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Introduction to Phylogenetics and Marine Invertebrates

Department: Scripps Institute of Oceanography

Instructor: Sonja Huc
Instructor Emails: shuc@ucsd.edu


Course Description

This course will explore phylogenetics, focusing on tree thinking and the use of current molecular methods and bioinformatics, while paying attention to historical context. Examples will be heavily marine invertebrate influenced, and we will use field trips to local tide pools, the Pelagic and Benthic Invertebrate Collections at Scripps Institution of Oceanography, and the Birch Aquarium for assignment inspiration, using phylogenetics to address questions regarding invertebrate biodiversity, ecology, and evolutionary biology. In order to better understand the organisms we will be using as examples, we will also dive into the diversity of marine invertebrates and learn about their defining features and traits

Course Goals / Learning Objective

  • A clear understanding of tree thinking
  • Understanding the different types of phylogenetic methods
  • Being able to independently execute a basic phylogenetic bioinformatic analysis by generating trees, and being able to interpret it
  • Understanding the importance and applications of phylogenetics
  • Being aware of the different groups of marine invertebrates and how to tell them apart in the field
  • Being able to write a report in the form of a short scientific paper

Course Topics

  • The history of phylogenetics
  • Tree thinking
  • Understanding DNA and its evolution
  • The parsimony principle, Maximum likelihood, Bayesian Inference
  • Phylogenetic models
  • Phylogenetic analysis computer programs and their use
  • Using trees
  • Comparative biology
  • Historical biogeography
  • Fossil calibration
  • Coevolution
  • Other applications of phylogenetics
  • Marine invertebrate biodiversity: sponges, cnidarians, mollusks, annelids, flat worms, bryozoans, brachiopods, crustaceans, echinoderms, and others

*Courses vary by experience and exposure to content. Instructors have the ability to change content and pace to serve the needs of students. Courses have been modified for online teaching.