Principles and Methods of Systematic Biology (EEB 5347)

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2009 Class on top of the AMNH

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

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

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.


Day Topics Reading/Assignment Lab
Aug 31 Organizational meeting, an introduction to biological systematics
Pdficon small.gifIntroduction 2009 class notes.pdf Pdficon small.gifSyllabus.pdf
Pdficon small.gifRules of Pronunciation Sci.Name.pdf
Pdficon small.gifHubbell.pdf
Lecture instead of lab this week
Sept 2 The many roles of biological systematics & collections tour
Sept 4 Species definitions & species intermediacy
Pdficon small.gifSpecies Definitions.pdf Pdficon small.gifSpecies Level Terminology 2009.pdf
Pdficon small.gifTempleton 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 & intermediacyPdficon small.gifSpecies.ppt Pdficon small.gifEhrlich&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)Pdficon small.gifSpecies II.pdf Pdficon small.gifFutuyma_pg239-263.pdf (For 9/18)
Sept 18 Subspecies and geographic variation Pdficon small.gifSubspecies 2009.ppt
Sept 21 Variation within a genotype: ontogeny & phenotypic plasticityPdficon small.gifInfrasubspecific Variation 2009.pdf Alpha Taxonomy
Tiger Beetle Exercise
Mesquite Morphological Matrices
Pdficon small.gifWinston 1999.pdf
Pdficon small.gifMesquite morphological tutorial.pdf
Sept 23 Supraspecfic taxa Pdficon small.gifHigher Categories 2009.pdf Pdficon small.gifPage & Holmes 1998.pdf(For 09/28)
Sept 25 Lab Pdficon small.gifTiger Beetle Intro 2009.pdf
Sept 28 Phylogenetic inference: Mostly a historical overview
Pdficon small.gifIntro to Phylogenetic Inference.pdf
Pdficon small.gifChart the evol history of life.pdf(For 09/30)
Pdficon small.gifModernizing 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 Pdficon small.gifCharacters1.pdf
Oct 2 Lab Pdficon small.gifKrell&Cranston.pdf(For 10/05)
Pdficon small.gifForey et al 1992 Chap2&3.pdf (For 10/05)
Oct 5 Taxonomic characters: polarity, outgroups, order, weighting, and step matrices
Pdficon small.gifCharacters II.pdf
Pdficon small.gifCladistics Review I.pdf
Pdficon small.gifCollin&Miglietta 2008 Dollo's Law.pdf
Mesquite II: manipulating DNA/amino acid sequences
Pdficon small.gifMesquite Lab II
Pdficon small.gifGenBank Tutorial
Oct 7 More on trees
Pdficon small.gifTrees.pdf
Pdficon small.gifCladistics Review II.pdf
Oct 9 Lab Pdficon small.gifFelsenstein2004.pdf(For 10/16)
Oct 12 Distance methods, UPGMA, neighbor-joining, correcting distance data, multivariate techniques
Pdficon small.gifMultivariate Methods 2009.pdf
Pdficon small.gifDistance Methods 2009.pdf
Pdficon small.gifPage&Holmes_Chap6.pdf (For 10/14&16) Intro to PAUP*:
corrected distances
Pdficon small.gifLab 5 PAUP Intro.doc
Oct 14 Molecular systematics in animals (Simon guest lecture)
Pdficon small.gifHow Molecules Evolve.pdf
Oct 16 Lab
Oct 19 Exam Pdficon small.gifMidterm Sample Questions 2009.pdf
Pdficon small.gifNeighbor-joining Exercise.pdf
American Museum of Natural History
Oct 21 Midterm Review
Pdficon small.gifMidterm Post-Exam Review.pdf
Oct 23 AMNH Trip
Oct 26 Parsimony; search algorithms;
algorithmic power, accuracy, and inconsistency
Pdficon small.gifParsimony.pdf
Pdficon small.gifPage&Holmes_Rest_of_Ch6.pdf Parsimony Lab
Pdficon small.gifLab6 Parsimony.doc
Oct 28 Likelihood(Guest Lecture: Paul Lewis)
Pdficon small.gifLikelihood.pdf
Oct 30 Lab
Nov 2 Swine flu class cancelled Modeltest, AIC & hLRT, Molecular clocks
Pdficon small.gifLab7.doc
Nov 4 Bayesian phylogenetics (Paul Lewis)
Pdficon small.gifBayesian phylogenetics.pdf
Nov 6 Lab
Nov 9 Molecular systematics in plants (Don Les)
Pdficon small.gifPlant Systematics Les.pdf
Pdficon small.gifPage&Holmes280-285.pdf Garli and MrBayes Lab
Pdficon small.gifLab8.doc
Nov 11 Reliability and measures of tree support: c.i., r.i.,
decay indices, bootstraps ; jackknifes; and sensitivity analyses;
bootstraps, randomization tests
Pdficon small.gifReliability 2009.pdf
Nov 13 Lab
Nov 16 Data partitions; consensus; ILD
Pdficon small.gifConsensus.pdf
Pdficon small.gifILD 2009.doc COI data set analysis
Pdficon small.gifLab9 COI Barcodes.doc
Nov 18 DNA Barcodes
Pdficon small.gifDNA Barcodes.pdf
Pdficon small.gifFunk & Omland.pdf
Pdficon small.gifHebert et al. 2004.pdf
Pdficon small.gifMeyer and Paulay.pdf
Nov 20 Lab
Nov 23-28 No class-Thanksgiving Break

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


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 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