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Molecular Phylogenetics (BiSc 225)

Instructor: TBD
Number of Credits: 4
Level of instruction: graduate
Description: Applying comparative evolutionary techniques to molecular data including data recovery, alignment, tree building methods, coding data, weighting effects, and general theory of quantitative systematics. The course is subdivided into three major sections: (1) Introduction and History of the use of molecular approaches (Immunology, Histocompatibility, DNA/DNA hybridization, Protein Electrophoresis, RFLP restriction mapping, Finger-printing, and Sequencing) and explanations of how these have been used and analyzed. (2) Molecular Data bases and related analytical software, for nucleic acids and proteins, will also be explored (GenBank, SwissProt, GCG); (3) Detailed phylogenetic analysis including parsimony, likelihood, neighbor-joining, and distance methods as well as Bremer support, the bootstrap, jackknife, tree constraints, successive approximation, estimating the level of saturation and combining data sets.
How often is the course offered: Every Spring Semester.
What is the average enrollment: 8-10
How broad a student audience is served by the course: graduate students from GWU (Departments of Biology, Genetics, and Anthropology), Howard University, and Georgetown University.

Lecture Syllabus

Week 1
Lab: Introduction, Grading, and other Logistics. Introduction to Macintosh and Novell. Finding and down-loading genetic data. Molecular Databases for Nucleic acids and Proteins:

Lecture: Molecular Biology and Phylogenetics a fusion of two fields. Why study phylogenetic inference. The power of comparative genetics examined in a phylogenetic framework. Introduction to Systematics, Characters, and Taxonomic groups.
** Get an e-mail, internet and a Novell account.

Week 2
Lab: Martin Luther King Holiday

Lecture: Introduction to Macintosh and Novell. Finding and down-loading genetic data. Molecular Data bases for Nucleic acids and Proteins:
** Choose a topic and submit a general proposal 1-2 pages.

Week 3
Lab: Finding and down-loading genetic data. Molecular Data bases for Nucleic acids and Proteins: NCBI, GenBank, SwissProt, EBI.

Lecture: Molecular Data bases.

Week 4
Lab: An introduction to Alignment of Molecular sequences. Use of available alignment software.

Lecture: An introduction to Alignment of Molecular sequences.
** Final Choice of taxa and genetic system.

Week 5
Lab: Alignment of your chosen gene. More Alignment of Molecules.

Lecture: More on the Alignment of Molecules.
** Submit alignment.

Week 6
Lab: George Washington's Birthday Holiday

Lecture: Data Matrix and weighting of Characters, Gap coding and weighting, missing data. Trees, roots, ingroups and outgroups. Tree construction and Effects of weighting.

Week 7
Lab: Tree construction, effects of weighting and determining branch lengths.

Lecture: Co-evolution and independence of characters, Consistency index (CI, RI). Character optimizations and calculations of branch length. Branch length effects.

Week 8
Lab: Testing support.

Lecture: Support for Nodes: Statistical and character based methods. Bremer support, Bootstrap, and Jack-knife. Tree constraints. Successive approximation and Experimental Phylogenies.

Week 9
Lab: Open period

Lecture: Consensus methods when trees don't agree. Character versus Taxonomic congruence or how molecular and morphological data can interact (Guest lecturer, Dr. J. Clark).

Week 10
Lab: Estimating saturation assessing consensus. Rate tests and estimating divergence dates.

Lecture: Transversion Parsimony, Saturation curves, and Transition to Transversion ratios. Molecular Clocks, Calibrating rates of change, and rate heterogeneity.

Week 11
Lab: Distance based methods.

Lecture: History of Molecular Approaches: Immunology, Histocompatibility, DNA/DNA hybridization.
** Papers due, first draft including all but discussion.

Week 12
Lab: Maximum Likelihood.

Lecture: History of Molecular Approaches: Protein Electrophoresis, RFLP restriction mapping, Finger-printing, Sequencing. Coding alleles, mapping versus fragment RFLP data.

Week 13
Lab: Open period

Lecture: Molecular Evolution, What is in the genome: Satellites (SINES and LINES), Gene families, ribosomal, and single copy genes. Determining the utility of a molecule. Data sampling theory (more data or more taxa). Testing monophyly.

Week 14
Lab: Open period

Lecture: Distance versus Character based approaches to Phylogenetics: Introduction to distance methods. Neighbor-joining, Minimum Distance trees, UPGMA, Maximum Likelihood, Evolutionary Parsimony.

Week 15
Lab: Designated Monday, we may have a lecture, otherwise
Open Lab period

Lecture: ** Data presentation, 10-12 min. with 3-5 min. discussion.