Document Type
Article
Publication Date
4-24-2026
Abstract
Freshwater mussels are a keystone species providing crucial ecosystem services and river composition resiliency. Globally, they remain one of the most imperiled invertebrate groups, facing threats of water quality declines and urban development. Traditional field sampling can often be laborious and ineffective in surveying rare species’ distributions. Anecdotal evidence suggests the presence of freshwater mussels within the Appomattox River; the specifics of population sizes and suitable habitat remains an open question. Environmental DNA (eDNA) usage in conservation ecology has increased dramatically within the past two decades, being a far less invasive and cost-demanding option than traditional surveys. In an effort to detect the presence of mussels in the Appomattox River basin and narrow the search within a given watershed for traditional field sampling and thus the associated cost, eDNA methods were implemented in the Appomattox River across 16 sites from first to fourth order streams. In collaboration with the U.S. Fish and Wildlife Service, we graciously received 134 freshwater mussel mitochondrial genomes to assist in the development of a 16S rRNA mitochondrial barcode. For this study, we aligned the mitogenomes and sequenced PCR product to construct a consensus region of the 16S rRNA gene in the interest of developing a barcode for Unionidae mussels. End point PCR and Sanger sequencing confirmed conservedness and variability across genera (PCR samples = 7, Sanger sequencing = 77). We present a prototype barcode primer pair that consists of two regions found in several extant freshwater mussel species. The development of a barcode is fundamental to assisting in prevalence monitoring using eDNA. Here, we show the challenges and outcomes of developing barcoding from the ground up for eDNA usage on non-model and understudied organisms.
Recommended Citation
Duellman, Nicholas, "Environmental DNA Barcoding for Non-Model Organisms: Challenges and Outcomes of Developing Barcodes for Freshwater Mussels" (2026). Longwood Senior Theses. 46.
https://digitalcommons.longwood.edu/senior_theses/46
