Difference between revisions of "Principles and Methods of Systematic Biology (EEB 5347)"
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− | <span style="font-size: large">Fall | + | <span style="font-size: large">Fall 2017<br/> |
− | <span style="font-size: large">Lecture MW 9: | + | <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 | + | office hours open; best to call or email ahead<br/> |
− | email: [mailto:david.wagner | + | email: [mailto:david.wagner'at'uconn.edu david.wagner'at'uconn.edu]<br/> |
<br/> | <br/> | ||
− | '''Graduate Teaching Assistant''': | + | |
− | Office hours: TLS 461 | + | '''Graduate Teaching Assistant''': Kevin Keegan<br/> |
− | Phone: | + | Office hours: TLS 461 F 10:45-11:45 or by appointment<br/> |
− | email: [mailto: | + | 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. | + | 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" | ||
− | !style="background:#99cccc;" width="90" align="center"| | + | !style="background:#99cccc;" width="90" align="center"|Day |
− | !style="background:#2A52BE;" width=" | + | !style="background:#2A52BE;" width="365"|Topics |
− | !style="background:#008080;" width=" | + | !style="background:#008080;" width="315"|Reading/Assignment |
− | !style="background:#00B7EB;" width=" | + | !style="background:#00B7EB;" width="275"|Lab |
− | + | ||
− | + | ||
− | + | ||
|- | |- | ||
− | | | + | |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 |
+ | |- | ||
+ | |Aug 30 ||An introduction to biological systematics; The many roles of biological systematics and collections <br/> || | ||
+ | |- | ||
+ | |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}} | ||
+ | |- | ||
+ | |Sep 4 ||Labor Day, No class || || rowspan="3"| Kevin away in Mexico<br/>Babbidge Library resources; taxonomic literature | ||
+ | |- | ||
+ | |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 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 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''' || 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 22 || lab || | ||
+ | |- | ||
+ | |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 27 || Phylogenetic inference: mostly a historical overview || | ||
+ | |- | ||
+ | |Sept 29 || lab || | ||
+ | |- | ||
+ | |Oct 2 || Trees and characters: types of dendrograms, rooting and polarization || || rowspan="3"| 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 || || rowspan="3"| 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) || || rowspan="3"| 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 || || rowspan="3"| Lab: Tree reliability and measures <br/>'''(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 || || rowspan="3"| Lab: neighbor-joining and correcting distance data '''(Meet in McCarthy Room, 4th floor TLS)''' | ||
+ | |- | ||
+ | |Nov 1 || Bayesian inference (Lewis Guest Lecture) {{pdf|http://hydrodictyon.eeb.uconn.edu/people/plewis/downloads/Bayesian_30Oct2013.key.pdf}} || | ||
+ | |- | ||
+ | |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 8 || Molecular systematics in plants (Les) || | ||
+ | |- | ||
+ | |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 15 || DNA barcoding || | ||
+ | |- | ||
+ | |Nov 17 || lab || | ||
+ | |- | ||
+ | |Nov 20 ||rowspan="3"| '''Thanksiving''' || rowspan="3"| '''Thanksiving''' || rowspan="3"| '''Thanksiving''' | ||
+ | |- | ||
+ | |Nov 22 | ||
+ | |- | ||
+ | |Nov 24 | ||
+ | |- | ||
+ | |Nov 27 || Nomenclature || || rowspan="3"| Lab: Mesquite; character optimization; character correlation | ||
+ | |- | ||
+ | |Nov 29 || Nomenclature; Phylocode || | ||
+ | |- | ||
+ | |Dec 1 || lab || | ||
+ | |- | ||
+ | |Dec 4 || Phylogenetic trees & evolutionary processes || || rowspan="3"| '''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'''== | =='''Grading'''== | ||
{| border="1" cellpadding="1" | {| border="1" cellpadding="1" | ||
− | | | + | !width="200"|Item |
+ | !width="25"|Percentage | ||
+ | !width="25"|Points | ||
|- | |- | ||
− | | | + | |Lab and take home exercises|| <div style="text-align: center">25</div> || <div style="text-align: center">250</div> |
|- | |- | ||
− | | | + | |Midterm Exam || <div style="text-align: center">20</div> || <div style="text-align: center">200</div> |
|- | |- | ||
− | | | + | |Paper || <div style="text-align: center">25</div> || <div style="text-align: center">250</div> |
|- | |- | ||
− | | | + | |Nomenclature Exercise || <div style="text-align: center">2</div> || <div style="text-align: center">20</div> |
|- | |- | ||
− | | '''Total''' || '''100 | + | |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/> | ||
− | + | 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 | + | |
− | that | + | |
<br/> | <br/> | ||
− | + | ||
− | + | '''Important Dates''' | |
− | + | {| border="1" cellpadding="1" | |
− | + | !width="150"|Date | |
− | + | !width="200"|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 | ||
+ | |- | ||
+ | |} |
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 | 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 |
Templeton (1989) | |
Sep 4 | Labor Day, No class | Kevin away in Mexico Babbidge Library resources; taxonomic literature | |
Sept 6 | Species definitions & species intermediacy Species 1 Lecture |
Finish reading/reread Templeton from Friday DeQuieroz (2007) | |
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 |
Erlich & Raven (1969) Mallet (2013) |
Meet in McCarthy Room Taxonomic resources: key websites; taxonomy exercise . Online Resource List 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 Notes Intro to Mesquite exercise (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 A bit on keys (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) | ||
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 |