From Restriction Maps to Cladograms

Barry McPhail, Aleta Sullivan and JoAnne Dombrowski

Target age or ability group: High school biology.
Class time required: One 55-minute class period.
Materials and equipment: Student handouts
Summary of activity: This activity simulates the activities of a population geneticist as he or she observes the likenesses and differences between related animal (primate) species and then plots the relationships on a cladogram.
Prior knowledge, concepts or vocabulary necessary to complete activity: Vocabulary: restriction endonuclease, enzyme, cladogram, random change
Reference:Brindle, P., Linke, S. and Monmimy, M., 1993. Nature 364:6440, 821-824.

Teacher instructions

Instruct students to develop a matrix to determine the number of differences between each set of primate species (sample data chart and answers below). Based on this information, the students should be able to determine closely related organisms. Using the number of differences, have the students complete the cladogram.

Answers to Cladogram:

17 (gibbon), 13 (orangutan), 10 (pygmy chimp), 4 (gorilla), 3 (chimp), 0 (human)

Answers to Student Questions:

  1. gibbon
  2. chimp
  3. no
  4. selected for (changed) as the environment changes
  5. less likely to change (will accumulate)
  6. the changes that offer an advantage in the "new" environment
  7. fewer

From Restriction Maps to Cladograms

Restriction Maps:

A particular restriction nuclease will cut DNA into a series of fragments called restriction fragments. If you treat DNA with a number of restriction nucleases, you can construct a map that shows the location of each of these cuts on a given length of DNA.


Below are restriction maps for a segment of DNA common to a number of mammals including humans: the genes which code for hemoglobin.
  1. Compare the restriction map for each species to the human map. Make a mark on the map for each difference. A difference is the addition or subtraction of a restriction site. (See the example).

  2. For each restriction map, count the number of differences that you find. Enter these data on a data chart.

  3. In the cladogram, enter the number of differences between each species and human. The species with the least number of differences should be entered closest to the human, and the species with the greatest number of differences, farthest from the human.


In the example below, Species 2 has three differences with Species 1.

Restriction Map of Human and Various Primate DNA in a Cluster of Genes Coding for Hemoglobin

Elizabeth Zimmer and Alan Wilson developed the map reproduced below (as cited in Alberts, et al. Molecular Biology of the Cell. Garland Publishing, 1983). From the following list, predict which are the most and which are the least closely related: human, chimp, pygmy chimp, gorilla, orangutan, and gibbon.

Cladogram: similarities of restriction maps between humans and other primates.


  1. Which species has the most differences with humans?

  2. Which species has the fewest differences with humans?

  3. Hemoglobin is the molecule in the bloodstream which transfers oxygen from the lungs to the body's cells; it is, therefore, important that it work properly. Is an animal born with large changes in its hemoglobin likely to survive to produce offspring? Reason?

  4. Some small changes in the hemoglobin molecule may give an animal an advantage in one environment and a disadvantage in some other environment. Are these sorts of changes likely to accumulate in the hemoglobin gene over long periods of time, or be changed back and forth as the outside environment changes? Explain.

  5. Some small changes in the hemoglobin molecule are selectively neutral--they do not affect the animal's fitness in any change of environment. Are these sorts of changes likely to accumulate in the hemoglobin gene over long periods of time, or be changed back and forth as the outside environment changes? Why?

  6. Of the three sorts of change introduced in questions 3 - 5, which sort is the most likely to accumulate in the hemoglobin gene from generation to generation?

  7. If the changes we are counting are a) random, b) selectively neutral, and c) tend to persist in the genes from generation to generation, would you expect the genes of two closely related organisms to have more differences or fewer differences than the genes of two distantly related organisms?

On to Constructing a Phylogenetic Tree
Using DNA Sequence Data

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