308 Monitoring Threatened Species and Ecological Communities
eDNA sampling
Recent advances in DNA-based techniques for taxonomic identification also offer
exciting opportunities for threatened species monitoring. One particularly
promising domain involves new methods for collecting and processing
environmental DNA – the extracellular material shed from organisms.
Environmental DNA, or eDNA, is particularly ubiquitous in aquatic environments.
The collection of environmental samples from aquatic habitats (e.g. using filter
capsules and syringes, or peristaltic pumps) can therefore provide management
agencies with an ability to rapidly assess the distributions of threatened species,
and to identify threatening processes, such as the presence of invasive species
(Table 23.1). What’s more, rapid declines in the cost of DNA sequencing are
making eDNA sampling increasingly cost-effective. In the year 2000, for example,
sequencing 1 million base pairs of DNA cost US$10 000; in 2010, that same feat
could be achieved for US$1 (Yoccoz 2012).
Environmental DNA sampling is particularly attractive for monitoring
threatened species, which are often elusive, widely dispersed or undergo substantial
population f luctuations. In addition, eDNA sampling is less invasive than most
traditional monitoring techniques, inf licting little or no damage on target species
or their environment.
eDNA sampling has the potential to revolutionise threatened species monitoring
in aquatic systems, but, as is often the case with new technologies, key uncertainties
remain. For example, empirical studies suggest that eDNA degrades quickly in most
aquatic environments – in the order of days to weeks. However, in some
environments, and for some species, eDNA can persist much longer, potentially
Table 23.1. Examples of studies that have used eDNA sampling to monitor threatened species and/or their
threats.
Environment Monitoring objective Application Reference
Streams Evaluate effectiveness of
management actions
Eradication of invasive
trout
Banks et al. (2016)
Ponds Disease surveillance Detecting chytrid fungus
Batrachochytrium
dendrobatidis
Schmidt et al. (2013)
Maritime
shipping ports
Biosecurity surveillance Early detection of
non-indigenous
zooplankton
Brown et al. (2016)
Estuaries Evaluate impacts of
human activities
Effects of urbanisation on
metazoan communities
Kelly et al. (2016)
Ponds Engaging the public to
leverage effort and
support
Develop a nation-wide
citizen science program
to evaluate status of
newts
Biggs et al. (2015)