PBIO 699K course description

PBIO 699K (to become CBMG 670): Molecular Systematics

Instructor: Charles Delwiche
3 credits, MW 10:00-11:50

Molecular Systematics is in development as a course for the Cell Biology and Molecular Genetics (CBMG) graduate program, and is also a core course in the BEES graduate program (core area 3, systematics).

Phylogenetic analysis, particularly analyses using molecular data, have provided a powerful tool for the study of the history of evolution of both organisms and genomes. We will study phylogenetic methods in current use, as well as examples of the application of these methods to questions of both organismal and molecular evolution.

The course is intended to provide a useful background both for organismal biologists interested in relations among organisms, and for molecular biologists interested in the evolution of genes and gene families. The course will cover the theory and practice of phylogenetic analysis, methods of data collection, alignment and homology assessment, data analysis (including parsimony, distance, and likelihood methods), and sources of error. Some class time will be spent on hands-on practice with software tools for analysis of molecular phylogenetic data, and there will be an emphasis on understanding the complete scientific process, from data collection to analysis, publication, and evaluation.

Partial list of topics to be covered:

Homology as the basis of phylogenetic comparison
Data types and sources
Optimality criteria: distance, parsimony, and likelihood methods
Taxon selection and tree rooting
Tree search algorithms
Assessing confidence in phylogenetic trees
Relative utility of different methods
Sources of error
Evolutionary events that confound phylogenetic analysis
Presentation of phylogenetic information
The use of computers in phylogenetic reconstruction
PAUP, MacClade, Phylip, GCG, and other analytical tools

Prerequisites: Consent of instructor. Prior coursework in biochemistry, genetics, evolution, and systematics or taxonomy is recommended, but may be waived in special circumstances, e.g., for graduate students in computer science.