Principles and Methods of Systematic Biology (EEB 5347)

From eebedia

(Difference between revisions)
Jump to: navigation, search
(Schedule)
(Schedule)
(33 intermediate revisions by one user not shown)
Line 13: Line 13:
 
<br/>
 
<br/>
 
'''Graduate Teaching Assistant''': Russ Meister<br/>
 
'''Graduate Teaching Assistant''': Russ Meister<br/>
Office hours: BioPharm 323 Fridays 10:35-11:35 or by appointment <br/>
+
Office hours: BioPharm 323 Stop by or by appointment <br/>
 
Phone: 486-3947<br/>
 
Phone: 486-3947<br/>
 
email: [mailto:russell.meister'at'uconn.edu russell.meister'at'uconn.edu]<br/>
 
email: [mailto:russell.meister'at'uconn.edu russell.meister'at'uconn.edu]<br/>
Line 30: Line 30:
 
|| || rowspan="3"| Lecture instead of lab this week
 
|| || rowspan="3"| Lecture instead of lab this week
 
|-
 
|-
|Aug 28 ||The many roles of biological systematics Species Definitions {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/7/72/Species_Definitions_2013.pdf}} || Hubbell Reading {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/8/8e/Hubbell%2818Aug13%29.pdf}}
+
|Aug 28 ||The many roles of biological systematics <br/> Species Definitions {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/7/72/Species_Definitions_2013.pdf}}  Species Level Terminology {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/d/d4/Species_Level_Terminology_2013.pdf}} || Hubbell Reading {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/8/8e/Hubbell%2818Aug13%29.pdf}}
 
|-
 
|-
 
| Aug 30 ||Species definitions & species intermediacy & collections tour  <!--Species definitions & species intermediacy<br/>
 
| Aug 30 ||Species definitions & species intermediacy & collections tour  <!--Species definitions & species intermediacy<br/>
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20Level%20Terminology%202009.pdf}}Species Level Terminology 2009.pdf-->||
+
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20Level%20Terminology%202009.pdf}}Species Level Terminology 2009.pdf-->|| Templeton 1989 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/e8/A_Templeton_1989.pdf}}  De Queiroz 2007 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/5/51/De_Queiroz_2007.pdf}}
 
|-
 
|-
 
|Sept 2 ||Labor Day, No class || || rowspan="3"| Babbidge Library resources; taxonomic literature''' Meet in Babbidge library electronic classroom 1 (EC1) on level 1, to the left and behind Info Cafe 1 (http://classguides.lib.uconn.edu/content.php?pid=238531&sid=1968055) '''
 
|Sept 2 ||Labor Day, No class || || rowspan="3"| Babbidge Library resources; taxonomic literature''' Meet in Babbidge library electronic classroom 1 (EC1) on level 1, to the left and behind Info Cafe 1 (http://classguides.lib.uconn.edu/content.php?pid=238531&sid=1968055) '''
 
|-
 
|-
|Sept 4 ||Species definitions & species intermediacy||
+
|Sept 4 ||Species definitions & species intermediacy <br/> Species II and III Lecture {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/e8/Species_II_and_III_2013New.pdf}} ||  Finish reading/reread Templeton from Friday, Read Prosek's article (http://www.orionmagazine.org/index.php/articles/article/2868/)<br/>Optional Readings: Futuyama Section (via email),  Coyne and Orr's Species Concepts Overview (via email)
 
|-
 
|-
|Sept 6 || Lab, Meet in library Room EC1 || Meet in library
+
|Sept 6 || Lab, Meet in library Room EC1, walking in through the main entrance, go straight back and up to level 1, then see this map (http://www.lib.uconn.edu/maps/Level1EC12013.pdf), you will be coming out of the stairs in the center of the map || Ehrlic & Raven 1969 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/7/7c/Ehrlich%26Raven_1969.pdf}} <br/>  Make a slide or two about geographic subspecific variation <br/>  Nichols Gene tree species tree discordance {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/3/37/Nichols_GeneSpecies_Tree.pdf}}
 
|-
 
|-
|Sept 9  || Species definitions & species intermediacy; variation within species  ||  || rowspan="3"| Taxonomic resources: key websites, taxonomy exercise assigned '''(Meet in McCarthy Room, 4th floor TLS)'''
+
|Sept 9  || Species definitions & species intermediacy; variation within species  || Mallet 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/a/a7/Mallet2013_Sub-semisp.pdf}}  Mallet 2013 Glossary if needed {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/d/d4/Mallet2013_SpeciesConcepts.pdf}} <br/> Wilson and Brown {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/File:WilsonBrown1953.pdf}} <br/>Winston Chapter (emailed) || rowspan="3"| Taxonomic resources: key websites, taxonomy exercise assigned '''(Meet in McCarthy Room, 4th floor TLS)''' Literature Search Activity {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/2/2a/Lab1_Literature_Search_2013.pdf}}  <br/> Online Resource List {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/e2/Lab1_tax_resources_online_2013.pdf}}
 
|-
 
|-
|Sept 11 || Subspecies and geographic variation ||
+
|Sept 11 || Subspecies and geographic variation {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/6/6c/Subspecies_2013.pdf}} ||  Read Futuyma's section on gene tree/species tree issues (from the Species chapter distributed earlier, pages 476-478) <br/> Mayr Chapter 4 (emailed) <br/> Send Dave or myself an example slide of infrasubspecific variation <br/>  Possibly read this too {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/ee/Agrawal_PhenotypicPlasticity.pdf}}
 
<!--Individual variation(population variation){{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20II.pdf}}Species II.pdf || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Futuyma_pg239to263master1.pdf}}Futuyma_pg239-263.pdf (For 9/18) -->
 
<!--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 13 || lab || lab
+
|Sept 13 || lab || lab <br/> Dave's names lecture {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/c/c6/A_bit_on_names.pdf}}
 
|-
 
|-
|Sept 16 || Variation within a genotype:  ontogeny & phenotypic plasticity  || || rowspan="3"| Lab:  Alpha taxonomy: finding taxonomic characters & keys; descriptions and diagnoses; introduction to Mesquite’s alpha taxonomic features  '''(Meet in McCarthy Room, 4th floor TLS)'''
+
|Sept 16 || Variation within a genotype:  ontogeny & phenotypic plasticity {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/e7/SubspeciesII_GeneTrees.pdf}} || || rowspan="3"| Lab:  Alpha taxonomy: finding taxonomic characters & keys; descriptions and diagnoses; introduction to Mesquite’s alpha taxonomic features  Mesquite I {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/d/de/MesquiteLabI.pdf}} '''(Meet in McCarthy Room, 4th floor TLS)''' <br/>  Dave's Tiger Beetle Intro {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/6/64/TigerBeetleIntro.pdf}}
 
|-
 
|-
|Sept 18 ||  Supraspecific taxa ||
+
|Sept 18 ||  Variation within a genotype || Macrotaxonomy and plant systematics readings sent out by Dave
 
|-
 
|-
 
|Sept 20 || lab || lab
 
|Sept 20 || lab || lab
 
|-
 
|-
|Sept 23 || Phylogenetic inference: mostly a historical overview || || rowspan="3"| Describing and diagnosing species; specimen/museumdatabases DELTA, MANTIS & other taxonomic computer tools Lab:  NYC field trip '''(Meet in McCarthy Room, 4th floor TLS)'''  
+
|Sept 23 || Supraspecific taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/2/2a/HigherCatagories2013.pdf}} || || rowspan="3"|   NYC field trip '''(Do NOT meet in McCarthy Room, 4th floor TLS)'''  
 
|-
 
|-
 
|Sept 25 || Phylogenetic inference:  mostly a historical overview  ||
 
|Sept 25 || Phylogenetic inference:  mostly a historical overview  ||
Line 60: Line 60:
 
|Sept 27 || lab || lab
 
|Sept 27 || lab || lab
 
|-
 
|-
|Sept 30 || Trees and characters; types of dendrograms;<br/>rooting and polarization || || rowspan="3"|  Lab: Mesquite II  '''(Meet in McCarthy Room, 4th floor TLS)'''
+
|Sept 30 || Trees and characters; types of dendrograms;<br/>rooting and polarization || || rowspan="3"|  Describing and diagnosing species; specimen/museumdatabases DELTA, MANTIS & other taxonomic computer tools Lab: OR Lab: Mesquite II  '''(Meet in McCarthy Room, 4th floor TLS)'''
 
|-
 
|-
 
|Oct 2 || Taxonomic characters: polarity, outgroups, order, weighting, and step matrices  ||  
 
|Oct 2 || Taxonomic characters: polarity, outgroups, order, weighting, and step matrices  ||  
Line 232: Line 232:
 
=='''Important dates (May change a bit)'''==
 
=='''Important dates (May change a bit)'''==
 
<span style="font-size: large">
 
<span style="font-size: large">
7 October, 2013: conference; topic selection<br/>
+
7 October, 2013: Paper Topic Due<br/>
17 October, 2013: midterm<br/>
+
14 October, 2013: Midterm<br/>
21 October, 2013: outline with 5+ references<br/>
+
16 October, 2013: Brief Outline with 5 references<br/>
18 November, 2013: first draft due<br/>
+
18 November, 2013: First draft due (May change)<br/>
2 December, 2013: paper due<br/>
+
2 December, 2013: Paper due (May change)<br/>
 
[[Category:EEB Courses]]
 
[[Category:EEB Courses]]
 
<br/>
 
<br/>
 
EEB5347 website from 2011 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/EEB5347_2011)
 
EEB5347 website from 2011 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/EEB5347_2011)

Revision as of 19:24, 23 September 2013

2009 Class on top of the AMNH
2011 Class on top of the AMNH

Fall 2013

Lecture MW 9:05-10:35 In the Bamford Conference Room TLS 171B
Lab F 9:05-10:35 Probably the McCarthy Room, 4th floor TLS

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

Graduate Teaching Assistant: Russ Meister
Office hours: BioPharm 323 Stop by or by appointment
Phone: 486-3947
email: russell.meister'at'uconn.edu

Contents

Textbook and readings

There is no assigned text. Generally you can expect one or two readings to be assigned for each lecture. Many readings will be available as pdfs, downloadable from the course website. Others, available in hard copy only, will be on reserve in the departmental office (TLS 312) in the filing cabinet next to the window. You are free to check out copy #2 for 3 hours; copy #1 should stay in the office, i.e., so one is always there for others to photocopy.

Schedule


Day Topics Reading/Assignment Lab
Aug 26 Organizational meeting; an introduction to biological systematics Basic Definitions Pdficon small.gif
Lecture instead of lab this week
Aug 28 The many roles of biological systematics
Species Definitions Pdficon small.gif Species Level Terminology Pdficon small.gif
Hubbell Reading Pdficon small.gif
Aug 30 Species definitions & species intermediacy & collections tour Templeton 1989 Pdficon small.gif De Queiroz 2007 Pdficon small.gif
Sept 2 Labor Day, No class Babbidge Library resources; taxonomic literature Meet in Babbidge library electronic classroom 1 (EC1) on level 1, to the left and behind Info Cafe 1 (http://classguides.lib.uconn.edu/content.php?pid=238531&sid=1968055)
Sept 4 Species definitions & species intermediacy
Species II and III Lecture Pdficon small.gif
Finish reading/reread Templeton from Friday, Read Prosek's article (http://www.orionmagazine.org/index.php/articles/article/2868/)
Optional Readings: Futuyama Section (via email), Coyne and Orr's Species Concepts Overview (via email)
Sept 6 Lab, Meet in library Room EC1, walking in through the main entrance, go straight back and up to level 1, then see this map (http://www.lib.uconn.edu/maps/Level1EC12013.pdf), you will be coming out of the stairs in the center of the map Ehrlic & Raven 1969 Pdficon small.gif
Make a slide or two about geographic subspecific variation
Nichols Gene tree species tree discordance Pdficon small.gif
Sept 9 Species definitions & species intermediacy; variation within species Mallet 2013 Pdficon small.gif Mallet 2013 Glossary if needed Pdficon small.gif
Wilson and Brown Pdficon small.gif
Winston Chapter (emailed)
Taxonomic resources: key websites, taxonomy exercise assigned (Meet in McCarthy Room, 4th floor TLS) Literature Search Activity Pdficon small.gif
Online Resource List Pdficon small.gif
Sept 11 Subspecies and geographic variation Pdficon small.gif Read Futuyma's section on gene tree/species tree issues (from the Species chapter distributed earlier, pages 476-478)
Mayr Chapter 4 (emailed)
Send Dave or myself an example slide of infrasubspecific variation
Possibly read this too Pdficon small.gif
Sept 13 lab lab
Dave's names lecture Pdficon small.gif
Sept 16 Variation within a genotype: ontogeny & phenotypic plasticity Pdficon small.gif Lab: Alpha taxonomy: finding taxonomic characters & keys; descriptions and diagnoses; introduction to Mesquite’s alpha taxonomic features Mesquite I Pdficon small.gif (Meet in McCarthy Room, 4th floor TLS)
Dave's Tiger Beetle Intro Pdficon small.gif
Sept 18 Variation within a genotype Macrotaxonomy and plant systematics readings sent out by Dave
Sept 20 lab lab
Sept 23 Supraspecific taxa Pdficon small.gif NYC field trip (Do NOT meet in McCarthy Room, 4th floor TLS)
Sept 25 Phylogenetic inference: mostly a historical overview
Sept 27 lab lab
Sept 30 Trees and characters; types of dendrograms;
rooting and polarization
Describing and diagnosing species; specimen/museumdatabases DELTA, MANTIS & other taxonomic computer tools Lab: OR Lab: Mesquite II (Meet in McCarthy Room, 4th floor TLS)
Oct 2 Taxonomic characters: polarity, outgroups, order, weighting, and step matrices
Oct 4 lab lab
Oct 7 Distance methods, UPGMA, neighbor-joining, correcting distance data, multivariate methods Lab: Neighbor-joining and corrected distances; PAUP* (introduction) (Meet in McCarthy Room, 4th floor TLS)
Oct 9 Parsimony; search algorithms; algorithmic power, accuracy, and inconsistency
Oct 11 lab lab
Oct 14 Midterm exam Parsimony with PAUP (Meet in McCarthy Room, 4th floor TLS)
Oct 16 Midterm Review
Oct 18 lab lab
Oct 21 lab lab Lab: PAUP*: tree searches; tree statistics
(Meet in McCarthy Room, 4th floor TLS)
Oct 23 Reliability and measures of tree support
Oct 25 No Lab/AMNH & Bronx Zoo Trip
Oct 28 lab lab Lab: Likelihood (Garli and/or RAxML) and Bayesian analyses (Meet in McCarthy Room, 4th floor TLS)
Oct 30 Maximum likelihood (Lewis Guest Lecture)
Nov 1 Bayesian inference (Lewis Guest Lecture)
Nov 4 Data partitions; consensus; comparing trees Lab: PAUP*: ModelTest; molecular clocks; AIC et al. (Meet in McCarthy Room, 4th floor TLS)
Nov 6 Molecular systematics in plants (Les Guest Lecture)
Nov 8 lab lab
Nov 11 Molecular systematics in animals (Simon Guest Lecture) COI Barcoding and analyzing your own data sets (Meet in McCarthy Room, 4th floor TLS)
Nov 13 lab lab
Nov 15 DNA barcoding
Nov 18 Nomenclature Lab: Mesquite; character optimization; character correlation (Meet in McCarthy Room, 4th floor TLS)
Nov 20 Nomenclature; Phylocode
Nov 22 Lab Lab
Nov 25 Thanksgiving Recess Thanksgiving Recess, Do NOT meet in McCarthy Room
Nov 27 Thanksgiving Recess
Nov 29 Thanksgiving Recess
Dec 2 Special topic: Phylogenetic trees & evolutionary processes No lab this week DO NOT Meet in McCarthy Room
Dec 4 Special topic: Taxonomic collections
Dec 6 Special topic: Systematics and conservation biology and the future of biological systematics
Dec 14 Final: 8-11 AM

Supplementary Reading

Topics Additional Reading
Species as ranked taxa and species concepts Pdficon small.gifApplication of Evolutionary Species concept.pdf Pdficon small.gifSpecies concept for prokaryotes.pdf Pdficon small.gifIs the BSC showing its age?.pdf
Pdficon small.gifImportance of stating species concept for conservation purposes.pdf Pdficon small.gifImpact of species concepts on biodiversity studies.pdf
Pdficon small.gifThe need for specifying species concepts.pdfPdficon small.gifOn the failure of modern species concepts.pdf Pdficon small.gifSpecies as ranked taxa.pdf

Pdficon small.gifDoes the choice of species concept result in an increase in bird species?.pdf Pdficon small.gifMethod for delimiting Cohesion speceis.pdf

DNA Barcodes Pdficon small.gifElias et al. 2007.pdf
Pdficon small.gifJanzen et al 2005.pdf
Pdficon small.gifTen Reasons For Barcoding.pdf
Pdficon small.gifWill & Rubinoff 2004.pdf
Pdficon small.gifHebert and Gregory 2005.pdf
Pdficon small.gifMoritz and Cicero 2004.pdf
Pdficon small.gifHebert et al.2003.pdf
Pdficon small.gifPLoS_Birds_Hebert et al. 2004.pdf

Grading

Lab and take home exercises 20% 200 pts
Midterm 20% 200 pts
Term paper 22% 220 pts
Nomenclature exercise 1% 10 pts
Participation 2% 20 pts
Final 35% 350 pts
Total 100% 1000 pts


Term paper

Each student will be required to prepare a paper that will be due on December 2nd. Styles that have been adopted in the past include (1) a literature review that could be incorporated into a thesis chapter or (2) an NSF Doctoral Dissertation Improvement Grant proposal. Another angle would be to (3) review a subject relevant to systematic theory or methodology. If you are considering the DDIG option this year's Dissertation Improvement Grants will be due on October 10th, 2013. Visit http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5234 htm

Funding sources for taxonomy and biodiversity

Here is a comprehensive guide to potential funding sources for taxonomy and biodiversity studies. It was created in 2010, so most sources are up to date.
Pdficon small.gifFunding for biodiversity and taxonomy 2010.pdf

Important dates (May change a bit)

7 October, 2013: Paper Topic Due
14 October, 2013: Midterm
16 October, 2013: Brief Outline with 5 references
18 November, 2013: First draft due (May change)
2 December, 2013: Paper due (May change)

EEB5347 website from 2011 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/EEB5347_2011)

Personal tools