PBIO/BINF 8350 Molecular Phylogenetics and Evolution (Spring 2016)

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Instructors - Liang Liu (Statistics; lliu@uga.edu) and Jim Leebens-Mack (Plant Sciences; jleebensmack@plantbio.uga.edu)


Syllabus


Goal: 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.  We will draw on review papers and the primary literature to learn how phylogentically-based comparative studies can be used in retrospective investigations of a wide range of biological processes.  Readings will be posted on the course website.  The lab will provide students with hands-on training in state-of-the-art methods of phylogenetic inference.


Course Website: newELC – PBIO 8350

Lecture MW 11:15-12:05  (1503A Miller Plant Sciences; 69341)

Lab F 11:15 - 1:45 (1503A Miller Plant Sciences)

Office Hours MWF after class and by appointment


Topics to be covered

Tree inference:

  • Gene tree estimation - parsimony, distance, likelihood, Bayesian....

  • Multiple sequence alignment

  • Model selection; hypothesis testing/tree comparisons; support values

  • Species tree estimation - coalescence model; reticulation (hybridization/recombination); duplication/loss;

  • Species tree gene tree reconciliation

Using inferred trees:

  • Divergence time estimation

  • Discrete trait evolution/ancestral state reconstruction

  • Molecular evolution

  • Continuous trait evolution/ancestral state reconstruction (individual traits)

  • Independent contrasts/phylogenetic least squares