BIOL 7020 Special Topics Cell/Molecular: Molecular Phylogenetics. Spring 2010
Department of Biology, College of Arts & Sciences, Valdosta State University
From the VSU Graduate Course Catalog: “Advanced study of cellular and molecular biology requiring reading of the
current literature and student presentations.”
Section A
Mon 6:00 – 7:50 PM
Bailey Science Center, room 1024
Instructor: Steve Thompson
Phone: 229-333-5773
Office: Bailey Science Center 1103
E-mail: stthompson@valdosta.edu
Web Home: http://www.bioinfo4u.net
Office Hours: 2:00 – 3:00 PM Mon & Wed. Drop by anytime within that slot, or any other time I’m in my office. I’m
also good at responding to e-mail — use it anytime and I’ll usually get back to you within the day.
Course Objectives: This course will attempt to familiarize participants in the basic premises, assumptions, models,
and capabilities of molecular phylogenetic and population parameter inference. Participants will learn the background
theory behind the software, they will install and learn how to operate the programs, and they will learn how to
understand and interpret the results. The power of these types of analyses will become apparent to participants in the
course, and they should be able to use the techniques mastered toward their own individual graduate research
projects. Topics to be covered include:
Finding appropriate data; getting it into the right format; getting it aligned, and the importance of that alignment;
building and interpreting evolutionary trees based on sequence data; understanding the differences and strengths
of weaknesses of the different algorithms — neighbor-joining and other distance-based methods, parsimony, and
probability-based methods, i.e. maximum likelihood and Bayesian inference; using and interpreting bootstrap
values and Bayesian confidence intervals; and estimating population parameters such as population size, and
migration, growth, and recombination rates based on population level data.
The format will be key readings from online PDF’s and discussion, some lecture, a lot of computer software
installation and learning, and, for at least half of the semester, work on individual projects where you get to work on
your own data — work that will hopefully help you toward finishing up your degree!
Understanding evolution is key to understanding biology, and this course should increase your grasp of many
evolutionary concepts. As the famous classical evolutionist Theodosius Dobzhansky stated back in 1973, “Nothing in
biology makes sense except in the light of evolution.”* Evolution provides the single, unifying, cohesive force that
allows all of life to be explained. It is to the life sciences what the long sought holy grail of the unified field theory is to
astrophysics.
And I’m required to give the VSU Biology Department Master of Science graduate school objectives:
1
“1. To demonstrate competency in factual content and interpretation of the major biological concept areas of cell
and molecular biology, genetics, organismal biology and evolution and ecology.
2. To demonstrate the ability to identify significant biological research questions, develop research protocols,
and properly analyze research questions through the use of the scientific method.
3. To produce a systematic and thoroughly researched thesis suitable for publication and appropriate to the
thesis sub-discipline.
4. To participate in activities related to the profession.”
This special topics course will address each and every one of these objectives.
Textbook: none required; however, many online primary and secondary sources will be required.
Attendance: I expect you to attend every session, but I do understand potential conflicts. Any missed material is
your own responsibility. Much will be available online, but class sessions will be very interactive and largely
discussion based — it will be very hard to recoup from missing any of it.
Assessment/Grading: There will be no exams in this course. Your grade will be based exclusively on your end-ofsemester term project, which should be based on something related to your graduate degree research, and a
subjective, ‘fudge-factor’ based on in-class participation. The term project will be done using a ‘portfolio’ system,
where I will review your work at various points throughout the semester.
Your final grade is based on the standard scale. A: 100–90%, B: 89–80%, C:79–70%, D: 69-60%, F: 59–0%.
Academic Honesty and Disruptive behavior: You are graduate students, and as such I shouldn’t even have to
mention this stuff, but I am required to do so. The VSU Academic and Non-Academic Conduct Codes (respectively
http://www.valdosta.edu/judicial/AcademicStudentConductCode.shtml and
http://www.valdosta.edu/judicial/ConductViolations.shtml) provide basic standards, and the Biology Department
Plagiarism page (http://www.valdosta.edu/biology/documents/biologyplagiarism.doc) lays out policy in further detail.
Family Educational Rights & Privacy Act: By Federal law, grades cannot be posted by Name, Social Security
Number, or other Personal Identifiers. Scores and student work will not be given over the telephone, by e-mail, or to
another student. You must speak to me personally or wait for your official grades.
American Disabilities Act: Students requiring classroom accommodations or modifications because of a
documented disability should discuss this need with me at the beginning of the semester. These students must
register with the Access Office (http://www.valdosta.edu/access/) located in Farber Hall, 229-245-2498 (V/VP) and
229-219-1348 (TTY), e-mail access@valdosta.edu.
Student Assistance: The Student Success Center is located in Langdale Residence Hall and is available to all
students. The SCC provides free professional and academic advising, peer tutoring in core courses, and campus job
information. Phone: 229-333-7570 or email: ssc@valdosta.edu.
Course Schedule (subject to change):
2
Date
Topic
(see http://www.valdosta.edu/~stthompson/Bio7020/7020-Thompson.html)
M Jan 11
Organizational meeting
M Jan 18
Martin Luther King Holiday — No Class!
M Jan 25
Lectures on: the basics of the inference methodologies
(what the main issues and problems are);
M Feb 1
and a little more detail — how to find the sequences
(BLAST and relatives and what they mean),
M Feb 8
— how to align them
(Clustal plus the way better methods, and SeaView) , and . . .
M Feb 15
— how to estimate their phylogeny
(PHYLIP, RAxML, MrBayes, and lots more).
M Feb 22
Plus, what about population data?
Guest from FSU’s Scientific Computing Dept. Dr. Peter Beerli.
M Mar 1
Let’s install LAMARC and Migrate-N and get them working.
M Mar 8
Project abstract presentation and discussion.
M Mar 15
Spring Break!
M Mar 22
Open session for project work and discussion
M Mar 29
Open session for project work and discussion
M Apr 5
Open session for project work and discussion
M Apr 12
Open session for project work and discussion
M Apr 19
Open session for project work and discussion
M Apr 26
Project presentations
M May 3
No Class (unofficial exam prep day)
* The source of the original 1973 quote is a bit obscure though it has been cited as being transcribed from an article
Dobzhansky wrote for the American Biology Teacher, 1973. 35, pp 125-129.
3