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Hidden in Plain Sight: Analysis of Biodiversity


Kristen H. Short
Department of Biology
Manchester University


This case study tells the story of John and Mary, two first-year college students learning about biodiversity while on a trip to Costa Rica where they become interested in studying butterflies (Astraptes fulgerator). Designed for use in a flipped classroom setting, the case includes a number of short videos that students watch on their own in order to prepare for a PowerPoint presentation shown in class. The presentation includes clicker questions that sometimes test application of knowledge directly, and at other times ask for predictions. Students will learn how genes are chosen for barcoding studies and how gene trees can be interpreted. By the end of the case, John and Marie ultimately discover that A. fulgerator is actually a complex of several cryptic species discovered through DNA barcoding, and additional applications of barcoding are discussed. The case was originally designed for an introductory biology course for biology or environmental studies majors, but could also be adapted for specialized courses such as conservation biology or molecular biology.


  • Define biodiversity and discuss its importance in ecosystems.
  • Explain several species concepts, and analyze the difficulties with identifying species.
  • Discuss factors involved in the evolution of DNA sequences and the choice of a gene for a barcoding study, and interpret a gene tree to make inferences about sequence evolution in that gene.
  • Define barcode gap and discuss the utility of DNA barcoding for species discovery and identification.
  • Discuss various ways that biodiversity is valued, and use this concept to evaluate the significance of cryptic biodiversity.


DNA barcoding; DNA sequence; phylogeny; biodiversity; species concept; evolution; cryptic species

Topical Areas


Educational Level

Undergraduate lower division, Undergraduate upper division


PDF, PowerPoint

Type / Methods

Clicker, Flipped



Subject Headings

Biology (General)  |   Evolutionary Biology  |  

Date Posted


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The following video(s) are recommended for use in association with this case study.

  • Biodiverstiy
    This Ted Ed video explains what biodiversity is, defining the three components (ecosystem, species, genetic), and establishes its importance to ecosystem functioning. Running time: 4:18 min. Created by Kim Preshoff for TED Ed, 2015.
  • What Is a Species?
    This video defines the biological species concept, the morphological species concept, the genotypic species concept, the ecological species concept, and evolutionary and phylogenetic species concepts, while also mentioning there are many species concepts used. It also addresses many problems with species concepts and classifications by using real examples from animals, and explains the importance of classifying organisms. Running time: 6:52 min. Produced by The Brain Scoop, 2016.
  • DNA Sequence Evolution
    This video explains DNA sequence mutations and how they can be used to document changes that have occurred in species over time and can be used to tell a story about the relationships between different forms of life. Running time: 7:22 min. Created by Kristen Short for the National Center for Case Study Teaching in Science, 2017.
  • Big Question
    This video explains how biodiversity (nature) can be valued by defining ecosystem services, aesthetic value, and other aspects of biodiversity value. Running time: 3:15 min. What is Nature Worth? Produced by the Institute on the Environment, University of Minnesota, 2010.
  • The History of DNA Barcoding
    This video discusses the history of DNA barcoding and covers some of its basic uses. Its content is not as central to the case as the content of the other videos, but some instructors may wish to use this video as a way to help students see the collaborative nature of science and how biological concepts are used in the context of real, current research projects. Running time: 2:33 min. Produced by the DNA Learning Center, 2011.