Research Index
Syllabus
COA 692/792 Special Problems in Systematics
Fall, Spring and Summer Semesters
Instructor: Dr. Jinx Campbell, Asst. Professor of Marine Mycology
Course Description:
This is a practical course in cladistics using the student's own data set to elucidate species phylogenies, classifications and taxonomic placement.
Each student must provide a molecular or morphological data set that will be analyzed over the duration of the course.
Course Objectives:
Students will be instructed on how to find phylogenetic data and how to build a data set. Using a number of phylogenetic software packages students will learn how to align their sequence data and produce cladistic trees using maximum parsimony, maximum likelihood and Bayesian analyses. Additionally statistical methods will be employed to determine the “best” tree for the dataset, and the robustness of the tree topologies using bootstrap, jack-knife, decay indices and posterior probabilities.
Software:
ClustalX
Se-Al
MacClade
PAUP*
MrBayes
Autodecay
Grading:
Mid-term (20%): Completion of a working data set (sequence data must be completely aligned), exported into Nexus format.
Final (80%): Construction of a cladistic tree indicating branch and clade support, suitable for publication.
A = 90–100%
B = 80–89%
C = 70–79%
D = 60–69%
F = below 59%
