A practical guide to DNA-based methods for biodiversity assessment

DNA-based methods for species detection and identification have revolutionised our ability to assess biodiversity in terrestrial, freshwater and marine ecosystems. Starting from the seminal study that used eDNA to detect invasive american bullfrogs in France (Gentile Francesco Ficetola et al. 2008)), research conducted over the last decade has demonstrated the power of these approaches for surveying a wide range of species and groups. Early applications included the use of eDNA to monitor Asian Carp in the USA (Jerde et al. 2013). Following heavy scrutiny, the method was eventually adopted, and is still employed today by the United States Geological Survey (USGS). A flurry of research followed, with tests designed for many threatened and invasive species including New zealand mudsnails (Goldberg et al. 2013), american crayfish (Geerts et al. 2018), gammarids (R. Blackman et al. 2017), and great crested newts (Biggs et al. 2015). The great crested newt eDNA test has been employed for regulatory monitoring in the UK since 2014. During the same time period, there was a proliferation of research studies that used high-throughput sequencing approaches to describe whole communities of organisms from mixed species and environmental samples, using an approach termed DNA metabarcoding (Taberlet et al. 2012).