Research
Our research utilzes a combination of field and laboratory techniques to address ecological questions. Most of our work currently focuses on environmental DNA (eDNA), the use of DNA animals shed to detect their presence. Several current or recent projects are described below.
Assessment of biodiversity in freshwater lotic Galápagos habitats (San Cristóbal) through the use of eDNA metabarcoding.
The Galápagos are an iconic location, Darwin having forever secured their place in history, and have been described as a living laboratory. Although the Galápagos have been the focus of many extensive biodiversity studies, few have focused on freshwater fauna, particularly of the relatively few lotic systems present on only some of the larger islands. This project utilizes eDNA to survey the freshwater invertebrate fauna in streams in the highlands of San Cristóbal on Finca Helena Maria, a privately owned 600-acre reserve. This project is supported by a Summer Research Grant from the Kentucky Academy of Science.
Assessment of salamander distribution in the GSMNP through the use of eDNA metabarcoding with an emphasis on a reexamination of the distribution of the rare salamander, E. junaluska.
The Great Smoky Mountains National Park is known as the salamander capital of the world, serving as home to an incredible 30 species of salamanders. The objectives of this project are to: 1) reassess salamander distribution throughout the park using environmental DNA and metabarcoding, and 2) to utilize a more targeted assay to reassess one of the Park’s rarest salamanders, the Junaluska salamander (Eurycea junaluska). In July of 2023 water samples were collected across the park and filtered in the field for transport to the lab, samples have been extracted and analysis is underway. This project is supported by a Carlos C. Campbell Memorial Fellowship from the Great Smoky Mountains Conservation Association. This project is ongoing but see a presentation of data obtained to date here: Junaluska 2023.
Brammell, Ben F., Sara A. Brewer, Elizabeth K. Strasko, Jarrett R. Johnson and Madeline Cox. 2023. eDNA monitoring of a rare salamander: The use of eDNA in detection of Eurycea junaluska in the Great Smoky Mountains National Park. 108th Annual Kentucky Academy of Science Meeting, Nov. 3-4, 2023, Northern KY Univ. Highland Heights, KY. Poster.
Detecting fossorial salamanders using eDNA; development and validation of quantitative and end-point PCR assays for the detection of five species of Ambystoma.
Salamanders of the family Ambystomatidae are some of the most interesting members of the order Caudata. They are large, fossorial species and adults are rarely encountered above ground outside of their brief reproductive season when they may sometimes be observed in huge numbers migrating to spawning habitats. Larvae develop rapidly in ephemeral pools or small streams and typically leave the water in a matter of months. A number of Ambystomatid species are of conservation interest. In this project we developed tools to detect five Ambystomatid species using eDNA. This work is now published in Conservation Genetics Resources, see this publication here: Amby 2023.
Brammell, B.F., Strasko, E.K., Brewer, S.A. et al. Detecting fossorial salamanders using eDNA: Development and validation of quantitative and end-point PCR assays for the detection of five species of Ambystoma. Conservation Genet Resour (2023). https://doi.org/10.1007/s12686-023-01322-6
Development and validation of qPCR assays for use in eDNA detection of southern two-lined (Eurycea cirrigera) and northern dusky (Desmognathus fuscus) salamanders.
The use of DNA to detect organsims in the environment requires both DNA sequences from the target organisms and oligos (short pieces of synthetic DNA that match these sequences). In this study Florene Bell, Angie Flores and other Asbury undergraduates sequenced DNA from northern dusky and southern two line salamanders and used these sequences to design oligos for use in eDNA detection of these species. Water samples were collected from streams in Robinson Forest in eastern Kentucky and these oliogs used to detect salamander DNA in these samples. See their publication here: Bell et al. 2022.
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Bell, Florene F., Angie F. Flores, Kenton L. Sena, Thomas A. Maigret, Chi Jing Leow, Ronald B. Sams, David K. Peyton, and Ben F. Brammell. 2022. Development and validation of qPCR assays for use in eDNA detection of southern two-lined (Eurycea cirrigera) and northern dusky (Desmognathus fuscus) salamanders. Herpetological Conservation and Biology 17(2):398-412.
One of the questions of greatest interest regarding eDNA is whether or not it is capable of determining the number of organsims (or at least biomass) present in addition to simply presence or absence or organisms. In this study Ramon Guivas (Asbury undergraduate) used qPCR to examine the relationship between eDNA concentration and biomass of fantail darters in a controlled laboratory setting. See his publication here: Guivas and Brammell 2020.
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Guivas, Ramon M. and Ben F. Brammell. 2020. Evaluation of biomass and filtration method on eDNA detection of fantail darters. International Journal of Zoology 3:1-7. https://doi.org/10.1155/2020/4731686
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Photo by Lev Frid, https://www.inaturalist.org/taxa/100476-Etheostoma-flabellare/browse_photos
Evaluation of biomass and filtration method on eDNA detection of fantail darters (Etheostoma flabellare).
Development of eDNA protocols for detection of four dater (Percidae: Etheostomatinae) species in central Kentucky streams
Darters are small, colorful, unique fish with complex behavior and phylogenetic histories and are abundant in nearly all central KY streams. We are working to develop eDNA tools to identify four common darter species in the KY River drainage and assess their effectivess with the same species in adjacent drainages. This project is in progress but see Abigail's presentaion here: Fletcher et al. 2022.
Fletcher, Abigail K., Mary R. Johnson, Cierla V. McGuire, Sara A. Brewer, Joanne Jung, Malinda A. Stull, and Ben F. Brammell. 2022. Development of eDNA protocols for detection of four dater (Percidae: Etheostomatinae) species in central Kentucky streams. Kentucky Water Resources Annual Symposium, September 18, 2022, Lexington, KY. Poster.
Multiple methods of detection of semiaquatic salamanders in small lotic systems: A comparison of eDNA and leaf liter bags.
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Another question of interest to biologist is "How does eDNA compare to tradtional methods of detection." In this study Rebecca Piche (undergraduate) compares the effectives of eDNA detection of salamanders to the more traditional method of leaf litter bags.
Piche, Rebecca R., Eliza M. Crawford, and Ben F. Brammell. 2021. Multiple methods of detection of semiaquatic salamanders in small lotic systems: A comparison of eDNA and leaf liter bags. 2021 Meeting of the Tennessee Herpetological Society, Dec. 6-7, 2021, Chattanooga, TN. Poster.
Analysis is still underway for this project but you can see a copy of Rebecca's presentation at the 2021 Tennessee Society of Herpetology meeting here: Piche et al. 2021.