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Introduction to Phylogenetic Trees for Comparative Genomic Analysis

By Deborah Tobiason1, William Davis2

1. Carthage College 2. Washington State University

In this activity, students are introduced to phylogenetic trees and networks as tools for analyzing evolutionary relationships.

Listed in Teaching Materials | resource by group HHMI Science Education Alliance (SEA) Faculty Group

Version 1.0 - published on 24 Aug 2020 doi:10.25334/HWSZ-Q412 - cite this

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

Phylogenetic tree image.jpg

Description

In this activity, students are introduced to phylogenetic trees and networks as tools for analyzing evolutionary relationships. An explanation of how phylogenetic trees are constructed is provided.  A pre-activity assignment reviews tree basics and requires students to practice analyzing pre-made phylogenetic trees. Students then collect data to analyze using two distinct methods for producing phylogenetic trees and networks. The students are also introduced to the concept of bootstrapping trees to verify branches. A final assessment requires students to investigate whether a single gene can be used to predict bacteriophage phylogeny using the tools that they have been introduced to.

Learning objectives

After completing this module, students will be able to…

  • Define the key concepts that underlie phylogenetic trees
  • Distinguish between a rooted and an unrooted tree
  • Prepare concatenated FASTA files
  • Construct phylogenic trees and networks
  • Analyze and interpret phylogenetic trees and networks
  • Generate hypotheses related to phylogeny using phylogenetic trees

How is the module structured to promote student development as a scientist? 

This activity supports elements important for student development as scientists in the following ways:

  • The activity introduces software (Splitstree) used by practicing scientists who publish the results of their analyses using this tool in scientific publications.
  • The module provides students with the theoretical background necessary to construct and interpret phylogenetic trees and networks.
  • Students are asked to share their answers, and to defend their answers to their peers.
  • Once completed, the students will have the skills to investigate further questions related to phylogeny

Intended Teaching Setting

Course level:  First-year and second-year science majors

Instructional Setting:  In-person classroom or online

Implementation Time Frame:

  1. Students read the overview and complete Exercise 1 either prior to class or during a class session. Before moving on, the facilitator assesses student comprehension and answers questions.
  2. For exercise 2, the concepts and tools can be introduced in class and the activity assigned for homework. Students can work in groups the following class period to discuss findings and correct any misconceptions.
  3. Exercise 3 can be assigned for homework along with Exercise 2 or separately. Again introducing the tool to students in class prior to assigning the exercise for homework may be helpful but is not necessary. Students can work in groups the following class period to discuss findings and correct any misconceptions.
  4. For Exercise 4, the multi-sequence fasta file can be created as a class in a shared document to be used independently to complete Exercise 4 for homework and investigate use of a single gene to determine phage phylogenetic relationships. The complete fasta file is also provided to instructors if they do not have time for students to gather data. Interpretation of the results from Exercise 4 can be discussed in groups the following class period, and additional hypotheses to test using phylogenetic trees can be shared.

Project Documents

Facilitator documents:

Teaching notes for phylogenetic tree module

Answer key for phylogenetic tree module

Major capsid fasta sequence file

Smith KC, Castro-Nallar E, Fisher JN, Breakwell DP, Grose JH, Burnett SH. Phage cluster relationships identified through single gene analysis. BMC Genomics. 2013;14:410. Published 2013 Jun 19. doi:10.1186/1471-2164-14-410 (can be accessed at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3698066/)

Learning activities with built-in assessments:

Overview: Introduction to Phylogenetic Trees

Exercise 1: Introduction to Phylogenetic Trees

Worksheet for Exercise 1: Introduction to Phylogenetic Trees

Exercise 2: Introduction to Phylogenetic Trees

Worksheet for Exercise 2: Introduction to Phylogenetic Trees

Exercise 3: Introduction to Phylogenetic Trees

Worksheet for Exercise 3: Introduction to Phylogenetic Trees

Exercise 4: Introduction to Phylogenetic Trees

Worksheet for Exercise 4: Introduction to Phylogenetic Trees

Facilitator Instructions

  1. Have students read the Overview document.
  2. Assign Exercise 1 and have students work through the activity and questions in class or for homework. Have students discuss their answers in small groups and correct any misconceptions with the class.
  3. Introduce students to phylogeny.fr site and fasta file formats (optional as instructions are embedded in the exercise). Assign Exercise 2 and have students work through the activity and questions in class or for homework. Have students discuss their answers in small groups and correct any misconceptions with the class.
  4. Introduce students to Splitstree4 program and have students download it to their computer (optional as instructions are embedded in the exercise). Assign Exercise 3 separately or with Exercise 2 and have students work through the activity and questions in class or for homework. Have students discuss their answers in small groups and correct any misconceptions with the class.
  5. Introduce students to the phagesdb.org website and demonstrate how to obtain capsid protein sequence (optional as instructions are embedded in the exercise). Have students work together as a class to build a shared fasta document containing the capsid sequences. Assign Exercise 4 and have students work through the activity and questions in class or for homework.
  6. Have students discuss in groups their results from Exercise 4 and develop other hypotheses that could be investigated using phylogenetic trees.

 

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