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Inquiry-based hypothesis testing using phylogenetic trees in MEGA

Author(s): Kristin Hultgren

Seattle University

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Summary:
A key learning objective in biology is applying bioinformatics tools to test a real-life question. These inquiry-based modules have students assemble and align data, and construct simple phylogenies using the program MEGA, to test evolutionary…

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A key learning objective in biology is applying bioinformatics tools to test a real-life question. These inquiry-based modules have students assemble and align data, and construct simple phylogenies using the program MEGA, to test evolutionary hypotheses.

Licensed under CC Attribution-NonCommercial-ShareAlike 4.0 International according to these terms

Version 1.0 - published on 17 Jun 2021 doi:10.25334/FYP1-0G44 - cite this

Adapted from: Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses v 5.0

Keywords

  1. phylogenetics
  2. bioinformatics
  3. FASTA
  4. NCBI
  5. BLAST
  6. multiple sequence alignment
  7. sequence similarity
  8. CourseSource
  9. Zika virus
  10. MEGA
  11. alcohol metabolism

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Description

For many undergraduates, one of the most challenging exercises in the study of evolutionary biology is developing and testing evolutionary hypotheses using phylogenetic trees.  In this series of modules, modified from Kleinschmit et al. (2019), students develop predictions about tree structure under different evolutionary hypotheses, and assemble data from FASTA-formatted sequence files and databases hosted by NCBI (The National Center for Biotechnology Information).  They then use the free, user-friendly program MEGA X to align sequence data and construct simple trees to test their hypotheses.  These modules cover a key learning objective in biology—application of bioinformatics tools to answer a real-life biological question.  Specifically, they allow students the opportunity to combine their knowledge of tree-thinking, skills in database searching (NCBI), and experience in making phylogenies (MEGA) to answer inquiry-based research questions on a range of applied topics.

Notes

  • Exercise Format
    • There are three stand-alone modular exercises
    • Each modular exercise, student postlab worksheet, and necessary FASTA sequences are bundled into a single document along with a preface page with implementation instructions for the instructor
    • The exercises have been modified to include a greater role for hypothesis development for students, and for integration with the program MEGA to align sequences and build phylogenetic trees.
  • Exercise title change to mirror the associated CourseSource manuscript by Kleinschmit et al., 2019

Reference

Kleinschmit, A., Brink, B., Roof, S., Goller, C., and Robertson, S.D.  2019. Sequence Similarity: An inquiry based and “under the hood” approach for incorporating molecular sequence alignment in introductory undergraduate biology courses. CourseSource. https://doi.org/10.24918/cs.2019.5

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