Catching Cheaters: Using Salmon Phylogenetic Analysis to Identify Atlantic Salmon Mislabeled in Local Stores as Pacific Salmon
This project consists of an analysis of salmon samples collected by the students from their local stores. The students use phylogenetic analysis to identify farmed Atlantic salmon mislabeled as wild Pacific salmon by local stores and suppliers. The first time this exercise was performed, we identified three salmon samples (of 16 tested) that had been sold as "wild Pacific salmon" but were in fact Atlantic salmon, which is exclusively farm-raised. In addition to the obvious consumer fraud issue (wild salmon can be more than twice as expensive), this mislabeling has wider implications due to the environmental impacts of salmon farming and the health implications due to higher concentrations of PCBs and heavy metals including mercury in farmed salmon and lower concentrations of omega-3 fatty acids. This project allows students to apply molecular methods such as polymerase chain reaction (PCR) and DNA sequencing to a real-world issue, while connecting to lecture topics throughout the majors introductory biology curriculum.
The learning objectives for this set of lecture modules and lab exercises are:
- To help the student to master the fundamental concepts of biology with application to a unifying theme (salmon ecology) and application to a real-world project connected to their local community.
- To develop an appreciation for the power of the scientific method and an understanding of how it is applied to specific questions or issues.
- To provide a context for understanding the usefulness and application of techniques of molecular biology by using these techniques to analyze field samples collected by the entire class.
- To explore sustainability through discussions of environmental impacts of salmon farming, toxicology and bioaccumulation of pollutants in salmon.
After completing these exercises, the student should be able to:
- Apply the scientific method to answer real-world questions.
- Understand the fundamental concepts of cellular chemistry, molecular and cellular biology, and how to apply these methods to bioregional environmental applications.
- Communicate the results of their own experiments, verbally and in writing, both informally and using standard scientific formats.
Each laboratory exercise has a specific objective, including:
- To understand the principles of gel electrophoresis, PCR amplification, DNA sequencing, and phylogenetic analysis.
- To learn how to apply DNA analysis to an environmental issue.
Students will demonstrate their abilities by performing a complete phylogenetic analysis (including salmon sample collection, DNA isolation, PCR, sequencing, and sequence analysis). They will answer questions informally (in weekly lab reports) and formally, after completing the project, in a group oral presentation.
Context for Use
TimeframeThis exercise is intended for the molecular and cellular biology quarter of a three-quarter introductory biology sequence. A sample class schedule has been included in the Instructor Lab Manual attached materials describing the exercise. The phylogenetic analysis from DNA extraction to sequence analysis requires a minimum of four (2-½ hour) lab sessions to complete, and therefore works best as the centerpiece of a quarter-long project culminating in a final paper or oral presentation.
There are other methods that could be applied to answering this question to allow the exercise to be completed in a shorter time, which might make this exercise adaptable for a one quarter non-majors biology survey course or a two quarter introductory biology sequence. For example, kits are available from various biology education supply companies to perform protein gel isozyme analysis of myosin, myoglobin, and actin to distinguish between different salmon species. We are currently experimenting with a method using spectrophotometry to quantify salmon pigment levels (typically higher in wild salmon), and chromatography to distinguish between artificial pigments in farmed salmon and natural pigments in wild salmon, both of which could be performed in a single lab session. This exercise could also be easily expanded for a more advanced genetics or phylogenetic analysis courses, by adding a molecular marker (DNA fingerprint) test in addition to the phylogenetic analysis, and by sequencing multiple genes such as Cox I in addition to the internal transcribed spacer (ITS).
Possible Use in Other Courses: It would also be useful to link this exercise to another course dealing with ethics, environmental law, consumer protection, food safety, or pollution and public policy.
Description and Teaching Materials
Students independently request wild Pacific salmon samples from their local stores and bring these tissue samples in to the lab for analysis. In a five week laboratory sequence, each student performs DNA isolations, PCR using salmon-specific primers, gel electrophoresis, and sets up sequencing reactions which are processed at a separate sequencing facility (approximately $6/sample). Sequences are analyzed using phylogenetic analysis software (available free on the Web) and the results are summarized in an oral presentation. The potential exists to expand this exercise by using protein gel isozyme analysis of myosin, myoglobin, and actin to distinguish between different salmon species, spectrophotometry to quantify salmon pigment levels (typically higher in wild salmon), and chromatography to distinguish between artificial pigments in farmed salmon and natural pigments in wild salmon.
Because salmon is such a Pacific Northwest icon, the exercise resonates with and strengthens the students' sense of connection to their local region (the bioregion). The exercises connect to the students' local communities by requiring them to bring in salmon samples from their own local stores. There is ample opportunity to involve community groups in using the results of the investigation to challenge local stores or local suppliers that are selling mislabeled salmon.
The laboratory exercises are most effective when integrated into a multi-quarter sequence of introductory biology. Salmon become a unifying theme for the whole sequence and a connection point for a series of learning modules relating to multiple topics throughout the year. For example, during the ecology section, topics such as bioaccumulation of pollutants, the environmental impacts of farmed vs. native fish, and conservation biology of salmon can be introduced. During the evolution section, topics such as phylogenetic trees and population genetics of salmon can be discussed. During the animal physiology section, muscle physiology (actin/myosin), toxicology, and osmoregulation changes from saltwater to freshwater can be incorporated. During the cell and molecular biology sections of the biology sequence, the labs provide a hands-on introduction to basic methods in molecular biology.
Anonymous comments from students participating in this exercise at University of Washington Tacoma in Winter 2007 included: "I liked the salmon labs because we were using real world issues to learn about a complicated process."
Description of the ActivityA complete Student Laboratory Manual, including pre-lab and post-lab questions, introduction and context, and detailed instructions, is attached below. An Instructor Manual provides additional information required to set up each lab. Example of student work and a rubric is also included below.
Teaching Notes and Tips
It is important to stress accountability and documentation of the sample collection. The potential for using this information to accuse local stores or suppliers of consumer fraud reinforces to the students the importance of keeping track of the identity of their samples and thoroughly documenting where the samples came from. All samples should be stored for confirmation of results.
We encourage other local educators to use any portions of this exercise that are appropriate to their courses. We hope to gather results from all local participants for eventual publication.