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

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<span style="font-size: large">Fall 2009<br/>
+
<span style="font-size: large">Fall 2017<br/>
  
<span style="font-size: large">Lecture MW 9:00-10:30, Lab F 9:00-10:30<br/>
+
<span style="font-size: large">Lecture MW 9:05-10:45  In TLS 313<br/>
 +
Lab F 9:05-10:45 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 as available<br/>
+
office hours open; best to call or email ahead<br/>
email: [mailto:david.wagner@uconn.edu david.wagner@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: TLS 461 Monday 10:30-11:30 (BioPharm 323 most other times) or by appointment<br/>
+
'''Graduate Teaching Assistant''': Kevin Keegan<br/>
Phone: 486-6650<br/>
+
Office hours: TLS 461 F 10:45-11:45 or by appointment<br/>
email: [mailto:christopher.l.owen@uconn.edu christopher.l.owen@uconn.edu]<br/>
+
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.
+
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 22: 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 31 || Organizational meeting, an introduction to biological systematics<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
 
|| {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hubbell.pdf}}Hubbell.pdf<br/>http://www.nytimes.com/2009/08/11/science/11naming.html || rowspan="3"| Lecture instead of lab this week
 
 
|-
 
|-
| Sept 2 || The many roles of biological systematics & collections tour ||
+
|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 4 || 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
+
|Aug 30 ||An introduction to biological systematics; The many roles of biological systematics and collections <br/> ||  
 
|-
 
|-
| Sept 7 No class ||No class ||No class || rowspan="3"| Babbidge Library resources; taxonomic literature''' Meet in Babbidge library Level 2 electronic classroom, across the lobby from the stairs and elevators'''
+
|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 9 || Species definitions & intermediacy{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20I.ppt}}Species.ppt || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Ehrlich%26Raven_1969.pdf}}Ehrlich&Raven1969.pdf (For 09/16)
+
|Sep 4 ||Labor Day, No class || || rowspan="3"| Kevin away in Mexico<br/>Lab: Babbidge Library resources; taxonomic literature
 
|-
 
|-
|Sept 11 Lab ||Lab ||Lab
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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 14 Lab ||Lab ||Lab || rowspan="3"| Taxonomic resoursces: 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 16 || Individual variation(population variation){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20II.pdf}}Species II.pdf
+
|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%20_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/>Lab 1: 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.
  || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Futuyma_pg239to263master1.pdf}}Futuyma_pg239-263.pdf (For 9/18)
+
 
|-
 
|-
|Sept 18 || Subspecies and geographic variation {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Subspecies%202009.ppt}}Subspecies 2009.ppt||
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|Sept 13 || Subspecies and geographic variation {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Subspecies_2017_Final.pdf}} || Send Wagner an example (~3 ppt slides) of intraspecific geographic variation '''before 11:59 PM Sunday'''
 
|-
 
|-
|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 15 || lab ||  
 
|-
 
|-
|Sept 23 ||Supraspecfic taxa ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%20%26%20Holmes%201998.pdf}}Page & Holmes 1998.pdf(For 09/28)
+
|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 2: 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 25 ||Lab {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Tiger%20Beetle%20Intro%202009.pdf}}Tiger Beetle Intro 2009.pdf ||
+
|Sept 20 || Supraspecific taxa or Higher Categories {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Higher_Categories_2017.pdf}}||
 
|-
 
|-
|Sept 28 ||Phylogenetic inference: an overview||{{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) || rowspan="3"| Alpha Taxonomy: taxonomic keys,<br/>specimen/museum databases DELTA,<br/> MANTIS & other taxonomic computer tools
+
|Sept 22 || lab ||
 
|-
 
|-
|Sept 30 ||Taxonomic characters: types, polarity and order,<br/>weighting and step ||
+
|Sept 25 || Supraspecific taxa or Higher Categories || || rowspan="3"| Lab 3: Describing and diagnosing species; Keys; Taxonomic cybertools: DELTA, Lucid, MANTIS{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab3_Presentation_2017.pdf}} <br/>A bit on keys {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab3_Handout_Keys_2017.pdf}}<br/>
 +
A bit on descriptions and reading taxonomic literature {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Winston%20_1999.pdf}}<br/>Example Description and Diagnoses {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Meister_Description_Diagnoses.pdf}}<br/>External anatomy of tiger beetles {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Tiger_Beetle_Morphology.pdf}} <br/> (Wagner away)
 
|-
 
|-
|Oct 2 ||Lab ||  
+
|Sept 27 || Start Infraspecific variation or "packaging" of variation {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Infrasubspecific_Variation_2017.pdf}}|| Schuh and Brower 2009 (pp 131-140) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Schuh_and_Brower_2009.pdf}}
|}
+
|-
<br/>
+
|Sept 29 || Continue Infraspecific variation or "packaging" of variation ||
=='''Supplementary Reading'''==
+
|-
{| border="1" cellpadding="2"  
+
|Oct 2 || Finish Infraspecific variation or "packaging" of variation || || rowspan="3"|  Lab 4: GenBank and DNA Sequence Data (right-click "save as") {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Genbank_2017.doc}}
!style="background:#2A52BE;" width="275"|Topics
+
|-
!style="background:#008080;" width="975"|Additional Reading
+
|Oct 4 || Phylogenetic inference:  mostly a historical overview {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Intro_to_Phylogenetic_Inference_2017.pdf}}, Begin: Trees and Characters {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters_and_Trees_2017.pdf}} || Page and Holmes Ch. 2 pp 11-36{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page_Holmes_Trees.pdf}}<br/> Krell and Cranston (2004){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Krell_Cranston2004.pdf}}<br/> Tree View of Life {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Tree%20_View_of_Life.pdf}}
|-  
+
|-
| 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/>
+
|Oct 6 || lab ||
{{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
+
|-
 +
|Oct 9 || End: Trees and characters, Parsimony {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Parsimony_2017.pdf}}  || || rowspan="3"| Lab: Trip to American Museum of Natural History and Bronx Zoo in NYC!!!<br/> [https://photos.app.goo.gl/UytYC85yxZx8Wm7F3 Photo Album]
 +
|-
 +
|Oct 11 ||''' Midterm exam''' Sample questions (right click "save as") {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Midterm_Sample_Questions_2017.rtf}}||
 +
|-
 +
|Oct 13 || '''Head to NYC'''<br/>NYC Trip Reference {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/NYC_Trip_Reference.pdf}} ||
 +
|-
 +
|Oct 16 || Tree reliability, sensitivity, and support measures I{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Reliability_2017.pdf}} || Page and Holmes Ch.6 pp. 209-227 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page_and_Holmes_Ch_6_209-227.pdf}} || rowspan="3"| Lab 5: Review midterm, Finish last week's lab, any extra time work on key/description/diagnoses
 +
|-
 +
|Oct 18 || Tree reliability, sensitivity, and support measures II||Page and Holmes Ch. 6 pp 172-208{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page_and_Holmes_Ch6_pp172-208.pdf}}
 +
|-
 +
|Oct 20 || lab ||
 +
|-
 +
|Oct 23 || Maximum Likelihood (Lewis) {{pdf|http://hydrodictyon.eeb.uconn.edu/people/plewis/downloads/eeb5347-2017/23Oct2017.pdf}} ||'''Key, Description, and Diagnoses due!!!''' || rowspan="3"| Lab 6: Phylogenetic Inference using distance and parsimony with PAUP*: UPGMA, neighbor-joining, bootstrap, and jackknife <br/> Lab 5 (right-click "save-as")  {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab_5.doc}}<br/>Primate COI data (right-click "save-as") {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/primate-mtDNA.nex}}
 +
|-
 +
|Oct 25 || Bayesian Inference (Lewis)  {{pdf|http://hydrodictyon.eeb.uconn.edu/people/plewis/downloads/eeb5347-2017/25Oct2017.pdf}} ||
 +
|-
 +
|Oct 27 || lab ||
 +
|-
 +
|Oct 30 || Midterm Q&A<br/>Multivariate and distance methods I<br/>Multivariate Methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Multivariate_Methods2017.pdf}}<br/>Distance Methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Distance_Methods_2017.pdf}}|| || rowspan="3"| Lab 7: Examining and correcting distance data in PAUP*<br/>Exercise (right click "save-as"){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab7_estimating_correcting_distance_data_PAUP.doc}}<br/>Nexus File (right click "save-as"){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/vertmtdna.nex}}
 +
|-
 +
|Nov 1 || Multivariate and distance methods II ||  
 +
|-
 +
|Nov 3 || lab  ||
 +
|-
 +
|Nov 6 || Molecular systematics in animals (Simon){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/How_Molecules_Evolve_Parts_I_&_II_2017.pdf}} (Wagner in Denver) || || rowspan="3"| Lab 8:  Maximum Likelihood, Model Choice, and CIPRES<br/>Exercise (right-click "save as") {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab8_ML_Inference_2017.doc}}
 +
|-
 +
|Nov 8 || Molecular systematics in plants (Les) (password for lecture PDF emailed to you) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Wagner_Systematics_2017_pw.pdf}}||
 +
|-
 +
|Nov 10 || lab ||
 +
|-
 +
|Nov 13 || Data partitions; consensus; comparing trees{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Consensus_2017.pdf}} || || rowspan="3"| Lab 9: Bayesian Inference with MrBayes<br/>Exercise (right-click "save-as"){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab9_Bayesian_Inference.doc}}<br/>Nexus File (right-click "Save-as"){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/primates.nex}}
 +
|-
 +
|Nov 15 || DNA barcoding {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/DNA_Barcoding_2017.pdf}} ||Hebert et al. 2004 (read first){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hebert_et_al_2004.pdf}}<br/>Ratnasingham & Hebert (read second){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Ratnasingham_Hebert_2013.pdf}}
 +
|-
 +
|Nov 17 || lab ||
 +
|-
 +
|Nov 20 ||rowspan="3"| '''Thanksiving''' || rowspan="3"| '''Thanksiving''' || rowspan="3"| '''Thanksiving'''
 +
|-
 +
|Nov 22
 +
|-
 +
|Nov 24
 +
|-
 +
|Nov 27 || DNA barcoding, Debate (Nice work everyone! Very few ad-hominem attacks!) || || rowspan="3"| Lab 10:  Spread Your Wings (Right-click,"save-as"){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab_10_Spread_Your_Wings.doc}}
 +
|-
 +
|Nov 29 || Nomenclature {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Nomenclature_2017.pdf}}<br/>Type Definitions{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Type_Definitions_2015.pdf}} ||
 +
|-
 +
|Dec 1 || lab ||
 +
|-
 +
|Dec 4 ||Nomenclature, Phylocode || || rowspan="3"| '''No lab this week'''
 +
|-
 +
|Dec 6 || Phylocode || Pennisi (2001) [read first: less technical explanation of pros/cons]{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Pennisi_2001.pdf}}<br/>
 +
Donoghue and Gauthier (2004}{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Donoghue_Gauthier_2004.pdf}}<br/>
 +
De Queiroz (2006){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/De_Queiroz_2006.pdf}}
 +
|-
 +
|Dec 8 || Phylogenetic Trees: Pattern and Process {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Patterns_and_Processes_2017.pdf}}||
 +
|-
 +
|Dec circa 15 || Final: 8-11 AM (Bamford) ||
 
|}
 
|}
 +
 
=='''Grading'''==
 
=='''Grading'''==
 
{| border="1" cellpadding="1"
 
{| border="1" cellpadding="1"
| Lab and take home exercises || 20% || 100 pts
+
!width="200"|Item
 +
!width="25"|Percentage
 +
!width="25"|Points
 
|-
 
|-
| Midterm || 20% || 100 pts
+
|Lab and take home exercises|| <div style="text-align: center">25</div> || <div style="text-align: center">250</div>
 
|-
 
|-
| Term paper || 25% || 115 pts
+
|Midterm Exam || <div style="text-align: center">20</div> || <div style="text-align: center">200</div>
 
|-
 
|-
| Nomenclature exercise || 2% || 10 pts
+
|Paper || <div style="text-align: center">25</div> || <div style="text-align: center">250</div>
 
|-
 
|-
| Final || 35% || 175 pts
+
|Nomenclature Exercise || <div style="text-align: center">2</div> || <div style="text-align: center">20</div>
 
|-
 
|-
| '''Total''' || '''100%''' || '''500 pts'''
+
|Class Participation || <div style="text-align: center">3</div> || <div style="text-align: center">30</div>
 +
|-
 +
|Final Exam || <div style="text-align: center">25</div> || <div style="text-align: center">250</div>
 +
|-
 +
|'''Total''' || <div style="text-align: center">'''100'''</div> || <div style="text-align: center">'''1000'''</div>
 
|}
 
|}
 +
 +
=='''Term Paper'''==
 
<br/>
 
<br/>
=='''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.
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://researchfunding.duke.edu/detail.asp?OppID=587 htm
+
 
<br/>
 
<br/>
=='''Important dates'''==
+
 
<span style="font-size: large">
+
'''Important Dates'''
9 October, 2009: conference; topic selection<br/>
+
{| border="1" cellpadding="1"
23 October, 2009: outline with 5+ references<br/>
+
!width="150"|Date
20 November, 2009: first draft due<br/>
+
!width="200"|Milestone
4 December, 2009: paper due<br/>
+
|-
[[Category:EEB Courses]]
+
|6 October 2017 || conference; topic selection
 +
|-
 +
|20 October 2017 || outline with 5+ references
 +
|-
 +
|17 November 2017 || first draft due
 +
|-
 +
|4 December 2017 || paper due
 +
|-
 +
|}

Latest revision as of 16:29, 14 December 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
Lab: 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
Lab 1: Taxonomic resources: key websites; taxonomy exercise Pdficon small.gif.
Online Resource List Pdficon small.gif
BioBlitz in Stamford.
Sept 13 Subspecies and geographic variation Pdficon small.gif 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 2: 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 or Higher Categories Pdficon small.gif
Sept 22 lab
Sept 25 Supraspecific taxa or Higher Categories Lab 3: Describing and diagnosing species; Keys; Taxonomic cybertools: DELTA, Lucid, MANTISPdficon small.gif
A bit on keys Pdficon small.gif

A bit on descriptions and reading taxonomic literature Pdficon small.gif
Example Description and Diagnoses Pdficon small.gif
External anatomy of tiger beetles Pdficon small.gif
(Wagner away)

Sept 27 Start Infraspecific variation or "packaging" of variation Pdficon small.gif Schuh and Brower 2009 (pp 131-140) Pdficon small.gif
Sept 29 Continue Infraspecific variation or "packaging" of variation
Oct 2 Finish Infraspecific variation or "packaging" of variation Lab 4: GenBank and DNA Sequence Data (right-click "save as") Pdficon small.gif
Oct 4 Phylogenetic inference: mostly a historical overview Pdficon small.gif, Begin: Trees and Characters Pdficon small.gif Page and Holmes Ch. 2 pp 11-36Pdficon small.gif
Krell and Cranston (2004)Pdficon small.gif
Tree View of Life Pdficon small.gif
Oct 6 lab
Oct 9 End: Trees and characters, Parsimony Pdficon small.gif Lab: Trip to American Museum of Natural History and Bronx Zoo in NYC!!!
Photo Album
Oct 11 Midterm exam Sample questions (right click "save as") Pdficon small.gif
Oct 13 Head to NYC
NYC Trip Reference Pdficon small.gif
Oct 16 Tree reliability, sensitivity, and support measures IPdficon small.gif Page and Holmes Ch.6 pp. 209-227 Pdficon small.gif Lab 5: Review midterm, Finish last week's lab, any extra time work on key/description/diagnoses
Oct 18 Tree reliability, sensitivity, and support measures II Page and Holmes Ch. 6 pp 172-208Pdficon small.gif
Oct 20 lab
Oct 23 Maximum Likelihood (Lewis) Pdficon small.gif Key, Description, and Diagnoses due!!! Lab 6: Phylogenetic Inference using distance and parsimony with PAUP*: UPGMA, neighbor-joining, bootstrap, and jackknife
Lab 5 (right-click "save-as") Pdficon small.gif
Primate COI data (right-click "save-as") Pdficon small.gif
Oct 25 Bayesian Inference (Lewis) Pdficon small.gif
Oct 27 lab
Oct 30 Midterm Q&A
Multivariate and distance methods I
Multivariate MethodsPdficon small.gif
Distance MethodsPdficon small.gif
Lab 7: Examining and correcting distance data in PAUP*
Exercise (right click "save-as")Pdficon small.gif
Nexus File (right click "save-as")Pdficon small.gif
Nov 1 Multivariate and distance methods II
Nov 3 lab
Nov 6 Molecular systematics in animals (Simon)Pdficon small.gif (Wagner in Denver) Lab 8: Maximum Likelihood, Model Choice, and CIPRES
Exercise (right-click "save as") Pdficon small.gif
Nov 8 Molecular systematics in plants (Les) (password for lecture PDF emailed to you) Pdficon small.gif
Nov 10 lab
Nov 13 Data partitions; consensus; comparing treesPdficon small.gif Lab 9: Bayesian Inference with MrBayes
Exercise (right-click "save-as")Pdficon small.gif
Nexus File (right-click "Save-as")Pdficon small.gif
Nov 15 DNA barcoding Pdficon small.gif Hebert et al. 2004 (read first)Pdficon small.gif
Ratnasingham & Hebert (read second)Pdficon small.gif
Nov 17 lab
Nov 20 Thanksiving Thanksiving Thanksiving
Nov 22
Nov 24
Nov 27 DNA barcoding, Debate (Nice work everyone! Very few ad-hominem attacks!) Lab 10: Spread Your Wings (Right-click,"save-as")Pdficon small.gif
Nov 29 Nomenclature Pdficon small.gif
Type DefinitionsPdficon small.gif
Dec 1 lab
Dec 4 Nomenclature, Phylocode No lab this week
Dec 6 Phylocode Pennisi (2001) [read first: less technical explanation of pros/cons]Pdficon small.gif

Donoghue and Gauthier (2004}Pdficon small.gif
De Queiroz (2006)Pdficon small.gif

Dec 8 Phylogenetic Trees: Pattern and Process Pdficon small.gif
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
4 December 2017 paper due