Phylogenetics problems

Debby Walser-Kuntz, Sarah Deel, and Susan Singer; Carleton College, Northfield, MN

This material is replicated on a number of sites as part of the SERC Pedagogic Service Project


Students receive information about cladistics and apply this phylogenetic approach to two different problems. In the first problem, involving dinosaurs, students determine whether traits are ancestral or derived and use this information to select the most parsimonious tree. In the second problem, students collect data from primate skulls and follow the same process.

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Learning Goals

These problems are designed to help introductory biology students understand the process of using cladistics to determine phylogenies. We want students to focus on the big picture, so while the concepts of reversal and convergence are introduced, the more sophisticated terminology associated with trees (paraphyletic, monophyletic, etc.) is not included. We expect students to participate in real data collection as well as application of cladistics techniques, so we bring primate skulls into the classroom. To encourage students to develop their own understanding of the process, students are asked to mark character state changes on trees to determine parsimony; though we encourage them to see patterns in their data, we do not provide "short cuts" to make the process faster.

Student holding primate skull
Concepts and content
  • phylogenetics
  • cladistics
  • reversal
  • convergence
  • parsimony
  • ancestral and derived characters
  • outgroup
Thinking skills
  • reading background to learn new concepts (as a replacement for lecture)
  • data analysis

Context for Use

These problems are used in an undergraduate introductory biology course, but could also be used for advanced high school students or in an upper level course (such as Evolution). The problems were designed so students solve the first problem in-class in small groups, with faculty present to provide feedback and coach as needed; students collect data for the second problem and complete the analysis either in class (time allowing) or as a homework assignment outside of class. All of the background information needed to work these problems is included in the handout, though we do provide a very brief overview of phylogenetic trees in a lecture format (focusing in particular on how cladistic phylogenies represent changes over time).

Primate skull replicas (see Teaching Materials) are made available to the students during class; groups of students take turns collecting data from the skulls. If skulls are not available, students could be given all the data to complete the second problem.

This activity can also be used as a laboratory exercise, and students can collect all of the primate skull data used in the second problem (in the lab, we use a total of six different primate species rather than just four). Please contact Sarah Deel ( for lab handouts, keys, or more information.

Description and Teaching Materials

Phylogenetics Problems (Acrobat (PDF) 856kB Aug19 09) Phylogenetics Problems (Microsoft Word 2007 (.docx) 624kB Aug19 09) Students need a copy of this handout, which includes enough background information on cladistics and phylogenies to complete the activity. Students also need access to the following skulls:
  • Alouatta
  • Lemur
  • Macaca
  • Human
Replicas of these skulls are available through Bone Clones. We use real human skulls for this activity, though replicas will work. Students can share the skulls, since the data collection process does not take long.

Teaching Notes and Tips

This activity takes place in a 65-minute class period. We open the class with a very brief (less than ten minutes) lecture about the information present in phylogenies. Then the students have time to read the handout and work through the first problem in small groups. Faculty are present to help students; students are sometimes confused about the process of annotating phylogenetic trees with marks indicating a change in character state (e.g. from "ancestral" to "derived"). It helps to show them that the ancestral trait "flows" up from the bottom of the tree until a mark indicates a change has occurred, and that after that point the derived trait is flowing up.

Students then work in their groups to collect data from skulls at the front of the classroom for the second problem. If there is time remaining (this depends on the working speed of the group), students may start working individually on determining which traits are ancestral and which are derived; otherwise they complete this outside of class and turn in their answers at the next class period. We post a full key to the first (dinosaur) problem online after class. After they have turned in the second (primate) problem, a key is posted for that as well.

Hints and Key for Dinosaur Problem (Microsoft Word 110kB Aug19 09) Hints and Key for Dinosaur Problem (Acrobat (PDF) 136kB Aug19 09)
Key for Primate Problem (Microsoft Word 2007 (.docx) 26kB Aug19 09) Key for Primate Problem (Acrobat (PDF) 173kB Aug19 09)


Faculty interact with students during class and perform formative assessment as they talk with each group of students. The second problem is graded and returned to students. Students are, therefore, accountable individually for the second problem (as described in the accompanying module, students solve most of the problems collaboratively and are not graded for their work). A phylogenetics question is included on the exam.

References and Resources