Principles and Methods of Systematic Biology (EEB 5347)

From EEBedia
Jump to: navigation, search

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'

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'

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.


Day Topics Reading/Assignment Lab
Aug 28 Organizational meeting Hubbell Reading Pdficon small.gif 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 Pdficon small.gif
Templeton (1989)Pdficon small.gif
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 Pdficon small.gif
Finish reading/reread Templeton from Friday
DeQuieroz (2007)Pdficon small.gif
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 (, 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 Pdficon small.gif
Erlich & Raven (1969)Pdficon small.gif
Mallet (2013) Pdficon small.gif
Meet in McCarthy Room
Lab 1: Taxonomic resources: key websites; taxonomy exercise Pdficon small.gif.
Online Resource List Pdficon small.gif
BioBlitz in Stamford.
Sept 13 Subspecies and geographic variation Pdficon small.gif 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 Pdficon small.gif
Notes Pdficon small.gif
Intro to Mesquite exercise Pdficon small.gif
(Wagner away on Friday)
Sept 20 Supraspecific taxa or Higher Categories Pdficon small.gif
Sept 22 lab
Sept 25 Supraspecific taxa or Higher Categories Lab 3: Describing and diagnosing species; Keys; Taxonomic cybertools: DELTA, Lucid, MANTISPdficon small.gif
A bit on keys Pdficon small.gif

A bit on descriptions and reading taxonomic literature Pdficon small.gif
Example Description and Diagnoses Pdficon small.gif
External anatomy of tiger beetles Pdficon small.gif
(Wagner away)

Sept 27 Start Infraspecific variation or "packaging" of variation Pdficon small.gif Schuh and Brower 2009 (pp 131-140) Pdficon small.gif
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") Pdficon small.gif
Oct 4 Phylogenetic inference: mostly a historical overview Pdficon small.gif, Begin: Trees and Characters Pdficon small.gif Page and Holmes Ch. 2 pp 11-36Pdficon small.gif
Krell and Cranston (2004)Pdficon small.gif
Tree View of Life Pdficon small.gif
Oct 6 lab
Oct 9 End: Trees and characters, Parsimony Pdficon small.gif 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") Pdficon small.gif
Oct 13 Head to NYC
NYC Trip Reference Pdficon small.gif
Oct 16 Tree reliability, sensitivity, and support measures IPdficon small.gif Page and Holmes Ch.6 pp. 209-227 Pdficon small.gif 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 172-208Pdficon small.gif
Oct 20 lab
Oct 23 Maximum Likelihood (Lewis) Pdficon small.gif 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") Pdficon small.gif
Primate COI data (right-click "save-as") Pdficon small.gif
Oct 25 Bayesian Inference (Lewis) Pdficon small.gif
Oct 27 lab
Oct 30 Midterm Q&A
Multivariate and distance methods I
Multivariate MethodsPdficon small.gif
Distance MethodsPdficon small.gif
Lab 7: Examining and correcting distance data in PAUP*
Exercise (right click "save-as")Pdficon small.gif
Nexus File (right click "save-as")Pdficon small.gif
Nov 1 Multivariate and distance methods II
Nov 3 lab
Nov 6 Molecular systematics in animals (Simon)Pdficon small.gif (Wagner in Denver) Lab 8: Maximum Likelihood, Model Choice, and CIPRES
Exercise (right-click "save as") Pdficon small.gif
Nov 8 Molecular systematics in plants (Les) (password for lecture PDF emailed to you) Pdficon small.gif
Nov 10 lab
Nov 13 Data partitions; consensus; comparing treesPdficon small.gif Lab 9: Bayesian Inference with MrBayes
Exercise (right-click "save-as")Pdficon small.gif
Nexus File (right-click "Save-as")Pdficon small.gif
Nov 15 DNA barcoding Pdficon small.gif Hebert et al. 2004 (read first)Pdficon small.gif
Ratnasingham & Hebert (read second)Pdficon small.gif
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")Pdficon small.gif
Nov 29 Nomenclature Pdficon small.gif
Type DefinitionsPdficon small.gif
Dec 1 lab
Dec 4 Nomenclature, Phylocode No lab this week
Dec 6 Phylocode Pennisi (2001) [read first: less technical explanation of pros/cons]Pdficon small.gif

Donoghue and Gauthier (2004}Pdficon small.gif
De Queiroz (2006)Pdficon small.gif

Dec 8 Phylogenetic Trees: Pattern and Process Pdficon small.gif
Dec circa 15 Final: 8-11 AM (Bamford)


Item Percentage Points
Lab and take home exercises
Midterm Exam
Nomenclature Exercise
Class Participation
Final Exam

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