The oceans are endlessly vast. Covering 71% of the surface of the Earth and reaching dizzying depths up to 11,000 metres, the our seas are made up of some 1,332,000,000,000,000,000,000 liters of water! With the scale of the mystery and the logistical challenges limiting our exploration of the ocean, it should come as no surprise that there are many, many animals in the water that we simply don't see. But that does not mean they are not there! Thankfully, new genetic technologies are being developed that can help us to identify when animals are nearby, even when we can't actually see them. So how does this method work? How can it help us to detect cryptic animals? And what are the implications for the conservation of threatened species?
Something's In the Water
The genetics revolution of recent decades has lead to a veritable explosion in new molecular techniques for scientists to use. You might imagine that such things are limited to the lab and have no value for field scientists, like shark experts, but you could not be more wrong! DNA barcoding has been used identify a species from only a tiny tissue sample, allowing scientists to monitor the trade in Endangered species. Genome sequencing has allowed us to identify new species, to learn about animal diseases, healing and immunity, and to study population genetics, all of which play a part in conservation plans, and assessing threatened species. DNA might be small, but what we can learn from it is endlessly vast!
eDNA
One relatively new technique that has made waves (no pun intended!) in recent years, is known as environmental DNA or eDNA for short. No, this is not some new Apple product. eDNA is a method that involves taking a sample of water from the ocean, a lake or a river and testing it for minute samples of DNA, in order to determine if a particular animal swam through that environment at some point. This is possible because every multicellular organism sloughs off DNA-rich cells into the environment all the time - whether it's losing hair, shedding microscopic skin cells or depositing drops of tears, saliva or semen - DNA is everywhere (DÃaz-Ferguson & Mover, 2014).
Room for Improvement
The methodologies that make eDNA have only recently been developed and so they are still being advanced and improved. This means there are limits to what eDNA can do. For instance, eDNA "primers" (chemicals that make the DNA sequencing process possible) must be developed for each species individually, so we still have a long way to go. Additionally, DNA does degrade in the environment to the point where it can't be recognised anymore, so this technique can only be used to tell us what animals were in the area very recently. As DNA is washed around and dispersed in currents, it can also sometimes be too diffuse to detect. As these currents can transport DNA over potentially long distances, there is also the possibility that this method will lead to false positives - indicating an animal is nearby when, in fact, they were actually quite far away (DÃaz-Ferguson & Mover, 2014).
However, as collecting eDNA samples is relatively easy and the method is quite cheap, it could represent a great data source for scientists and have applications in all kinds of projects (DÃaz-Ferguson & Mover, 2014).
eDNA in Action
eDNA has been used extensively to to explore the diversity of sharks and rays (known collectively as "chondrichthyans") in many places around the world. To give you an example, scientists used  two different eDNA techniques (known as COI eDNA and 12S eDNA) to investigate the waters around Singapore. Urbanised marine areas with great turbidity and a lot of ocean traffic can be notoriously challenging to sample, but eDNA made this relatively easy and inexpensive. Whatsmore, the results broadened our knowledge about the area, because eDNA showed that these waters are far richer in chondrichthyan diversity than previous sightings and museum records might have had us believe. In fact, the researchers even discovered that two species of rays live around Singapore, despite neither of these animals ever having been seen there before: the Bangal whipray (Brevitrygon imbricata) and the cowtail stingray (Pastinachus sephen) (Ip et al, 2021).
Being able to identify that a particular species lives in an area where they have not previously been seen (or not been seen in a long time) is especially important for threatened species that are very rare (Simpfendorfer et al, 2016).
For example, in Australia, eDNA has been used to detect Critically Endangered largetooth sawfish (Pristis pristis) in freshwater river systems. Similarly, eDNA has been used to identify regions in the Mediterranean Sea that are used by Critically Endangered angel sharks (Squatina squatina, S. aculeata and S. oculata). Therefore, eDNA can be used to map how rare animals use their habitats, which could be vital for identifying critical regions and prioritising particular areas for protection (Simpfendorfer et al, 2016; Faure et al, 2023).
eDNA methodologies have also been developed to be able to detect potentially dangerous species of sharks, like great whites (Carcharodon carcharias), bull sharks (Carcharias leucas) and tiger sharks (Galeocerdo cuvier). In countries where sharks and humans come into conflict, this technology may have applications in shark monitoring programs and the protection of ocean users (van Rooyen et al, 2020).
Who knows what the future holds and what potential this technology may have in the future...
References
DÃaz-Ferguson EE & Moyer GR (2014). History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments. Revista de biologia tropical, 62:4. Access online.
Ip YCA, Chang JJM, Lim KK, Jaafar Z, Wainwright BJ & Huang D (2021). Seeing through sedimented waters: environmental DNA reduces the phantom diversity of sharks and rays in turbid marine habitats. BMC Ecology and Evolution, 21. Access online.
Faure N, Manel S, Macé B, Arnal V, Guellati N, Holon F, Barroil A, Pichot F, Riutort J-J, Insacco G, Zava B, & Deter J (2023). An environmental DNA assay for the detection of Critically Endangered angel sharks (Squatina spp.). Aquatic Conservation: Marine and Freshwater Ecosystems, 33:10. Access online.
Jenrette JF, Jenrette JL, Truelove NK, Moro S, Dunn NI, Chapple TK, Gallagher AJ, Gambardelle C, Schallert R, Shea BD, Curnick DJ, Block BA & Ferretti F (2023). Detecting Mediterranean white sharks with environmental DNA. Oceanography, 36. Access online.
van Rooyen A, Miller AD, Clark Z, Sherman CD, Butcher PA, Rizzari JR & Weeks AR (2021). Development of an environmental DNA assay for detecting multiple shark species involved in human–shark conflicts in Australia. Environmental DNA, 3:5. Access online.
Suarez-Bregua P, Alvarez-Gonzalez M, Parsons KM, Rotllant J, Pierce GJ & Saavedra C (2022). Environmental DNA (eDNA) for monitoring marine mammals: Challenges and opportunities. Frontiers in Marine Science, 9:987774. Access online.
Simpfendorfer CA, Kyne PM, Noble TH, Goldsbury J, Basiita RK, Lindsay R, Shields A, Perry C & Jerry DR (2016). Environmental DNA detects Critically Endangered largetooth sawfish in the wild. Endangered Species Research, 30. Access online.
By Sophie A. Maycock for SharkSpeak
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