PBIO/BINF 8350– Molecular Phylogenetics and Evolution Instructors - Liang Liu (242 Statistics; 706-542-3309; firstname.lastname@example.org), Jim LeebensMack 4504 Miller Plant Sciences; 706-583-5573; email@example.com) TA- Lauren Eserman (firstname.lastname@example.org) 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.