A publication from the Asbury University Shaw School of Sciences recently earned the distinction of being selected as the cover article for an issue of the journal Fishes. Dr. Ben Brammell (professor of biology), Dr. Ben McLaughlin ’07 (assistant professor of mathematics and computer science), Sara Brewer ’24, Karly Fetter ’26, Lauren Slone ’27, and Matt Kulp (lead fisheries biologist, Great Smoky Mountains National Park) authored the article titled “Ichthyofaunal Metabarcoding in the Southern Appalachians: Use of eDNA Metabarcoding in Fish Surveys in Lotic Systems of the Great Smoky Mountains National Park with Comparisons to Historic Electrofishing Data.”
The authors collected water samples from streams and rivers throughout the Great Smoky Mountains National Park. They used a combination of molecular procedures and next-generation DNA sequencing to survey park fish populations by extracting DNA from the water—a technique called environmental DNA (eDNA) metabarcoding.
“Metabarcoding is about 1/3 field work, 1/3 lab work, and 1/3 computer science,” Brammell said. “So it provides a great opportunity for cross-disciplinary collaborations.”
The authors detected a total of 40 fish species, including two threatened species, and recorded one of the first observations of high congruence between eDNA metabarcoding and traditional electrofishing data in streams and rivers, a relationship that remains uncertain.
Brammell explained that the rapid development of DNA sequencing technology enabled this work. The researchers used “second generation” DNA sequencing in the project (the same technology that scientists use to sequence genomes and conduct biomedical research today), thereby offering students a valuable opportunity to gain broadly applicable experience. The study also underscored the growing role of computer science in biology.
“In this study, we obtained over 43 million DNA sequences; there’s no way to deal with this volume of data aside from computer science,” Brammell said. “Developments in DNA sequencing technology have largely transformed the field of biology over the past two decades and given rise to the field of bioinformatics. If I were a student interested in a biology research career today, I would take all of the computer science classes that I could.”
Dr. Ben McLaughlin performed much of the bioinformatic and statistical analysis for the project. AU undergraduates played an instrumental role in the research. Second author Sara Brewer helped with the field work and carried out an extensive portion of the lab work, gaining significant molecular biology experience. This paper marks Sara’s third publication from her undergraduate research at Asbury; she is now pursuing a Ph.D. in Molecular and Cellular Biochemistry at the University of Kentucky.
Coauthors and current AU students Karly Fetter and Lauren Slone also contributed significantly to the laboratory work. Both Fetter and Slone have secured spots in the University of Kentucky Medical School’s Early Assurance Program and continue conducting research in Dr. Brammell’s lab.
“I love getting to work with our students,” Brammell said. “The most rewarding part of my career is the opportunity to observe students go through a transformation from enthusiastic but inexperienced young people to competent colleagues that share an interest in and love for the natural world. Partnering with them in research is extremely rewarding.”
The project was funded by a grant from the Great Smoky Mountains Conservation Association. The article cover photo and full publication are available here: https://www.mdpi.com/2410-3888/10/4.