In the Year 2525… Using Real Time PCR Data to Analyze a Founder Scenario

Overview & Concepts

This activity will place the concepts of Hardy-Weinberg equilibrium into a contemporary context.  During the activity students will interpret data from real-time PCR and use it to calculate allele frequencies.  These allele frequencies will then serve as a hypothetical founder population, for which students will run simulations using Allele A1 software to predict possible future allele frequencies.

Grade Level: 

Concepts Covered: 

Hardy-Weinberg equilibrium, founder effect, alleles, single nucleotide polymorphism, genetic drift, real-time PCR, genotype vs. phenotype.

Prior Knowledge Required: 


Activity Notes

Days to Teach: 

2 days in class, plus homework components


Student activity packet, data sheet (laminated color print out or electronic), computer, Allele A1 software (available at

Teaching Tips / Activity Overview: 

The activity is intended for a college prep level intro biology course.  As such, I have limited the scope to the rather straightforward allele referenced in the student handout. This activity can be implemented during a genetics unit as an application of the Hardy-Weinberg principle or during a biotechnology unit as an application of the light-cycler/real time PCR.To make the activity run smoothly, I would post any hyperlinks to an on-line environment if available, such as moodle, blackboard, or a class wiki.

  1. Read introduction and complete pre-lab questions: homework, or about 30 minutes in class.
  2. Review Pre-lab: 15 to 20 minutes.
  3. Discussion of blue vs. non-blue allele and associated SNP: 5 to 10 minutes
  4. Interpret light cycler data and calculate allele frequencies: 20 minutes.
    • I would interpret one light-cycler result with the class, to ensure understanding.
    • If you have access to color copying, the data can be handed out as a laminated set in color.  Otherwise, post it electronically so that students are able to read the data sheets in color.
  5. Analyze allele data: 10 minutes.
  6. Run ‘Allele A1’ simulations: 15 minutes
    • I would direct students in how to download “Allele A1” and, depending upon class ability, might demonstrate how to work it.
  7. Analyze ‘Allele A1’ simulations: 15 minutes
  8. Final summary: homework.

Please note:

  • In reference to “Data Task Three”, I would not ask intro bio students to calculate Chi Square.  Rather, I would want them to both observe that the expected and actual frequencies of zygosities differ and infer that this may be due to chance alone.



  • Student responses to questions in the activity packet will be evaluated for accuracy.
  • The final written summary will be evaluated using a rubric appropriate to the activity.


  • Have students calculate and interpret Chi square values for the data.
  • Run additional simulations using Allele A1 that take into account migration, population growth rates, and other factors which disrupt Hardy-Weinberg equilibrium.
  • Critical analysis: Recognizing that the initial scenario is idealized, have students conduct additional research into what such a Mars mission might look like from a biological/genetic standpoint.  Have students present a more informed and realistic outlook for this group of explorers.
  • The curious and scientifically inclined students may want to check out some of the acknowledged resources below.
  • If access to equipment is available, have students run their own light-cycler data and perform a similar analysis.



These teacher notes and resources were produced by Ray Mount based upon the following resources:

  • Franklin & Marshall and the Clinic for Special Children Bioinformatics seminar documents;  ‘Eye color data 2010 and 2012’ and ‘Light cycler sample preparation’. 
  • Eiberg H., et al. 2008. Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the H ERC2 gene inhibiting OCA2 expression.  Human Genetics, 123.  177-187.
  • Mary Roach, Packing for Mars.  W.W. Norton, 2010.  This work provided the inspiration for the scenario, as she discusses, in entertaining fashion, the various facets of an extended manned Mars mission.
  • Jon C Herron, Allele A1.  Jon Herron is the author of the Allele A1 software, which can be downloaded from his website at
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