|right|''2009 Class on top of the AMNH'']]
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<span style="font-size: large">Fall 2017<br/>
[[Image:AMNH2011_roof.jpg|right|''2011 Class on top of the AMNH'']]
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<span style="font-size: large">Fall 2011<br/>
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<span style="font-size: large">Lecture MW 9:05-10:45  In TLS 313<br/>
 
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Lab F 9:05-10:45 McCarthy Room, 4th floor TLS<br/>
<span style="font-size: large">Lecture MW 9:00-10:30, Lab F 9:00-10:30<br/>
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<br/>
 
<br/>
 
<span style="font-size: large">'''Instructor''': Dr. David L. Wagner, TLS Rm 471<br/>
 
<span style="font-size: large">'''Instructor''': Dr. David L. Wagner, TLS Rm 471<br/>
 
Phone: 486-2139<br/>  
 
Phone: 486-2139<br/>  
office hours as available<br/>
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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/>
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Office hours: BioPharm 325 Wednesdays 10:30-11:30 or by appointment<br/>
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'''Graduate Teaching Assistant''': Kevin Keegan<br/>
Phone: 486-6650<br/>
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Office hours: TLS 461 F 10:45-11:45 or by appointment<br/>
email: [mailto:christopher.l.owen'at'uconn.edu christopher.l.owen'at'uconn.edu]<br/>
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Phone: 617-272-5054<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.
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There is no assigned text. Generally you can expect one or two readings to be assigned for each lecture. Most readings will be available as PDFs, downloadable from the course website.
 
<br/>
 
<br/>
 +
 
=='''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/><!--{{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 31 ||Organizational meeting, an introduction to biological systematics||{{pdf|http://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/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mayr_Ashlock1991_pgs1-18.pdf}}Mayr&Ashlock1991_pgs1-18.pdf (optional)
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|Aug 28 ||Organizational meeting || Hubbell Reading {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/8/8e/Hubbell%2818Aug13%29.pdf}} || rowspan="3"| Dave away in Fort Collins<br/>Introduction to McCarthy Room;<br/>Collections tour with Dr. Jane O'Donnell;<br>Species concept discussion and letter to yourself
 
|-
 
|-
| Sept 2 ||The many roles of biological systematics & collections tour <!--Species definitions & species intermediacy<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20Definitions.pdf}}Species Definitions.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20Level%20Terminology%202009.pdf}}Species Level Terminology 2009.pdf-->||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/A_Templeton%201989.pdf}}Templeton 1989.pdf<br/>{{pdf|http://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/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Futuyma_spconcepts_445-451.pdf}}Futuyma_spconcepts_445-451.pdf
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|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 '''
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|Sep 1 ||Species definitions & species intermediacy<br/> A Bit on Names {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/A_bit_on_names_2017.pdf}}|| Templeton (1989){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/A_Templeton%201989.pdf}}
 
|-
 
|-
|Sept 7 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20I%202011.pdf}}Species I 2011.pdf ||
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|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
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|Sept 6 ||Species definitions & species intermediacy <br/> Species 1 Lecture {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species_I_2017.pdf}}||  Finish reading/reread Templeton from Friday<br/> DeQuieroz (2007){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/De%20Queiroz%202007.pdf}}
 
|-
 
|-
|Sept 12  || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20II%202011.pdf}}Species II 2011.pdf || {{pdf|http://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)'''
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|Sept 8 || Lab, Meet in library Room EC1, walking in through the main entrance, go straight back and up to level 1, then see this map (http://www.lib.uconn.edu/maps/Level1EC12013.pdf), you will be coming out of the stairs in the center of the map ||
 
|-
 
|-
|Sept 14 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20III%202011.pdf}}Species III 2011.pdf ||
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|Sept 11  || Finish species definitions & species intermediacy; start variation within species <br/> Species II Lecture {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species_II_2017.pdf}} || Erlich & Raven (1969){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Ehrlich&Raven_1969.pdf}} <br/> Mallet (2013)  {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mallett_2013.pdf}} || rowspan="3"| '''Meet in McCarthy Room'''<br/>Taxonomic resources: key websites; taxonomy exercise {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab1_Literature_Search_2017_dlw.doc}}.<br/>Online Resource List {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab1_tax_resources_online_2017_dlw.pdf}}<br/> BioBlitz in Stamford.
<!--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 16 || lab || lab
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|Sept 13 || Subspecies and geographic variation || Send Wagner an example (~3 ppt slides) of intraspecific geographic variation '''before 11:59 PM Sunday'''
 
|-
 
|-
|Sept 19 || {{pdf|http://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)'''
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|Sept 15 || lab ||  
 
|-
 
|-
|Sept 21 || Infrapopulation variation (lecture sent via email) ||
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|Sept 18 || Variation within a genotype:  ontogeny & phenotypic plasticity || Send Wagner an example (~3 ppt slides) of intraspecific non-geographic variation '''before 11:59 PM Tuesday''' || rowspan="3"| Lab: Alpha taxonomy: finding taxonomic characters & keys; descriptions and diagnoses; taxonomic cybertools for alpha taxonomy and phylogenetics <br/> Slides {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab2_Presentation_2017.pdf}} <br/> Notes {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab2_Presentation_2017_notes.pdf}} <br/>Intro to Mesquite exercise {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab2_mesquite_exercise_2017.pdf}} <br> (Wagner away on Friday)
 
|-
 
|-
|Sept 23 || lab || lab
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|Sept 20 || Supraspecific taxa ||
 
|-
 
|-
|Sept 26 || {{pdf|http://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)'''
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|Sept 22 || lab ||
 
|-
 
|-
|Sept 28 || {{pdf|http://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 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Meister_Description_Diagnoses.pdf}}<br/>A bit on keys {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab3_Handout_Keys_2017.pdf}}<br/>(Wagner away)
 
|-
 
|-
|Sept 30 || lab || lab
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|Sept 27 || Phylogenetic inference:  mostly a historical overview ||
 
|-
 
|-
|Oct 3 || Trees and characters; types of dendrograms;<br/>rooting and polarization ||{{pdf|http://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/>{{pdf|http://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 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters_1%202011.pdf}}Characters_1 2011.pdf ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Krell%26Cranston.pdf}}Krell&Cranston.pdf<br/>{{pdf|http://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
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|Oct 4 || Taxonomic characters: polarity, outgroups, order, weighting, and step matrices ||  
 
|-
 
|-
|Oct 10 ||{{pdf|http://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)'''
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|Oct 6 || lab ||
 
|-
 
|-
|Oct 12 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Distance%20Methods%202011.pdf}}Distance Methods 2011.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Parsimony%202011.pdf}}Parsimony 2011.pdf <br/> {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/ParsimonyLectureForMidTerm.ppt}}ParsimonyLectureForMidTerm.ppt ||{{pdf|http://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
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|Oct 11 ||''' Midterm exam''' ||
 
|-
 
|-
|Oct 17 || Midterm exam ||{{pdf|http://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 ||
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|Oct 16 || Maximum likelihood (lecture by Lewis; Wagner away) || || rowspan="3"| Lab: likelihood (Garli and/or RAxML) and Bayesian analyses
 
|-
 
|-
|Oct 21 || lab || lab
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|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)'''
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|Oct 20 || lab ||
 
|-
 
|-
|Oct 26 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Reliability%202011.pdf}}Reliability 2011.pdf||
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|Oct 23 || Tree reliability, sensitivity, and support measures I ||  || rowspan="3"| Lab: Tree reliability and measures  <br/>'''(Meet in McCarthy Room, 4th floor TLS)'''
 
|-
 
|-
|Oct 28 || No Lab/AMNH & Bronx Zoo Trip || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lewis_2001-TREE-16-1.30-37.pdf}}Lewis_2001_TREE.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Holder%26Lewis2003NatRevGen.pdf}}Holder&Lewis2003_NatRevGen.pdf
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|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)'''
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|Oct 27 || lab ||  
 
|-
 
|-
|Nov 2 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Likelihood_2Nov2011.pdf}}Guest Lecture Paul Lewis ||  
+
|Oct 30 || Multivariate and distance methods || || rowspan="3"| Lab: neighbor-joining and correcting distance data  '''(Meet in McCarthy Room, 4th floor TLS)'''
 
|-
 
|-
|Nov 4 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Bayesian_4Nov2011.pdf}}Guest Lecture Paul Lewis ||
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|Nov 1 || Bayesian inference (Lewis Guest Lecture) {{pdf|http://hydrodictyon.eeb.uconn.edu/people/plewis/downloads/Bayesian_30Oct2013.key.pdf}} ||  
 
|-
 
|-
|Nov 7 || Data partitions; consensus; comparing tree topologies<br/>{{pdf|http://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)'''
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|Nov 3 || lab  ||
 
|-
 
|-
|Nov 9 || Guest lecture by Don Les:<br/>Molecular systematics in plants(lecture too big, so I emailed it to you) ||
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|Nov 6 || Molecular systematics in animals (Simon) (Wagner in Denver) || || rowspan="3"| Lab:  PAUP*: ModelTest; molecular clocks; AIC et al.  '''(Meet in McCarthy Room, 4th floor TLS)'''
 
|-
 
|-
|Nov 11 || lab || lab
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|Nov 8 || Molecular systematics in plants (Les) ||
 
|-
 
|-
|Nov 14 || Guest lecture by Chris Simon:<br/>Molecular systematics in animals<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/CSimon%20Lecture-How%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)'''
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|Nov 10 || lab ||
 
|-
 
|-
|Nov 16 || lab || lab
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|Nov 13 || Data partitions; consensus; comparing trees || || rowspan="3"| Lab:  Find and analyze your own data set; COI problem '''(Meet in McCarthy Room, 4th floor TLS)'''
 
|-
 
|-
|Nov 18 || Procedural flow chart for phylogenetic analysis; DNA barcoding<br/>{{pdf|http://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'''
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|Nov 17 || lab ||
 
|-
 
|-
|Nov 23 || Thanksgiving recess ||  
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|Nov 20 ||rowspan="3"| '''Thanksiving''' || rowspan="3"| '''Thanksiving''' || rowspan="3"| '''Thanksiving'''
 
|-
 
|-
|Nov 25 || Thanksgiving recess||
+
|Nov 22
 
|-
 
|-
|Nov 28 || Nomenclature<br/>{{pdf|http://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 ||  
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|Nov 27 || Nomenclature || || rowspan="3"| Lab:  Mesquite; character optimization; character correlation
 
|-
 
|-
|Dec 2 || lab || lab
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|Nov 29 || Nomenclature; Phylocode ||
 
|-
 
|-
|Dec 5 ||Patterns and process<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Patterns%20and%20Processes%202011%20One.pdf}}Patterns and Processes 2011 One.pdf<br/>{{pdf|http://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/>{{pdf|http://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/>{{pdf|http://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{{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
+
|Dec 8 || Special topic: Systematics and conservation biology and the future of biological systematics ||
 
|-
 
|-
|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)
+
|Dec circa 15 || Final: 8-11 AM (Bamford) ||
 +
|}
 +
 
 +
=='''Grading'''==
 +
{| border="1" cellpadding="1"
 +
!width="200"|Item
 +
!width="25"|Percentage
 +
!width="25"|Points
 
|-
 
|-
|Sept 25 ||Lab {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Tiger%20Beetle%20Intro%202009.pdf}}Tiger Beetle Intro 2009.pdf ||
+
|Lab and take home exercises|| <div style="text-align: center">25</div> || <div style="text-align: center">250</div>
 
|-
 
|-
|Sept 28 ||Phylogenetic inference: Mostly a historical overview<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Intro%20to%20Phylogenetic%20Inference.pdf}}Intro to Phylogenetic Inference.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Chart%20the%20evol%20history%20of%20life.pdf}}Chart the evol history of life.pdf(For 09/30)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Modernizing%20the%20tree%20of%20life.pdf}}Modernizing the tree of life.pdf(For 09/30) || rowspan="3"| Alpha Taxonomy: taxonomic keys,<br/>specimen/museum databases DELTA,<br/> MANTIS & other taxonomic computer tools
+
|Midterm Exam || <div style="text-align: center">20</div> || <div style="text-align: center">200</div>
 
|-
 
|-
|Sept 30 ||Trees and characters: types of dendrograms, rooting and polarization<br/>weighting and step matrices {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters1.pdf}}Characters1.pdf ||
+
|Paper || <div style="text-align: center">25</div> || <div style="text-align: center">250</div>
 
|-
 
|-
|Oct 2 ||Lab ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Krell%26Cranston.pdf}}Krell&Cranston.pdf(For 10/05)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Forey%20et%20al%201992%20Chap2%263.pdf}}Forey et al 1992 Chap2&3.pdf (For 10/05)
+
|Nomenclature Exercise || <div style="text-align: center">2</div> || <div style="text-align: center">20</div>
 
|-
 
|-
|Oct 5 ||Taxonomic characters: polarity, outgroups, order, weighting, and step matrices<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters%20II.pdf}}Characters II.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/CompleatCladist.pdf}}Cladistics Review I.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Collin%26Miglietta%202008%20Dollo%20Law.pdf}}Collin&Miglietta 2008 Dollo's Law.pdf|| rowspan="3"| Mesquite II: manipulating DNA/amino acid sequences<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mesquite%20Lab%20II}}Mesquite Lab II<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/GenBank%20Tutorial%202009}}GenBank Tutorial
+
|Class Participation || <div style="text-align: center">3</div> || <div style="text-align: center">30</div>
 
|-
 
|-
|Oct 7 ||More on trees<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/More%20on%20Trees.pdf}}Trees.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Cladistics.pdf}}Cladistics Review II.pdf
+
|Final Exam || <div style="text-align: center">25</div> || <div style="text-align: center">250</div>
 
|-
 
|-
|Oct 9 ||Lab ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Felsenstein2004.pdf}}Felsenstein2004.pdf(For 10/16)
+
|'''Total''' || <div style="text-align: center">'''100'''</div> || <div style="text-align: center">'''1000'''</div>
|-
+
|}
|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
+
 
|-
+
=='''Term Paper'''==
|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||
+
<br/>
|-
+
Each student will be required to prepare a paper that will be due on December 2. Acceptable styles: (1) a literature review that is structured to be a thesis chapter; (2) grant proposal; (3) stand-alone review a subject relevant to systematic theory or methodology.
|Oct 16 ||Lab ||
+
|-
+
|Oct 19 ||Exam||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Midterm%20Sample%20Questions%202009.pdf}}Midterm Sample Questions 2009.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Neighbor-joining%20Exercise.pdf}}Neighbor-joining Exercise.pdf||rowspan="3"|American Museum of Natural History
+
|-
+
|Oct 21 ||Midterm Review<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Midterm%20Post-Exam%20Review.pdf}}Midterm Post-Exam Review.pdf||
+
|-
+
|Oct 23 ||AMNH Trip ||
+
|-
+
|Oct 26 ||Parsimony; search algorithms;<br/>algorithmic power, accuracy, and inconsistency<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Parsimony.pdf}}Parsimony.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes_Part2_1.pdf}}Page&Holmes_Rest_of_Ch6.pdf||rowspan="3"|Parsimony Lab<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab6_parsimony_2009.doc}}Lab6 Parsimony.doc
+
|-
+
|Oct 28 ||Likelihood(Guest Lecture: Paul Lewis)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Likelihood_28Oct2009_1perpage.pdf}}Likelihood.pdf||
+
|-
+
|Oct 30 ||Lab ||
+
|-
+
|Nov 2 ||Swine flu class cancelled||||rowspan="3"|Modeltest, AIC & hLRT, Molecular clocks<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab7_2009_corrected.doc}}Lab7.doc
+
|-
+
|Nov 4 ||Bayesian phylogenetics (Paul Lewis)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Bayesian_2Nov2009_1perpage.pdf}}Bayesian phylogenetics.pdf||
+
|-
+
|Nov 6 ||Lab ||
+
|-
+
|Nov 9 ||Molecular systematics in plants (Don Les)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Systematics_2009_Les.pdf}}Plant Systematics Les.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes280_285.pdf}}Page&Holmes280-285.pdf||rowspan="3"|Garli and MrBayes Lab<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab8_2009.doc}}Lab8.doc
+
|-
+
|Nov 11 ||Reliability and measures of tree support:  c.i., r.i.,<br/>decay indices, bootstraps ; jackknifes; and sensitivity analyses;<br/>bootstraps, randomization tests<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Reliability%202009.pdf}}Reliability 2009.pdf||
+
|-
+
|Nov 13 ||Lab ||
+
|-
+
|Nov 16 ||Data partitions; consensus; ILD<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Consensus%202009.pdf}}Consensus.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/ILD%202009.doc}}ILD 2009.doc||rowspan="3"|COI data set analysis<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab9_barcoding_2009_corrected.doc}}Lab9 COI Barcodes.doc
+
|-
+
|Nov 18 ||DNA Barcodes<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/DNA%20Barcodes.pdf}}DNA Barcodes.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/FunkOmlandARev.pdf}}Funk & Omland.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Astraptes%20fulgerator.pdf}}Hebert et al. 2004.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Meyer%20and%20Paulaypdf%20copy.pdf}}Meyer and Paulay.pdf
+
|-
+
|Nov 20 ||Lab ||
+
|-
+
|Nov 23-28 ||No class-Thanksgiving Break||
+
|-
+
|Nov 30 ||Nomenclature<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Nomenclature%202009.pdf}}Nomenclature 2009.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Berenbaum%20Article.pdf}}Berenbaum Article.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Conniff%20article.pdf}}Conniff article.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Gould_Bully%20for%20Bront.pdf}}Gould_Bully for Bront.pdf||rowspan="3"|Mesquite: Ancestral States Reconstruction
+
|-
+
|Dec 2 ||Nomenclature; Phylocode||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mares2009.pdf}}Mares2009.pdf
+
|-
+
|Dec 4 ||Lab ||
+
|-
+
|Dec 7 ||Special topic: Taxonomic collections<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Importance%20of%20Collections.pdf}}Importance of Collections.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Nomenclature%20Exercise.doc}}Nomenclature Exercise.doc (due Dec 11)||rowspan="3"|No Lab
+
|-
+
|Dec 9 ||Special topic:  Phylogenetic trees & evolutionary processes;<br/>the comparative method<br/>:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Patterns%20and%20Processes%202011%20One.pdf}}Patterns and Processes 2011 One.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Patterns%20and%20Processes%202011%20Two.pdf}}Patterns and Processes 2011 Two.pdf||
+
|-
+
|Dec 11 ||Special topic: Biodiversity crisis and future of systematics<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Conservation_and_Systematics.pdf}}Conservation and Systematics.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Looking%20Ahead%202009.pdf}}||
+
|}-->
+
 
<br/>
 
<br/>
=='''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 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Application%20of%20Evol%20Spp%20concept.pdf}}Application of Evolutionary Species concept.pdf    {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20concept%20for%20prokaryotes%202001.pdf}}Species concept for prokaryotes.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Noor%202002%20BSC%20showing%20age%3F.pdf}}Is the BSC showing its age?.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Sites%20and%20Crandall%20Con.Bio%201997.pdf}}Importance of stating species concept for conservation purposes.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/AgapowSpeciesQRB04.pdf}}Impact of species concepts on biodiversity studies.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Urge%20to%20state%20species%20concept.pdf}}The need for specifying species concepts.pdf{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hey%202007.pdf}}On the failure of modern species concepts.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20as%20Ranked%20Taxa%20Baum%202009.pdf}}Species as ranked taxa.pdf<br/>
+
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Increase%20in%20bird%20species.pdf}}Does the choice of species concept result in an increase in bird species?.pdf {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Bond%20and%20Stockman%202008.pdf}}Method for delimiting Cohesion speceis.pdf
+
|-
+
|DNA Barcodes||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/elias%202007.pdf}}Elias et al. 2007.pdf<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
+
|}
+
=='''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/>
 
{{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'''==
 
<span style="font-size: 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]]
 

Latest revision as of 12:24, 25 September 2017

Fall 2017

Lecture MW 9:05-10:45 In TLS 313
Lab F 9:05-10:45 McCarthy Room, 4th floor TLS

Instructor: Dr. David L. Wagner, TLS Rm 471
Phone: 486-2139
office hours open; best to call or email ahead
email: david.wagner'at'uconn.edu

Graduate Teaching Assistant: Kevin Keegan
Office hours: TLS 461 F 10:45-11:45 or by appointment
Phone: 617-272-5054
email: kevin.keegan'at'uconn.edu

Textbook and readings

There is no assigned text. Generally you can expect one or two readings to be assigned for each lecture. Most readings will be available as PDFs, downloadable from the course website.

Schedule

Day Topics Reading/Assignment Lab
Aug 28 Organizational meeting Hubbell Reading Pdficon small.gif Dave away in Fort Collins
Introduction to McCarthy Room;
Collections tour with Dr. Jane O'Donnell;
Species concept discussion and letter to yourself
Aug 30 An introduction to biological systematics; The many roles of biological systematics and collections
Sep 1 Species definitions & species intermediacy
A Bit on Names Pdficon small.gif
Templeton (1989)Pdficon small.gif
Sep 4 Labor Day, No class Kevin away in Mexico
Babbidge Library resources; taxonomic literature
Sept 6 Species definitions & species intermediacy
Species 1 Lecture Pdficon small.gif
Finish reading/reread Templeton from Friday
DeQuieroz (2007)Pdficon small.gif
Sept 8 Lab, Meet in library Room EC1, walking in through the main entrance, go straight back and up to level 1, then see this map (http://www.lib.uconn.edu/maps/Level1EC12013.pdf), you will be coming out of the stairs in the center of the map
Sept 11 Finish species definitions & species intermediacy; start variation within species
Species II Lecture Pdficon small.gif
Erlich & Raven (1969)Pdficon small.gif
Mallet (2013) Pdficon small.gif
Meet in McCarthy Room
Taxonomic resources: key websites; taxonomy exercise Pdficon small.gif.
Online Resource List Pdficon small.gif
BioBlitz in Stamford.
Sept 13 Subspecies and geographic variation Send Wagner an example (~3 ppt slides) of intraspecific geographic variation before 11:59 PM Sunday
Sept 15 lab
Sept 18 Variation within a genotype: ontogeny & phenotypic plasticity Send Wagner an example (~3 ppt slides) of intraspecific non-geographic variation before 11:59 PM Tuesday Lab: Alpha taxonomy: finding taxonomic characters & keys; descriptions and diagnoses; taxonomic cybertools for alpha taxonomy and phylogenetics
Slides Pdficon small.gif
Notes Pdficon small.gif
Intro to Mesquite exercise Pdficon small.gif
(Wagner away on Friday)
Sept 20 Supraspecific taxa
Sept 22 lab
Sept 25 Supraspecific taxa Lab: Describing and diagnosing species; Keys; Taxonomic cybertools: DELTA, Lucid, MANTIS
Example: Descriptions and Diagnoses Pdficon small.gif
A bit on keys Pdficon small.gif
(Wagner away)
Sept 27 Phylogenetic inference: mostly a historical overview
Sept 29 lab
Oct 2 Trees and characters: types of dendrograms, rooting and polarization Lab: Mesquite II, Parsimony???
Oct 4 Taxonomic characters: polarity, outgroups, order, weighting, and step matrices
Oct 6 lab
Oct 9 Parsimony; tree searches; tree statistics Lab: Trip to American Museum of Natural History and Bronx Zoo in NYC!!!
Oct 11 Midterm exam
Oct 13 Head to NYC
Oct 16 Maximum likelihood (lecture by Lewis; Wagner away) Lab: likelihood (Garli and/or RAxML) and Bayesian analyses
Oct 18 Bayesian inference (lecture by Lewis; Wagner away)
Oct 20 lab
Oct 23 Tree reliability, sensitivity, and support measures I Lab: Tree reliability and measures
(Meet in McCarthy Room, 4th floor TLS)
Oct 25 Tree reliability, sensitivity, and support measures II
Oct 27 lab
Oct 30 Multivariate and distance methods Lab: neighbor-joining and correcting distance data (Meet in McCarthy Room, 4th floor TLS)
Nov 1 Bayesian inference (Lewis Guest Lecture) Pdficon small.gif
Nov 3 lab
Nov 6 Molecular systematics in animals (Simon) (Wagner in Denver) Lab: PAUP*: ModelTest; molecular clocks; AIC et al. (Meet in McCarthy Room, 4th floor TLS)
Nov 8 Molecular systematics in plants (Les)
Nov 10 lab
Nov 13 Data partitions; consensus; comparing trees Lab: Find and analyze your own data set; COI problem (Meet in McCarthy Room, 4th floor TLS)
Nov 15 DNA barcoding
Nov 17 lab
Nov 20 Thanksiving Thanksiving Thanksiving
Nov 22
Nov 24
Nov 27 Nomenclature Lab: Mesquite; character optimization; character correlation
Nov 29 Nomenclature; Phylocode
Dec 1 lab
Dec 4 Phylogenetic trees & evolutionary processes No lab this week
Dec 6 Special topic: Taxonomic collections
Dec 8 Special topic: Systematics and conservation biology and the future of biological systematics
Dec circa 15 Final: 8-11 AM (Bamford)

Grading

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

Term Paper


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

Important Dates

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