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− | [[Image:AMNH2009.jpg|right|''2009 Class on top of the AMNH'']]
| + | <span style="font-size: large">Fall 2017<br/> |
− | <span style="font-size: large">Fall 2011<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'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''': Chris Owen<br/> | + | |
− | Office hours: BioPharm 325 Wednesdays 10:30-11:30 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'at'uconn.edu christopher.l.owen'at'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" |
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| !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 29 ||Class canceled due to Hurricane Irene<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-->
| |
− | || || rowspan="3"| Lecture instead of lab this week
| |
| |- | | |- |
− | | Aug 31 ||Organizational meeting, an introduction to biological systematics||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hubbell.pdf}}Hubbell.pdf (for Friday)<br/>http://www.nytimes.com/2009/08/11/science/11naming.html (for Friday)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mayr_Ashlock1991_pgs1-18.pdf}}Mayr&Ashlock1991_pgs1-18.pdf (optional) | + | |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 2 ||The many roles of biological systematics & collections tour <!--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<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/De%20Queiroz%202007.pdf}}De Queiroz 2007.pdf<br/>http://en.wikipedia.org/wiki/Species#Definitions_of_species<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Futuyma_spconcepts_445-451.pdf}}Futuyma_spconcepts_445-451.pdf | + | |Aug 30 ||An introduction to biological systematics; The many roles of biological systematics and collections <br/> || |
| |- | | |- |
− | | Sept 5 ||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 ''' | + | |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 7 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20I%202011.pdf}}Species I 2011.pdf || | + | |Sep 4 ||Labor Day, No class || || rowspan="3"| Kevin away in Mexico<br/>Babbidge Library resources; taxonomic literature |
| |- | | |- |
− | |Sept 9 || Meet in library || Meet in library | + | |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 12 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20II%202011.pdf}}Species II 2011.pdf || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Ehrlich%26Raven_1969.pdf}}Ehrlich&Raven1969.pdf || rowspan="3"| Taxonomic resources: 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 14 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Species%20III%202011.pdf}}Species III 2011.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_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. |
− | <!--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 16 || lab || lab | + | |Sept 13 || Subspecies and geographic variation || Send Wagner an example (~3 ppt slides) of intraspecific geographic variation '''before 11:59 PM Sunday''' |
| |- | | |- |
− | |Sept 19 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Subspecies%202011.pdf}}Subspecies 2011.pdf || || rowspan="3"| Intro to Mesquite and Morphological Matrices '''(Meet in McCarthy Room, 4th floor TLS)''' | + | |Sept 15 || lab || |
| |- | | |- |
− | |Sept 21 || Infrapopulation variation (lecture sent via email) || | + | |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 23 || lab || lab | + | |Sept 20 || Supraspecific taxa || |
| |- | | |- |
− | |Sept 26 || {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Higher%20Categories%202011.pdf}}Higher Categories 2011.pdf || || rowspan="3"| Keys, species descriptions, and cybertaxonomy '''(Meet in McCarthy Room, 4th floor TLS)''' | + | |Sept 22 || lab || |
| |- | | |- |
− | |Sept 28 || || | + | |Sept 25 || Supraspecific taxa || || rowspan="3"| Lab: Describing and diagnosing species; specimen/museum databases; Taxonomic cybertools: DELTA, MANTIS, Mesquite & others (Wagner away) |
| + | Phylogenetic inference |
| |- | | |- |
− | |Sept 30 || lab || lab | + | |Sept 27 || Phylogenetic inference: mostly a historical overview || |
| |- | | |- |
− | <!--|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 29 || lab || |
| |- | | |- |
− | |Sept 23 ||Supraspecfic taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Higher%20Categories%202009.pdf}}Higher Categories 2009.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%20%26%20Holmes%201998.pdf}}Page & Holmes 1998.pdf(For 09/28) | + | |Oct 2 || Trees and characters: types of dendrograms, rooting and polarization || || rowspan="3"| Lab: Mesquite II, Parsimony??? |
| |- | | |- |
− | |Sept 25 ||Lab {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Tiger%20Beetle%20Intro%202009.pdf}}Tiger Beetle Intro 2009.pdf || | + | |Oct 4 || Taxonomic characters: polarity, outgroups, order, weighting, and step matrices || |
| |- | | |- |
− | |Sept 28 ||Phylogenetic inference: Mostly a historical overview<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Intro%20to%20Phylogenetic%20Inference.pdf}}Intro to Phylogenetic Inference.pdf||{{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)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Modernizing%20the%20tree%20of%20life.pdf}}Modernizing the tree of life.pdf(For 09/30) || rowspan="3"| Alpha Taxonomy: taxonomic keys,<br/>specimen/museum databases DELTA,<br/> MANTIS & other taxonomic computer tools | + | |Oct 6 || lab || |
| |- | | |- |
− | |Sept 30 ||Trees and characters: types of dendrograms, rooting and polarization<br/>weighting and step matrices {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters1.pdf}}Characters1.pdf|| | + | |Oct 9 || Parsimony; tree searches; tree statistics || || rowspan="3"| Lab: Trip to American Museum of Natural History and Bronx Zoo in NYC!!! |
| |- | | |- |
− | |Oct 2 ||Lab ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Krell%26Cranston.pdf}}Krell&Cranston.pdf(For 10/05)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Forey%20et%20al%201992%20Chap2%263.pdf}}Forey et al 1992 Chap2&3.pdf (For 10/05) | + | |Oct 11 ||''' Midterm exam''' || |
| |- | | |- |
− | |Oct 5 ||Taxonomic characters: polarity, outgroups, order, weighting, and step matrices<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Characters%20II.pdf}}Characters II.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/CompleatCladist.pdf}}Cladistics Review I.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Collin%26Miglietta%202008%20Dollo%20Law.pdf}}Collin&Miglietta 2008 Dollo's Law.pdf|| rowspan="3"| Mesquite II: manipulating DNA/amino acid sequences<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mesquite%20Lab%20II}}Mesquite Lab II<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/GenBank%20Tutorial%202009}}GenBank Tutorial | + | |Oct 13 || '''Head to NYC''' || |
| |- | | |- |
− | |Oct 7 ||More on trees<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/More%20on%20Trees.pdf}}Trees.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Cladistics.pdf}}Cladistics Review II.pdf | + | |Oct 16 || Maximum likelihood (lecture by Lewis; Wagner away) || || rowspan="3"| Lab: likelihood (Garli and/or RAxML) and Bayesian analyses |
| |- | | |- |
− | |Oct 9 ||Lab ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Felsenstein2004.pdf}}Felsenstein2004.pdf(For 10/16) | + | |Oct 18 || Bayesian inference (lecture by Lewis; Wagner away) || |
| |- | | |- |
− | |Oct 12 ||Distance methods, UPGMA, neighbor-joining, correcting distance data, multivariate techniques<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Multivariate%20Methods%202009.pdf}}Multivariate Methods 2009.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Distance%20Methods%202009.pdf}}Distance Methods 2009.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes_Chap6.pdf}}Page&Holmes_Chap6.pdf (For 10/14&16)|| rowspan="3"|Intro to PAUP*:<br/>neighbor-joining<br/>corrected distances<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab%205_PAUP%20Intro%20revised-1.doc}}Lab 5 PAUP Intro.doc | + | |Oct 20 || lab || |
| |- | | |- |
− | |Oct 14 ||Molecular systematics in animals (Simon guest lecture)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Guest%20Lecture%20Wagner%27s%20Systematics-%20How%20Molecules%20Evolve.%20Fall%2009.pdf}}How Molecules Evolve.pdf|| | + | |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 16 ||Lab || | + | |Oct 25 || Tree reliability, sensitivity, and support measures II || |
| |- | | |- |
− | |Oct 19 ||Exam||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Midterm%20Sample%20Questions%202009.pdf}}Midterm Sample Questions 2009.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Neighbor-joining%20Exercise.pdf}}Neighbor-joining Exercise.pdf||rowspan="3"|American Museum of Natural History | + | |Oct 27 || lab || |
| |- | | |- |
− | |Oct 21 ||Midterm Review<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Midterm%20Post-Exam%20Review.pdf}}Midterm Post-Exam Review.pdf|| | + | |Oct 30 || Multivariate and distance methods || || rowspan="3"| Lab: neighbor-joining and correcting distance data '''(Meet in McCarthy Room, 4th floor TLS)''' |
| |- | | |- |
− | |Oct 23 ||AMNH Trip || | + | |Nov 1 || Bayesian inference (Lewis Guest Lecture) {{pdf|http://hydrodictyon.eeb.uconn.edu/people/plewis/downloads/Bayesian_30Oct2013.key.pdf}} || |
| |- | | |- |
− | |Oct 26 ||Parsimony; search algorithms;<br/>algorithmic power, accuracy, and inconsistency<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Parsimony.pdf}}Parsimony.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes_Part2_1.pdf}}Page&Holmes_Rest_of_Ch6.pdf||rowspan="3"|Parsimony Lab<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab6_parsimony_2009.doc}}Lab6 Parsimony.doc | + | |Nov 3 || lab || |
| |- | | |- |
− | |Oct 28 ||Likelihood(Guest Lecture: Paul Lewis)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Likelihood_28Oct2009_1perpage.pdf}}Likelihood.pdf|| | + | |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)''' |
| |- | | |- |
− | |Oct 30 ||Lab || | + | |Nov 8 || Molecular systematics in plants (Les) || |
| |- | | |- |
− | |Nov 2 ||Swine flu class cancelled||||rowspan="3"|Modeltest, AIC & hLRT, Molecular clocks<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab7_2009_corrected.doc}}Lab7.doc | + | |Nov 10 || lab || |
| |- | | |- |
− | |Nov 4 ||Bayesian phylogenetics (Paul Lewis)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Bayesian_2Nov2009_1perpage.pdf}}Bayesian phylogenetics.pdf|| | + | |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 6 ||Lab || | + | |Nov 15 || DNA barcoding || |
| |- | | |- |
− | |Nov 9 ||Molecular systematics in plants (Don Les)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Systematics_2009_Les.pdf}}Plant Systematics Les.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Page%26Holmes280_285.pdf}}Page&Holmes280-285.pdf||rowspan="3"|Garli and MrBayes Lab<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/lab8_2009.doc}}Lab8.doc | + | |Nov 17 || lab || |
| |- | | |- |
− | |Nov 11 ||Reliability and measures of tree support: c.i., r.i.,<br/>decay indices, bootstraps ; jackknifes; and sensitivity analyses;<br/>bootstraps, randomization tests<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Reliability%202009.pdf}}Reliability 2009.pdf|| | + | |Nov 20 ||rowspan="3"| '''Thanksiving''' || rowspan="3"| '''Thanksiving''' || rowspan="3"| '''Thanksiving''' |
| |- | | |- |
− | |Nov 13 ||Lab || | + | |Nov 22 |
| |- | | |- |
− | |Nov 16 ||Data partitions; consensus; ILD<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Consensus%202009.pdf}}Consensus.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/ILD%202009.doc}}ILD 2009.doc||rowspan="3"|COI data set analysis<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Lab9_barcoding_2009_corrected.doc}}Lab9 COI Barcodes.doc | + | |Nov 24 |
| |- | | |- |
− | |Nov 18 ||DNA Barcodes<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/DNA%20Barcodes.pdf}}DNA Barcodes.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/FunkOmlandARev.pdf}}Funk & Omland.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Astraptes%20fulgerator.pdf}}Hebert et al. 2004.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Meyer%20and%20Paulaypdf%20copy.pdf}}Meyer and Paulay.pdf | + | |Nov 27 || Nomenclature || || rowspan="3"| Lab: Mesquite; character optimization; character correlation |
| |- | | |- |
− | |Nov 20 ||Lab || | + | |Nov 29 || Nomenclature; Phylocode || |
| |- | | |- |
− | |Nov 23-28 ||No class-Thanksgiving Break|| | + | |Dec 1 || lab || |
| |- | | |- |
− | |Nov 30 ||Nomenclature<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Nomenclature%202009.pdf}}Nomenclature 2009.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Berenbaum%20Article.pdf}}Berenbaum Article.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Conniff%20article.pdf}}Conniff article.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Gould_Bully%20for%20Bront.pdf}}Gould_Bully for Bront.pdf||rowspan="3"|Mesquite: Ancestral States Reconstruction | + | |Dec 4 || Phylogenetic trees & evolutionary processes || || rowspan="3"| '''No lab this week''' |
| |- | | |- |
− | |Dec 2 ||Nomenclature; Phylocode||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Mares2009.pdf}}Mares2009.pdf | + | |Dec 6 || Special topic: Taxonomic collections || |
| |- | | |- |
− | |Dec 4 ||Lab || | + | |Dec 8 || Special topic: Systematics and conservation biology and the future of biological systematics || |
| |- | | |- |
− | |Dec 7 ||Special topic: Taxonomic Collections<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Importance%20of%20Collections.pdf}}Importance of Collections.pdf||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Nomenclature%20Exercise.doc}}Nomenclature Exercise.doc (due Dec 11)||rowspan="3"|No Lab | + | |Dec circa 15 || Final: 8-11 AM (Bamford) || |
− | |-
| + | |
− | |Dec 9 ||Special topic: Phylogenetic trees & evolutionary processes;<br/>the comparative method<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Patterns%20and%20Processes%202009%20Class%20Version.pdf}}Patterns and Processes.pdf||
| + | |
− | |-
| + | |
− | |Dec 11 ||Conservation, Systematics, and looking ahead<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Conservation_and_Systematics.pdf}}Conservation and Systematics.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Looking%20Ahead%202009.pdf}}Looking Ahead 2009.pdf||
| + | |
− | |}-->
| + | |
− | <br/>
| + | |
− | =='''Supplementary Reading'''==
| + | |
− | {| border="1" cellpadding="2"
| + | |
− | !style="background:#2A52BE;" width="275"|Topics
| + | |
− | !style="background:#008080;" width="975"|Additional Reading
| + | |
− | |-
| + | |
− | | 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/>
| + | |
− | {{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
| + | |
− | |-
| + | |
− | |DNA Barcodes||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/elias%202007.pdf}}Elias et al. 2007.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Barcoding%20Leps%20of%20Costa%20Rica%20Guanacaste%20red.%20Janzen%20et%20al.pdf}}Janzen et al 2005.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/TenReasonsBarcoding.pdf}}Ten Reasons For Barcoding.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Will%20%26%20Rubinoff%202004.pdf}}Will & Rubinoff 2004.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hebert%20and%20Gregory%202005.pdf}}Hebert and Gregory 2005.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/PLoS_PromisesAndPitfalls.pdf}}Moritz and Cicero 2004.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Hebert_et_al_2003_DNABarcodes.pdf}}Hebert et al.2003.pdf<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/PLoS_Birds_Hebert_et_al_2004.pdf}}PLoS_Birds_Hebert et al. 2004.pdf
| + | |
| |} | | |} |
| + | |
| =='''Grading'''== | | =='''Grading'''== |
| {| border="1" cellpadding="1" | | {| border="1" cellpadding="1" |
− | | Lab and take home exercises || 20% || 200 pts | + | !width="200"|Item |
| + | !width="25"|Percentage |
| + | !width="25"|Points |
| |- | | |- |
− | | Midterm || 20% || 200 pts | + | |Lab and take home exercises|| <div style="text-align: center">25</div> || <div style="text-align: center">250</div> |
| |- | | |- |
− | | Term paper || 22% || 220 pts | + | |Midterm Exam || <div style="text-align: center">20</div> || <div style="text-align: center">200</div> |
| |- | | |- |
− | | Nomenclature exercise || 1% || 10 pts | + | |Paper || <div style="text-align: center">25</div> || <div style="text-align: center">250</div> |
| |- | | |- |
− | | Participation || 2% || 20 pts | + | |Nomenclature Exercise || <div style="text-align: center">2</div> || <div style="text-align: center">20</div> |
| |- | | |- |
− | | Final || 35% || 350 pts | + | |Class Participation || <div style="text-align: center">3</div> || <div style="text-align: center">30</div> |
| |- | | |- |
− | | '''Total''' || '''100%''' || '''1000 pts''' | + | |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://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5234 htm | + | |
| <br/> | | <br/> |
− | =='''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.<br/>
| + | '''Important Dates''' |
− | {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Funding%20for%20biodiversity%20and%20taxonomy%202010.pdf}}Funding for biodiversity and taxonomy 2010.pdf
| + | {| border="1" cellpadding="1" |
− | <br/>
| + | !width="150"|Date |
− | =='''Important dates'''== | + | !width="200"|Milestone |
− | <span style="font-size: large">
| + | |- |
− | 7 October, 2011: conference; topic selection<br/>
| + | |6 October 2017 || conference; topic selection |
− | 21 October, 2011: outline with 5+ references<br/>
| + | |- |
− | 18 November, 2011: first draft due<br/>
| + | |20 October 2017 || outline with 5+ references |
− | 2 December, 2011: paper due<br/>
| + | |- |
− | [[Category:EEB Courses]]
| + | |17 November 2017 || first draft due |
| + | |- |
| + | |1 December 2017 || paper due |
| + | |- |
| + | |} |
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.
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; specimen/museum databases; Taxonomic cybertools: DELTA, MANTIS, Mesquite & others (Wagner away)
Phylogenetic inference
|
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) |
|