Authentic Lessons for 21st Century Learning

Phylogenetic Mana-trees

Using Genomic Data to Evaluate Evolutionary Relationships

Heather Shaffery, Amy Willhoite, Krissy Atnip | Published: August 10th, 2022 by K20 Center

  • Grade Level Grade Level 9th, 10th, 11th, 12th
  • Subject Subject Science
  • Course Course Biology I, Biology II
  • Time Frame Time Frame 200 minutes
  • Duration More 3-4 class periods


In this lesson, students will develop cladograms and phylogenetic trees to predict manatees' evolutionary relationships to several other mammals. By comparing trees based on morphological characteristics with trees made from protein sequences, students will deepen their understanding of why scientists use multiple lines of evidence to determine relationships among organisms. This lesson includes the use of UniProt, a free online database, as a tool to collect and analyze protein sequences.

Essential Question(s)

How do molecular data and morphological data compare when predicting phylogenetic relationships? How are molecular and morphological data used to determine manatees' evolutionary relationships?



Students draw cladograms to predict how manatees are classified.


Students analyze protein sequence data from the UniProt online database to determine phylogenetic relationships among several organisms of their choice.


Students synthesize what they learned from the Explore investigation and discuss the value of using molecular and morphological data for classifying organisms and their evolutionary relationships.


Students use UniProt to construct a phylogenetic tree for manatees and compare it with their previous prediction(s), as well as recently published phylogenetic trees.


Using the tree comparisons from the Extend section, students explain how genetic and morphological data serve as evidence for manatees’ evolutionary relationships.


  • Lesson Slides (attached)

  • Student Slides (attached and linked)

  • Protein Alignment Notation handout (attached; optional)

  • Chromebooks or laptops

  • Internet access



15 Minute(s)

Begin the lesson using the attached Lesson Slides. Display lesson slide 3 to share the lesson’s essential questions. Display lesson slide 4 to go over the lesson’s learning objectives. Review these slides with students to the extent you feel necessary.

Display lesson slide 5 (student slide 2) and review cladogram structure as a formative assessment before continuing. Revisit this in greater detail in the Explain section if students struggle to remember the relationships illustrated in a cladogram or need more practice interpreting the models.

Display lesson slide 6. Share with students the list of organisms (manatee, seal, hyrax, narwhal, elephant) that they will investigate later in the lesson. Ask students to create their own cladograms based on how these five organisms look and what they know about these organisms on lesson slide 7 (student slide 3). Students should be able to defend with evidence why they placed each organism where they did.

Go to lesson slide 8. Discuss why students’ cladograms look different from one another even though they have the same organisms. Using the strategy Partner Speaks, have students give their reasoning for placing organisms where they did. Ask students what they could do to see which cladogram is most accurate, or how they could make a more accurate one.


90 Minute(s)

Before students begin the UniProt investigation, display lesson slide 9. Take some time to discuss the information on the slide so students have context for their work and a basic understanding of the UniProt database. Go to lesson slide 10 (student slide 5) to help students prepare their setup for the activities.

Go to lesson slide 11 (student slide 6). In partners or in small groups, have students select five organisms to investigate. Each animal should be in the same class (e.g., Mammalia, Amphibia, etc.). Once students have selected their animals, have students read the directions on student slide 7. Then, demonstrate how to use the UniProt database for Part 1 using lesson slides 12–13 (student slide 8).


40 Minute(s)

Display lesson slide 22. Have student groups share out their findings from the investigation. They should specifically address how well their predicted tree and molecular protein tree align and why there are (presumably) differences between them.

Display lesson slide 24. Provide students with some background information about conserved sequences (HBA) and why scientists might prefer them over other molecular data for these analyses. It is assumed that students already understand the relationship between DNA and protein synthesis (HS-LS3-1), concepts which are necessary for students to understand before the upcoming discussions.

Display lesson slides 25–26. Using the Roundabout Conversations strategy, have students answer the following questions one at a time through movement and discussion:

  • How do we know which of our phylogenetic trees is most likely to be accurate?

  • What steps could we take to find more evidence to support the tree(s) we have constructed or to improve the accuracy of our tree(s)? 

  • Why is analyzing protein sequences a useful way to classify organisms or to determine organisms’ evolutionary relationships?

  • Is a tree made from molecular data (e.g., DNA or protein sequences) more or less reliable than one made from derived (i.e., morphological) characteristics? Why?

Before moving on to the next activity, have a whole-class discussion to validate the information that students shared in their small groups and address any knowledge gaps or misconceptions that came up.

From their conversations, students should conclude that there is value in using both morphological and molecular data, but molecular data is more reliable. Additionally, students should recognize that protein sequences are useful for classification since proteins are what give organisms their characteristics. This detail may not be immediately obvious to them.

Display lesson slide 27. To transition to the Extend section of the lesson, remind students they have constructed a morphological tree for manatees' evolutionary relationships. Ask students what their next step would be if they were scientists trying to improve or support their original manatee trees.


40 Minute(s)

Display lesson slide 28 (student slide 20). Ask students to return their focus to manatees and the other four organisms from the Engage section. Using student slides 21–24, students should repeat the same processes from the Explore investigation to collect HBA sequences and construct a phylogenetic tree for the manatee.

Go to lesson slide 29 (student slide 25). Once students have the HBA tree from UniProt, ask them to compare it with the cladogram they made in the Engage section using morphological characteristics. They should identify similarities and differences between their predicted morphological cladogram and the molecular protein tree.

Finally, provide students with a simplified version of the manatee’s phylogenetic tree on lesson slide 30 to compare it with the other two.

Display lesson slide 31. Facilitate a group discussion addressing the following:

  1. What patterns did you notice among your three phylogenetic trees?

  2. What did your group find interesting or surprising?

  3. What patterns did you notice across all groups’ observations of their trees?

For the first two questions, have student groups share out the similarities and differences they noticed among the three manatee phylogenetic trees and what they found interesting or surprising. For the third question, have students participate in a whole-class discussion to identify patterns across all groups' observations.

Go to lesson slide 32 and pose the following question: How is it possible for scientists to get different trees for the same organisms? After students have shared their thoughts, provide a summary of the major ideas from the discussion. This should reinforce what students have just discussed, but it also is an opportunity to clarify alternative conceptions or fill gaps in students’ knowledge.

Go to lesson slides 33–34. Based on these conversations, facilitate consensus-building for the class to determine manatees' closest living relative(s). Conclude the discussion by asking students to explain why having different “mana-trees” contributes to our understanding of evolution broadly.


15 Minute(s)

Display lesson slide 35. Each student should submit two completed trees: the morphological cladogram they created in the Engage section and the HBA molecular tree created in the Extend section using UniProt. If the class consensus tree differs from these, ask students to explicitly identify manatees’ closest living relative(s). In addition to the trees, students should include their answers and explanations for the following questions:

  1. What evidence did you use and how did you use it to determine manatees’ evolutionary relationships?

  2. Why do scientists use multiple lines of evidence to determine evolutionary relationships among organisms?

Explanations might be written, oral, or completed as formal class presentations as is appropriate for a given group of students.