Principles and Methods of Systematic Biology (EEB 5347)

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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
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
Taxonomic resources: key websites; taxonomy exercise Pdficon small.gif.
Online Resource List Pdficon small.gif
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 (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) Pdficon small.gif
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)


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
1 December 2017 paper due