Comparing the Performance of Three Different Primer Sets for Detecting Mammals Using Environmental DNA (eDNA) Samples

Smith, Elin

Abstract

Efficient and cost-effective methods of monitoring vertebrate species are critical for future
conservation management. Environmental DNA (eDNA) metabarcoding from aquatic
environments has been increasingly utilised for biodiversity assessments for vertebrates, and
particularly mammalian species in recent years. The majority of studies published to date
however focus on aquatic species, and as a result, the efficacy of eDNA as a tool for
detecting terrestrial vertebrates is not as well understood. Additionally, there is a lack of
studies comparing the performance of metabarcoding primer sets for the detection of specific
taxonomic groups. In this study I compare three widely-used primer sets, designed for
targeting mammals, fish and vertebrates (MiMammal, MiFish and Vert-12S) in order to
determine which primer set or combination of primer sets would be most effective at
detecting specific taxonomic groups, with a particular focus on monitoring the mammalian
community. Environmental DNA samples were collected from 15 sites across nine different
rivers in North-Eastern Spain. Overall, 72 species were detected using the three primer sets,
consisting of 24 mammal species, 19 fish species, 26 bird species and 3 amphibian species.
Of the 72 detected species, 15 species were detected uniquely to the MiMammal primer, 1
species was uniquely detected by the MiFish primer, and 22 unique species were detected
using the Vert-12S primer. Subsequently, out of the 24 mammal species, 19 were detected
using the MiMammal and consisted of 3 species detected uniquely by this primer set. 14
mammal species were detected using the MiFish primer with 1 species being detected
uniquely to the MiFish. The Vert-12S primer detected a total of 18 mammal species, 4 of
which were unique detections to the primer set. This study has demonstrated that primer
choice is a crucial factor in eDNA based studies, depending on target taxa and habitat type.
Finally, this study has shown that while one primer might perform well enough to meet the
objectives of one study, to generate a more comprehensive understanding of species in a
community the use of multiple primer sets should be considered.

Citation

Smith, E. (2024). Comparing the Performance of Three Different Primer Sets for Detecting Mammals Using Environmental DNA (eDNA) Samples. (Thesis). University of Salford

• Thesis Type: Thesis
• Deposit Date: Feb 7, 2024
• Publicly Available Date: Mar 27, 2026
• Award Date: Mar 26, 2024