Mapping the evolutionary history of organisms by phylogenetic analysis
Emma Alenius; Bromangymnasiet Hudiksvall
Target Group
17-18 years old
Brief Description
This simulation allows the students to apply and deepen their knowledge of evolution, to use a scientific approach and to get familiar with different methods of phylogenetic analysis.


Student´s instruction sheet

Simulation of evolution

- phylogenetic analysis

Imagine your classroom as a nature area populated by unique living creatures that look like muffins. They belong to an unique group of organisms calle d M uffions. You and your classmates are biologists with the task to investigate these Muffions.

Your job is to observe and collect information about the different species of Muffions you can find in the area. You need this information to propose a hypothesis on the evolutionary relationships among the Muffions. Construct an evolutionary family tree, so-called cladogram, to illustrate your hypothesis.

Work systematically, look for details and make notes on the various clues you can find. Be careful not to miss any important information by moving the Muffions before you have studied their environment. Don´t taste the Muffions, the may be toxic.

Cladogram questions

1. Examine the evidence and determine the order in which the Muffion species appeared. Which species developed first and branched into other species? Which species are most closely related?

2. Identify the natural ( monophyletic ) groups in the cladogram. Name the groups systematically based on the most important common character of each group.

3. Which Muffion character may be a result of convergent evolution? Motivate your answer!

Discussion questions

1. Which methods did you use to identify the evolutionary relationships between the different Muffion species?

2. Did the methods work well? Motivate your answer.

3. How would you draw your cladogram if you only used o ne method to investigate the Muffions?

4. Evaluate your performance. Should you have done anything differently? If so, what?

5. Is it possible to interpret your observations and results in a different way?

6. Are your conclusions valid?

7. What did you learn from this assignment?

Teacher’s guide

Simulation of evolution

Mapping the evolutionary history of organisms by phylogenetic analysis

This simulation allows the students to apply and deepen their knowledge of evolution, to use a scientific approach and to get familiar with different methods of phylogenetic analysis.

The assignment is about mapping and comparing characters of fictitious organisms in order to formulate a hypothesis about the development of and relationship between the organisms and present these in a cladogram. Read the Student’s guide for further information.

Previous knowledge

The students should have basic knowledge in evolutionary theory, fossils and cladogram to be able to carry out the simulation in the best way. The assignment is suitable for students participating in Biology classes teaching the theory of evolution (in Sweden, Biology 1 for upper secondary school).


The students examine morphological and genetic characters of fictitious organisms, so called Muffions. Each Muffion is symbolized by a muffin (alternatively a picture of a muffin) with specific morphological characters. Inside each muffin there is genetic information, symbolized by a piece of folded aluminium foil with a unique letter code (alternatively the code is seen on the picture) .

Extinct Muffions are preserved as fossils in different layers of sediment. The fossils are symbolized by muffins inside a gypsum shell (or of a picture of the same) and placed at different depths in a box with sand (figure 1). The genetic information in the fossil Muffions is partly destroyed, which is symbolized by some letters missing in the code.

Living Muffions are placed in different parts of the classroom, next to different kind of objects to make the students discover relationships between the organisms characters and their environment.

By combining and comparing results from the observations of the morphological and genetic characters respectively in the living and fossilized Muffions the students can make conclusions and formulate hypotheses about their development and relationships. The students describes and analyses their methods, results and conclusions and illustrates their hypotheses in a cladogram.

Preparation: real muffins (~5 hours)

The teacher prepares eleven different kind of muffins, see Muffion recipe and video instruction . At the bottom of each muffin liner a piece of folded aluminium foil is placed. The foil contains the letter code corresponding to each kind of muffin .

The muffins which should symbolize extinct Muffions is covered with a layer of gypsum.

These muffins are placed at different levels in buckets containing sand so that the most original Muffion is located at the bottom and the latest developed at the top.

The muffins are placed at different locations in the classroom where the student will perform the investigation:

? The sand buckets with Muffions in gypsum is placed on the floor together with empty boxes, small shovels and hammers.

? The Muffions with raisin is placed on the floor.

? The Muffions without raisin is placed on the benches.

? The Muffions with cacao is placed on a particularly bright place, e.g. under a lamp or next to a window.

? The Muffions with mint and lemon flavour respectively is placed next to stuffed birds.

? The Muffions with white sprinkles is placed on a white surface.

? The Muffions with red sprinkles is placed on a red surface.

? The Muffions without sprinkles is placed on a surface which is neither red or white.

The teacher also brings trays (for the students to investigate the Muffions on), tweezers and scalpels.

Preparation: Pictures of muffins (~30 min) 

The teacher prints pictures of the Muffions and cuts them out, see Pictures of Muffions . The pictures are placed the same way as the real 

muffins, see above.

Procedure (with muffins 3-4 hours, with pictures 1-2 hours)

The students are divided in groups (4-5 students per group) and gets instructions to get the investigation started, see Student´s

instruction sheet . The teacher points out the importance of working systematically and thoroughly and request the students to take notes of all observations in their laboratory protocol.

The assignment is “open ended” where the idea is that the students themselves should find out how to determine the relationships between the different Muffion species. If the students don´t know how to proceed the teacher can give the following clues:

1. Note where the different Muffions are placed.

2. What is placed close to the Muffions.

3. How are you going to tell the different Muffions apart? How can you name them?

4. What's in the bottom of every muffin? (use a tweezer to pick up what you find)

5. Split every muffin in two.

6. Smell the muffins!

7. Carefully and systematically explore the sand buckets.

8. Note at which depth you find something in the sand buckets. Which index fossil do you find around the extinct Muffions? When did they live?

9. Smash the muffins in gypsum with a hammer.

10. Compare the Muffions in the bucket with the Muffions placed at different locations around the room.

11. Compare the combination of letters.

12. Which letters in the code fits with the different character?

The students will describe and analyze their methods, results and conclusions. They will also illustrate their hypothesis with a cladogram which they present to the rest of the class. At the end of the lesson the teacher may show the video on how the muffins were made and view the Muffion cladogram and overview chart .


Don't eat the muffins as they contain aluminium foil. Instead of a scalpel you can use a table knife to split the muffins.

Student comments

“We got to use our knowledge in a practical way. The assignment was very fun and educational.”

“We’ve learnt how to construct a cladogram, how evolution works and how researchers cut and paste among clues in order to draw conclusions. We have also learnt how to, with the aid of different methods leading up to different clues, construct a possible speciation scenario.”

“We’ve learnt how to investigate the relationship between species and to analyse different hypotheses and error sources concerning these.”

“We’ve learnt that there are several aspects of how species and characters evolve. We’ve also learnt to work in a systematic and structured way. Additionally, we’ve learnt that it can be cumbersome to work out the connection between species and come to a conclusion.”


Student´s instruction sheet

Muffion recipe

Pictures of Muffions

Muffion cladogram and overview chart

Video (preparation of Muffions)

Related files

Muffionrecipe 69 KB
PicturesofMuffions 127 KB
Simulation of evolution - student´s instruction sheet 90 KB
Simulation of evolution - teacher´s guide 790 KB
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