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

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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 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 <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.
+
|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/>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.
 
|-
 
|-
|Sept 13 || Subspecies and geographic variation || Send Wagner an example (~3 ppt slides) of intraspecific geographic variation '''before 11:59 PM Sunday'''
+
|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 15 || lab ||  
 
|Sept 15 || lab ||  
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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 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 20 ||  Supraspecific taxa ||
+
|Sept 20 ||  Supraspecific taxa or Higher Categories {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Higher_Categories_2017.pdf}}||
 
|-
 
|-
 
|Sept 22 || lab ||
 
|Sept 22 || lab ||
 
|-
 
|-
|Sept 25 || Supraspecific taxa || || rowspan="3"| Lab: Describing and diagnosing species; Taxonomic cybertools: DELTA, Lucid, MANTIS <br/> Example:
+
|Sept 25 || Supraspecific taxa or Higher Categories || || rowspan="3"| Lab: 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/>
Descriptions and Diagnoses {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Meister_Description_Diagnoses.pdf}} (Wagner away)
+
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)
Phylogenetic inference
+
 
|-
 
|-
|Sept 27 || Phylogenetic inference: mostly a historical overview ||
+
|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}}
 
|-
 
|-
|Sept 29 || lab ||
+
|Sept 29 || Continue Infraspecific variation or "packaging" of variation ||
 
|-
 
|-
|Oct 2 || Trees and characters: types of dendrograms, rooting and polarization || || rowspan="3"|  Lab: Mesquite II, Parsimony???
+
|Oct 2 || Finish Infraspecific variation or "packaging" of variation || || rowspan="3"|  Lab: GenBank and DNA Sequence Data (right-click "save as") {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Genbank_2017.doc}}
 
|-
 
|-
|Oct 4 || Taxonomic characters: polarity, outgroups, order, weighting, and step matrices ||  
+
|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}}
 
|-
 
|-
 
|Oct 6 || lab ||
 
|Oct 6 || lab ||
 
|-
 
|-
|Oct 9 || Parsimony; tree searches; tree statistics || || rowspan="3"| Lab: Trip to American Museum of Natural History and Bronx Zoo in NYC!!!
+
|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''' ||
+
|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''' ||
+
|Oct 13 || '''Head to NYC'''<br/>NYC Trip Reference {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/NYC_Trip_Reference.pdf}} ||
 
|-
 
|-
|Oct 16 || Maximum likelihood (lecture by Lewis; Wagner away) || || rowspan="3"| Lab: likelihood (Garli and/or RAxML) and Bayesian analyses
+
|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: Review midterm, Finish last week's lab, any extra time work on key/description/diagnoses
 
|-
 
|-
|Oct 18 || Bayesian inference (lecture by Lewis; Wagner away) ||
+
|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 20 || lab ||
 
|-
 
|-
|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 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: 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 || Tree reliability, sensitivity, and support measures II ||
+
|Oct 25 || Bayesian Inference (Lewis)  {{pdf|http://hydrodictyon.eeb.uconn.edu/people/plewis/downloads/eeb5347-2017/25Oct2017.pdf}} ||
 
|-
 
|-
 
|Oct 27 || lab ||  
 
|Oct 27 || lab ||  
 
|-
 
|-
|Oct 30 || Multivariate and distance methods || || rowspan="3"| Lab: neighbor-joining and correcting distance data '''(Meet in McCarthy Room, 4th floor TLS)'''
+
|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: 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 || Bayesian inference (Lewis Guest Lecture) {{pdf|http://hydrodictyon.eeb.uconn.edu/people/plewis/downloads/Bayesian_30Oct2013.key.pdf}} ||  
+
|Nov 1 || Multivariate and distance methods II ||  
 
|-
 
|-
 
|Nov 3 || lab  ||
 
|Nov 3 || lab  ||
 
|-
 
|-
|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 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:  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) ||
 
|Nov 8 || Molecular systematics in plants (Les) ||
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|Nov 10 || lab ||
 
|Nov 10 || 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 13 || Data partitions; consensus; comparing trees{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Consensus_2017.pdf}} || || rowspan="3"| Lab:  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  ||
+
|Nov 15 || DNA barcoding  ||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 17 || lab ||
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|Nov 24
 
|Nov 24
 
|-
 
|-
|Nov 27 || Nomenclature || || rowspan="3"| Lab:  Mesquite; character optimization; character correlation
+
|Nov 27 || Nomenclature || || rowspan="3"| Lab:  Spread Your Wings
 
|-
 
|-
 
|Nov 29 || Nomenclature; Phylocode ||
 
|Nov 29 || Nomenclature; Phylocode ||

Revision as of 13:47, 17 November 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 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: 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: 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: 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: 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: 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: 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: Maximum Likelihood, Model Choice, and CIPRES
Exercise (right-click "save as") Pdficon small.gif
Nov 8 Molecular systematics in plants (Les)
Nov 10 lab
Nov 13 Data partitions; consensus; comparing treesPdficon small.gif Lab: 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 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 Nomenclature Lab: Spread Your Wings
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