It is often valuable to be able to detect when a species is present in an ecosystem at low population levels. This could apply to rare or endangered species requiring conservation measures, or to pest/invasive species, the presence of which would trigger control or management interventions.
However, detecting species at low population density can be extremely difficult (and therefore expensive) when the species are small, morphologically intractable, behaviourally cryptic, nocturnal, or live in remote or inaccessible habitats. DNA-based methods offer a host of valuable tools for overcoming these obstacles, allowing earlier intervention and improved likelihood of achieving a successful outcome.
Using species-specific primers, aquatic and semi-aquatic species can be detected using environmental DNA (‘eDNA’) at a fraction of the time and effort of conventional surveying techniques. This has been used to great effect for monitoring the invasion front of Asian carp in the US Great Lakes river system and is accepted by DEFRA as a method of determining the presence or absence of the Great Crested Newt.
Terrestrial invertebrates can be detected using metabarcoding or metagenomics. This involves carrying out mass trapping, sequencing the unsorted trap samples and bioinformatically screening the sequence output for the DNA of the target species. This could be particularly relevant for early detection of agricultural, horticultural or domestic insect pests. Meanwhile, all of the non-target species that are sequenced as ‘by-catch’ can provide useful insights into local biodiversity.
Terrestrial vertebrates can be detected by sequencing the invertebrate parasites or scavengers that have fed on them. Next-generation sequencing can simultaneously sequence the DNA of predator, prey, and microbiome – so by collecting and sequencing blood-feeders such as leeches, mosquitoes, midges, and ticks, it is also possible to survey their vertebrate prey. WWF is using this approach to search for the critically endangered saola (Pseudoryx nghetinhentis) in the rainforests of South-East Asia.