Difference between revisions of "Principles and Methods of Systematic Biology (EEB 5347)"
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− | + | <span style="font-size: large">Fall 2017<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/> | |
− | <span style="font-size: large">Lecture MW 9:05-10: | + | |
− | Lab F 9:05-10: | + | |
<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/> | ||
Line 12: | Line 9: | ||
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''': | + | |
− | Office hours: | + | '''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" | ||
Line 27: | Line 27: | ||
!style="background:#00B7EB;" width="275"|Lab | !style="background:#00B7EB;" width="275"|Lab | ||
|- | |- | ||
− | |Aug | + | |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 | + | |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}} |
− | {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/ | + | |
|- | |- | ||
− | | | + | |Sep 4 ||Labor Day, No class || || rowspan="3"| Kevin away in Mexico<br/>Lab: Babbidge Library resources; taxonomic literature |
|- | |- | ||
− | |Sept | + | |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 | + | |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 | + | |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. |
|- | |- | ||
− | |Sept | + | |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 | + | |Sept 15 || lab || |
|- | |- | ||
− | |Sept | + | |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 | + | |Sept 20 || Supraspecific taxa or Higher Categories {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Higher_Categories_2017.pdf}}|| |
|- | |- | ||
− | |Sept | + | |Sept 22 || lab || |
|- | |- | ||
− | |Sept | + | |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) | ||
|- | |- | ||
− | |Sept | + | |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 | + | |Sept 29 || Continue Infraspecific variation or "packaging" of variation || |
|- | |- | ||
− | | | + | |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}} |
|- | |- | ||
− | |Oct | + | |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 | + | |Oct 6 || lab || |
|- | |- | ||
− | |Oct | + | |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 | + | |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 | + | |Oct 13 || '''Head to NYC'''<br/>NYC Trip Reference {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/NYC_Trip_Reference.pdf}} || |
|- | |- | ||
− | |Oct | + | |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 | + | |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 | + | |Oct 20 || lab || |
|- | |- | ||
− | |Oct | + | |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 | + | |Oct 25 || Bayesian Inference (Lewis) {{pdf|http://hydrodictyon.eeb.uconn.edu/people/plewis/downloads/eeb5347-2017/25Oct2017.pdf}} || |
|- | |- | ||
− | |Oct | + | |Oct 27 || lab || |
|- | |- | ||
− | |Oct | + | |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 | + | |Nov 3 || lab || |
|- | |- | ||
− | |Nov | + | |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 | + | |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 | + | |Nov 10 || lab || |
|- | |- | ||
− | |Nov | + | |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 | + | |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 | + | |Nov 17 || lab || |
|- | |- | ||
− | |Nov | + | |Nov 20 ||rowspan="3"| '''Thanksiving''' || rowspan="3"| '''Thanksiving''' || rowspan="3"| '''Thanksiving''' |
|- | |- | ||
− | |Nov | + | |Nov 22 |
|- | |- | ||
− | |Nov | + | |Nov 24 |
|- | |- | ||
− | |Nov | + | |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 | + | |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 | + | |Dec 4 ||Nomenclature, Phylocode || || rowspan="3"| '''No lab this week''' |
|- | |- | ||
− | |Dec | + | |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 | + | |Dec 8 || Phylogenetic Trees: Pattern and Process {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Patterns_and_Processes_2017.pdf}}|| |
|- | |- | ||
− | |Dec | + | |Dec circa 15 || Final: 8-11 AM (Bamford) || |
+ | |} | ||
+ | |||
+ | =='''Grading'''== | ||
+ | {| 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> |
|- | |- | ||
− | | | + | |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/> | |
− | + | 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. | |
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− | + | '''Important Dates''' | |
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− | | | + | !width="150"|Date |
+ | !width="200"|Milestone | ||
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− | | | + | |6 October 2017 || conference; topic selection |
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− | | | + | |20 October 2017 || outline with 5+ references |
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− | | | + | |17 November 2017 || first draft due |
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− | | | + | |4 December 2017 || paper due |
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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 | 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 Lab: 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 Lab 1: 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 2: 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 or Higher Categories | ||
Sept 22 | lab | ||
Sept 25 | Supraspecific taxa or Higher Categories | Lab 3: Describing and diagnosing species; Keys; Taxonomic cybertools: DELTA, Lucid, MANTIS A bit on keys A bit on descriptions and reading taxonomic literature | |
Sept 27 | Start Infraspecific variation or "packaging" of variation | Schuh and Brower 2009 (pp 131-140) | |
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") | |
Oct 4 | Phylogenetic inference: mostly a historical overview , Begin: Trees and Characters | Page and Holmes Ch. 2 pp 11-36 Krell and Cranston (2004) Tree View of Life | |
Oct 6 | lab | ||
Oct 9 | End: Trees and characters, Parsimony | 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") | ||
Oct 13 | Head to NYC NYC Trip Reference |
||
Oct 16 | Tree reliability, sensitivity, and support measures I | Page and Holmes Ch.6 pp. 209-227 | 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 | |
Oct 20 | lab | ||
Oct 23 | Maximum Likelihood (Lewis) | 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") Primate COI data (right-click "save-as") |
Oct 25 | Bayesian Inference (Lewis) | ||
Oct 27 | lab | ||
Oct 30 | Midterm Q&A Multivariate and distance methods I Multivariate Methods Distance Methods |
Lab 7: Examining and correcting distance data in PAUP* Exercise (right click "save-as") Nexus File (right click "save-as") | |
Nov 1 | Multivariate and distance methods II | ||
Nov 3 | lab | ||
Nov 6 | Molecular systematics in animals (Simon) (Wagner in Denver) | Lab 8: Maximum Likelihood, Model Choice, and CIPRES Exercise (right-click "save as") | |
Nov 8 | Molecular systematics in plants (Les) (password for lecture PDF emailed to you) | ||
Nov 10 | lab | ||
Nov 13 | Data partitions; consensus; comparing trees | Lab 9: Bayesian Inference with MrBayes Exercise (right-click "save-as") Nexus File (right-click "Save-as") | |
Nov 15 | DNA barcoding | Hebert et al. 2004 (read first) Ratnasingham & Hebert (read second) | |
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") | |
Nov 29 | Nomenclature Type Definitions |
||
Dec 1 | lab | ||
Dec 4 | Nomenclature, Phylocode | No lab this week | |
Dec 6 | Phylocode | Pennisi (2001) [read first: less technical explanation of pros/cons] | |
Dec 8 | Phylogenetic Trees: Pattern and Process | ||
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 |