PBIO/BINF 8350– Molecular Phylogenetics and Evolution
Instructors - Liang Liu (242 Statistics; 706-542-3309; lliu@uga.edu), Jim LeebensMack 4504 Miller Plant Sciences; 706-583-5573; jleebensmack@uga.edu)
TA- Lauren Eserman (lauren.eserman@gmail.com)
Course Website: ELC – PBIO 8350
Lecture MW 11:15-12:05 (1503A Miller Plant Sciences; 69341)
Lab F 11:15 - 1:10 (1503A Miller Plant Sciences)
Office Hours MWF after class and by appointment
Since Darwin and Haeckel published their iconic tree figures over 150 years ago,
phylogenetic analyses have provided a historical framework for interpreting the evolution
of form and function. In recent years, phylogenetic inference has come to play a central
role in Ecology, Genetics, Genomics and Molecular Biology.
The primary aim of this course is to provide students with the training and experience
necessary to frame, execute and correctly interpret phylogenetic, comparative and
molecular evolutionary analyses relating to their own research. This year we will be
covering foundational topics in phylogentic inference and comparative analysis through
lectures, discussion and hands-on computational work. Topics will be covered over four
class periods as follows:
 Class period 1 - background lecture,
 Class period 2 - student-led discussion of primary literature,
 Class period 3 - hands-on computational analysis, and
 Class period 4 - discussion of and interpretation of computational results.
This format will promote active learning over more passive lecture-based learning.
Students will master how to build and use phylogenetic trees to address their research
interests. Throughout the course students will have opportunities to analyze their own
data or data compiled to address their specific research interests. This work will
culminate in an original term project.
Course Schedule (Evolving!):
Day Date
M
Jan. 11
Topic
Course introduction
M
Jan. 18
M-F Mar 7-11
No Class - MLK Day
No Class Spring Break
Instr
Jim &
Liang
Readings/References
Reading: Baum et al. 2005
Topics to be covered over four meetings as described above (schedule with dates is
being developed - check https://faculty.franklin.uga.edu/lliu/content/pbiobinf-8350molecular-phylogenetics-and-evolution-spring-2016 before the end of December):

Tree inference:
o Gene tree estimation - parsimony, distance, likelihood, Bayesian....
o Multiple sequence alignment

o Model selection; hypothesis testing/tree comparisons; support values
o Species tree estimation - coalescence model; reticulation
(hybridization/recombination); duplication/loss;
o Species tree gene tree reconciliation
Using inferred trees:
o Divergence time estimation
o Discrete trait evolution/ancestral state reconstruction
o Molecular evolution
o Continuous trait evolution/ancestral state reconstruction (individual traits)
o Independent contrasts/phylogenetic least squares
Grading:
Assessment will be based class participation, two exams and a term project:
Lab Projects
Class Discussions
Term project
Midterm Exam
Final Exam
Total
20%
20%
20%
20%
20%
100%
Class assignments: Problem-based computational lab projects will be framed for each
topic by instructors and class participants.
Class Discussions: Students will lead discussion on a publication related to their term
project.
Term Project: Students will design and execute a phylogenetic, comparative and/or
molecular evolutionary study related to their research interests. Short project proposals
(2-3 pages) will be evaluated in March. Final term papers should be 10-12 double-spaced
pages with Abstract, Introduction, Methods, Results and Discussion sections and figures.
Do not include references in page count. See
http://www.oxfordjournals.org/our_journals/sysbio/for_authors/ms_preparation.html and
Systematic Biology publications for formatting guidelines.
Exams: Take-home mid-term and final exams will each account for 20% of the final
grade. Exams may be written by students individually or in pairs. The final exam will be
handed out the last day of class and due a week later.