In identifying the oyster, the students did all the research from start to finish: DNA extraction, amplified a gene that’s typically used for DNA barcoding, did the analysis, and then wrote a report on what they found.
A previously undocumented oyster species has been recognized for the first time in Hawai‘i by a team of undergraduates, graduate students, and faculty at the University of Hawai‘i at Hilo in a collaborative project with community partners.
The work was done as part of a Course-based Undergraduate Research Experience, commonly called a CURE project, by a genetics class with lab work (BIOL 376L) taught by Jolene Sutton, assistant professor of biology at UH Hilo. CURE projects are large-scale, where an entire class works together to tackle a single research question.
“We brought the oysters into the class and the students did everything from start to finish,” says Sutton, an evolutionary geneticist specializing in conservation biology. “They did the DNA extraction, amplified a gene that’s typically used for DNA barcoding, did the analysis, and then wrote a report on what they found.”
Oyster species are difficult to identify based on morphology alone, but their identities can be resolved by applying genetic and genomic technologies. Until now, four extant species of true oyster have been documented in Hawai‘i. The genetic study by the UH Hilo students expands the known range of the western Pacific Ostrea equestris, a species previously documented in China, Japan, and New Zealand, by providing the first verification of its occurrence in Hawai‘i.
The discovery has been submitted to a journal for peer review and is currently available as a paper on the pre-print server biorxiv.org.
Sutton’s coauthors on the paper include the nine students in the genetics class: Keinan Agonias, Nicole Antonio, Brandi Bautista, Riley Cabarloc, Maata Fakasieiki, Noreen Aura Mae Gonong, Torey Ramangmou, Lavin Uehara, and Jade Wong.
Other coauthors are the course’s two teaching assistants, Jared Nishimoto and Jeremy Schrader, both graduate students from the tropical conservation biology and environmental science program; Maria Haws, professor of aquaculture and director of the UH Hilo Pacific Aquaculture and Coastal Resources Center, along with colleagues Marni Rem-McGeachy, Hope Helg, Daniel Wilkie, and David Littrell; and Rhiannon Chandler, executive director of Waterkeepers Hawaiian Islands.
The project arose serendipitously when Haws approached Sutton with samples of oysters she had collected but could not identify. Sutton, who was already having her CURE students do DNA barcoding in the genetics lab class using pre-specified training samples, had been looking for a project that had more relevance to the community. “I wanted my students to do a project with a purpose.”
The previously undocumented oyster identified by the class as part of a large species complex known as Ostrea stentina/aupouria/equestris. “It’s a group of oysters that are closely related and very difficult to distinguish from one another,” says Sutton. “We took the analyses a little bit further and it turns out that the samples that we have in Hawai‘i are most closely related to the western Pacific branch of Ostrea equestris, which are associated with China, Japan, and New Zealand.”
The students’ findings may prove useful for the state’s aquaculture industry.
“Here in Hawai‘i we have a resurgence of aquaculture and traditional fishponds and using locally available species for aquaculture purposes, both for food and, in the case of oysters, for environmental remediation,” explains Sutton. “This task of identifying the different oysters in Hawai‘i offers some potential to diversify the markets. This could be something is marketable for food, since people do eat the Ostrea species. If this is a species that grows really well and is already here, maybe this a good option for aquaculture purposes.”
The value of a CURE classroom
Sutton says the CURE classroom format is extremely valuable for student learning and engagement.
“There are data showing that CUREs increase retention and student success,” she explains. “But we need more support for CUREs as they are a lot more effort and time given that it is real research. They require much more planning and flexibility than my other courses. The role of graduate student teaching assistants was critical to accomplishing this project the way we did and in the timeframe that we did it.”
The CURE format also made it possible for every undergraduate enrolled in the class to be published as a coauthor of a scientific paper. “It was really exciting for the students when we told them that we have this result that we think is worth publishing and we want you to be coauthors,” says Sutton.
Based on the results from spring 2019, Sutton secured additional seed funding to continue similar research for the spring 2020 semester. “We have a cohort of twelve students plus an undergraduate teaching assistant. They have been working on more oysters from more locations in Hawai‘i.”
Even with the COVID-19 interruption and the challenges associated with online lab classes, Sutton says she is prepared to teach the students remotely how to analyze the collected data using a combination of different free programs used in genetic analysis.
The work of the two graduate students was partially supported by the National Science Foundation. On the Pacific Aquaculture and Coastal Resources Center side, the work was partially supported by the Center for Tropical and Subtropical Aquaculture and the UH Sea Grant Program.
Story by Leah Sherwood, a graduate student in the tropical conservation biology and environmental science program at UH Hilo. She received her bachelor of science in biology and bachelor of arts in English from Boise State University.