Hjelmen Lab @ UVU

Phylogenetics (ALWAYS UNDER CONSTRUCTION)

BIOL 4300--01 Fall 2024

This course is co-instructed with Dr. Heath Ogden

Course description:

This course delves into the principles and methodologies of phylogenetics, equipping
students with the necessary skills to explore evolutionary relationships among organisms and
genes. Emphasizing the importance of "tree-thinking," students will learn to interpret and
construct phylogenetic trees, gaining insights into their implications for evolutionary biology
and specific disciplines for their major. Key topics will include sequence alignment techniques,
parsimony, maximum likelihood, and Bayesian tree reconstruction methods, and concepts of
nodal support and trait evolution. Through hands-on projects, students will design reproducible
workflows for phylogenetic inference and compile novel molecular datasets from reputable
online databases. The course culminates in the application of phylogenetic reconstruction
methodologies on datasets created by students. Participants will also develop skills in
professional communication by synthesizing their analysis and results into formats suitable for
scientific presentation, including posters, oral presentations, and manuscripts. By the end of
this course, students will possess a comprehensive understanding of phylogenetic analysis and
the ability to contribute meaningfully to the field of evolutionary biology and beyond through
rigorous scientific inquiry and effective communication.

Upon completion of this course, students will be able to:

1. Demonstrate tree-thinking and its relation to phylogenetic trees.

2. Understand the basic principles of phylogenetic methods, such as: sequence alignment;
parsimony, likelihood and Bayesian tree reconstruction; nodal support; trait evolution; among others.

3. Design a reproducible pipeline for phylogenetic inference

4. Compile a novel molecular dataset from appropriate online databases.

5. Execute phylogenetic reconstruction methodologies on the generated dataset

6. Synthesize a professional communication (poster, oral, manuscript, etc.) of the analysis,
results, and interpretation of the phylogenetic project.