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.
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.
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.
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
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.