To overcome these challenges, DNA barcoding is now regularly
used in dietary analysis of native and invasive predators (e.g., Côté
et al., 2013; Jo et al., 2016). DNA barcoding relies on species-specific mutations within a short, standardized region of the
genome to determine the identity of an unknown sample. While no
single gene region has been found to resolve all taxa, a ~700 base
pair (bp) region of the mitochondrial cytochrome oxidase subunit
1 (CO1) gene can be used to unambiguously identify most animal
species (Hebert et al., 2003). The specific advantages of DNA
barcoding over traditional taxonomic approaches include identification of degraded or partial samples, identification of morphologically
similar species, and reduced need for taxonomic expertise (Hajibabaei
et al., 2007).
By integrating DNA barcoding into the classroom, students
gain experience with molecular tools and methods currently used
in a broad range of research and clinical applications, including
forensic science, molecular diagnostic science, environmental
monitoring, microbiology, ecology, and evolutionary biology.
The five-lab unit guides students through each step in the DNA
barcoding process, from fish dissection through DNA sequence
cleanup and species identification. In addition to providing practical hands-on training, the DNA barcoding unit provides an
engaging opportunity for students to develop their conceptual
understanding of fundamental molecular processes and applications, including DNA synthesis, replication, and mutation; enzyme
function and temperature dependence; polymerase chain reaction
(PCR) methodology and principles; and DNA sequencing technologies and bioinformatics.
The learning outcomes presented here are for DNA barcoding of
fish prey. A summary of linked Advanced Placement (AP) and
International Baccalaureate (IB) standards is provided in Table 1.
Foundational Knowledge Learning Outcomes:
• Describe DNA structure and the importance of mutation and
inheritance in DNA barcoding
• Explain how DNA data are generated using DNA sequencing,
including describing the requirements and results of PCR
• Describe the process and application of agarose gel electrophoresis
• Construct a hypothetical food web using student-generated
• Describe potential ecological and economic impacts of invasive
Application Learning Outcomes:
• Perform a fish dissection and identify major internal organs
• Demonstrate an ability to generate DNA sequence data
• Explain how to locate and extract information from public
DNA sequence databases
• Evaluate and interpret DNA sequence data
• Identify applications for DNA barcoding in natural resource
Conceptualization: Setting the Stage
management and conservation
This project leverages interest in citizen science to guide students
through a five-class conservation genetics unit of study, which includes
dissection, followed by genomic DNA isolation, CO1 gene cloning
(PCR), and DNA sequence analysis to identify dissected prey items.
The objective of the conceptualization stage is to pique student
interest in the project and identify prior knowledge through an
entry event. Some effective strategies to consider include an article,
video, or activity in conjunction with a discussion using predetermined questions. A good entry event is to have students read and
discuss one of the many widely available articles highlighting the
impact of invasive fish on native ecosystems (e.g., National Geographic’s “It all started with a few trout. Now Yellowstone’s iconic
birds face collapse”). Conceptual questions for the students to consider include
• Where did the invasive species come from and what was their
mode of introduction?
• What is the species’ current invasive distribution and possible
means of dispersal?
• What are documented and hypothesized impacts on native
• Are there potential impacts to fisheries and tourism-related
Instruction: Building Understanding &
The purpose of the instruction phase is to build student knowledge,
understanding, and skills through hands-on investigation (Figure 1).
Strategies for effective practices include focused instruction on core
knowledge, scientific practices, and crosscutting themes; formative
assessment of student knowledge understanding and skills; and
guided collection of accurate scientific data.
Table 1. International Baccalaureate and
Advanced Placement Biology assessment standards
linked to this activity.
Concept IB Topic
Origin of cells 1.5 1.D.1, 2.B.3
function of enzymes
DNA structure 2.6, 3.2, 7.1 3.A.1, 3.A.2, 3.A.3,
DNA replication 2.7, 7.1 1.B.1, 3.A.1, 4.A.1
Biotechnology 3.5 3.A.1
4.1 2.D.1, 2.D.3, 4.A.5,
4.A.6, 4.B.3, 4.C.4
5.3, 5.4 1.B.1, 1.B.2