Difference between revisions of "Principles and Methods of Systematic Biology (EEB 5347)"
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|Oct 9 ||Lab ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Felsenstein2004.pdf}}Felsenstein2004.pdf(For 10/16) | |Oct 9 ||Lab ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Felsenstein2004.pdf}}Felsenstein2004.pdf(For 10/16) | ||
|- | |- | ||
− | |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 | + | |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 |
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|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 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|| | ||
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|Oct 23 ||AMNH Trip || | |Oct 23 ||AMNH Trip || | ||
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− | |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 | + | |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 |
|- | |- | ||
|Oct 28 ||Likelihood(Guest Lecture: Paul Lewis)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Likelihood_28Oct2009_1perpage.pdf}}Likelihood.pdf|| | |Oct 28 ||Likelihood(Guest Lecture: Paul Lewis)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Likelihood_28Oct2009_1perpage.pdf}}Likelihood.pdf|| | ||
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|Oct 30 ||Lab || | |Oct 30 ||Lab || | ||
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− | |Nov 2 ||Swine flu class cancelled||||rowspan="3"|Modeltest, AIC & hLRT, Molecular clocks | + | |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 4 ||Bayesian phylogenetics (Paul Lewis)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Bayesian_2Nov2009_1perpage.pdf}}Bayesian phylogenetics.pdf|| | |Nov 4 ||Bayesian phylogenetics (Paul Lewis)<br/>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/systematics/restricted/Bayesian_2Nov2009_1perpage.pdf}}Bayesian phylogenetics.pdf|| | ||
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|Nov 6 ||Lab || | |Nov 6 ||Lab || | ||
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− | |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 | + | |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 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 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|| |
Revision as of 06:08, 24 November 2009
Fall 2009
Lecture MW 9:00-10:30, Lab F 9:00-10:30
Instructor: Dr. David L. Wagner, TLS Rm 471
Phone: 486-2139
office hours as available
email: david.wagner@uconn.edu
Graduate Teaching Assistant: Chris Owen
Office hours: TLS 461 Monday 10:30-11:30 (BioPharm 323 most other times) or by appointment
Phone: 486-6650
email: christopher.l.owen@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 31 | Organizational meeting, an introduction to biological systematics Introduction 2009 class notes.pdf Syllabus.pdf Rules of Pronunciation Sci.Name.pdf |
Hubbell.pdf http://www.nytimes.com/2009/08/11/science/11naming.html |
Lecture instead of lab this week |
Sept 2 | The many roles of biological systematics & collections tour | ||
Sept 4 | Species definitions & species intermediacy Species Definitions.pdf Species Level Terminology 2009.pdf |
Templeton 1989.pdf | |
Sept 7 No class | No class | No class | Babbidge Library resources; taxonomic literature Meet in Babbidge library Level 2 electronic classroom, across the lobby from the stairs and elevators |
Sept 9 | Species definitions & intermediacySpecies.ppt | Ehrlich&Raven1969.pdf (For 09/16) | |
Sept 11 Lab | Lab | Lab | |
Sept 14 Lab | Lab | Lab | Taxonomic resoursces: key websites, taxonomy exercise assigned (Meet in McCarthy Room, 4th floor TLS) |
Sept 16 | Individual variation(population variation)Species II.pdf | Futuyma_pg239-263.pdf (For 9/18) | |
Sept 18 | Subspecies and geographic variation Subspecies 2009.ppt | ||
Sept 21 | Variation within a genotype: ontogeny & phenotypic plasticityInfrasubspecific Variation 2009.pdf | Alpha Taxonomy Tiger Beetle Exercise Mesquite Morphological Matrices Winston 1999.pdf Mesquite morphological tutorial.pdf | |
Sept 23 | Supraspecfic taxa Higher Categories 2009.pdf | Page & Holmes 1998.pdf(For 09/28) | |
Sept 25 | Lab Tiger Beetle Intro 2009.pdf | ||
Sept 28 | Phylogenetic inference: Mostly a historical overview Intro to Phylogenetic Inference.pdf |
Chart the evol history of life.pdf(For 09/30) Modernizing the tree of life.pdf(For 09/30) |
Alpha Taxonomy: taxonomic keys, specimen/museum databases DELTA, MANTIS & other taxonomic computer tools |
Sept 30 | Trees and characters: types of dendrograms, rooting and polarization weighting and step matrices Characters1.pdf |
||
Oct 2 | Lab | Krell&Cranston.pdf(For 10/05) Forey et al 1992 Chap2&3.pdf (For 10/05) | |
Oct 5 | Taxonomic characters: polarity, outgroups, order, weighting, and step matrices Characters II.pdf |
Cladistics Review I.pdf Collin&Miglietta 2008 Dollo's Law.pdf |
Mesquite II: manipulating DNA/amino acid sequences Mesquite Lab II GenBank Tutorial |
Oct 7 | More on trees Trees.pdf |
Cladistics Review II.pdf | |
Oct 9 | Lab | Felsenstein2004.pdf(For 10/16) | |
Oct 12 | Distance methods, UPGMA, neighbor-joining, correcting distance data, multivariate techniques Multivariate Methods 2009.pdf Distance Methods 2009.pdf |
Page&Holmes_Chap6.pdf (For 10/14&16) | Intro to PAUP*: neighbor-joining corrected distances Lab 5 PAUP Intro.doc |
Oct 14 | Molecular systematics in animals (Simon guest lecture) How Molecules Evolve.pdf |
||
Oct 16 | Lab | ||
Oct 19 | Exam | Midterm Sample Questions 2009.pdf Neighbor-joining Exercise.pdf |
American Museum of Natural History |
Oct 21 | Midterm Review Midterm Post-Exam Review.pdf |
||
Oct 23 | AMNH Trip | ||
Oct 26 | Parsimony; search algorithms; algorithmic power, accuracy, and inconsistency Parsimony.pdf |
Page&Holmes_Rest_of_Ch6.pdf | Parsimony Lab Lab6 Parsimony.doc |
Oct 28 | Likelihood(Guest Lecture: Paul Lewis) Likelihood.pdf |
||
Oct 30 | Lab | ||
Nov 2 | Swine flu class cancelled | Modeltest, AIC & hLRT, Molecular clocks Lab7.doc | |
Nov 4 | Bayesian phylogenetics (Paul Lewis) Bayesian phylogenetics.pdf |
||
Nov 6 | Lab | ||
Nov 9 | Molecular systematics in plants (Don Les) Plant Systematics Les.pdf |
Page&Holmes280-285.pdf | Garli and MrBayes Lab Lab8.doc |
Nov 11 | Reliability and measures of tree support: c.i., r.i., decay indices, bootstraps ; jackknifes; and sensitivity analyses; bootstraps, randomization tests Reliability 2009.pdf |
||
Nov 13 | Lab | ||
Nov 16 | Data partitions; consensus; ILD Consensus 2009.pdf ILD 2009.doc |
COI data set analysis | |
Nov 18 | DNA Barcodes DNA Barcodes.pdf Funk & Omland.pdf |
Hebert et al. 2004.pdf Meyer and Paulay.pdf | |
Nov 20 | Lab | ||
Nov 23-28 | No class-Thanksgiving Break |
Supplementary Reading
Grading
Lab and take home exercises | 20% | 100 pts |
Midterm | 20% | 100 pts |
Term paper | 25% | 115 pts |
Nomenclature exercise | 2% | 10 pts |
Final | 35% | 175 pts |
Total | 100% | 500 pts |
Term paper
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://researchfunding.duke.edu/detail.asp?OppID=587 htm
Important dates
9 October, 2009: conference; topic selection
23 October, 2009: outline with 5+ references
20 November, 2009: first draft due
4 December, 2009: paper due