This approach is used when detecting a target species within a particular sample from the environment. In some cases, the target species might be at very low abundance, which makes the process even more challenging in terms of determining how many samples are required to achieve a probability of detection level appropriate for the study.
Species-specific markers are designed using available DNA sequence information from that species, along with other closely related species in order to ensure the assay being designed only will detect the target species. Using that DNA information, PCR primers are developed and then trialed firstly against reference samples of DNA extracted from the species of interest. The PCR primers are used to amplify the species-specific markers using Real-Time Quantitative PCR to detect the target-species’ DNA. Once the specificity of these markers are determined, samples from the environment are then obtained where there is physical evidence of the target species. This helps determine whether there are issues regarding DNA extraction from environmental samples that might limit the effectiveness of the species-specific assay. Those factors, along with the sensitivity of the assay, are able to be determined prior to using the assay for a particular purpose
Applications of single-species detection;
- Rare species: Many threatened species can difficult to detect through traditional monitoring but eDNA can be another tool used by conservation managers as part of survey programmes
- Invasive species incursion: New incursions of invasive species need to be acted on quickly in order to prevent establishment. Sensitive single-species eDNA detection tools can assist by being able to be deployed rapidly and across a wide area as part of surveillance operations.
- Monitoring success of reintroductions: It can be difficult to assess the effectiveness of reintroductions, especially if traditional monitoring relies on later life stages for detection. eDNA can provide evidence of success or failure at various life stages for particular species where managers are seeking to establish viable populations
- Detecting evidence of breeding: Being able to detect whether particular species are spawning is another application of single-species detection tools, where eDNA can be used to look at the relative abundance of different types of DNA in the environment.
- Border detection: Prevention of biosecurity threats entering the country is much more cost-effective than trying to eradicate an unwanted arrival. The development of more sensitive real-time detection tools for application at the border as part of biosecurity operations shows great potential.