- Environmental DNA (eDNA) is genetic material extracted directly from environmental samples, such as soil, water and air, rather than from an evident biological source. eDNA analysis is revolutionizing species detection and genetic analyses for conservation, management and research.
- Researchers in northern Australia are using eDNA to locate and help conserve critically endangered largetooth sawfish.
- eDNA technology is rapidly evolving; it could become completely field-based and be used to determine abundance and applied to meta-genomic ecosystem surveys to predict spatial and temporal biodiversity patterns.
What has a body like a shark’s, a saw protruding from its head and critically endangered status according to the IUCN?
The largetooth sawfish is a species of ray that grows up to 23 feet long, named for its long flat tapered bill, or rostrum, flanked on either side by 14 to 23 teeth in a bizarre testament to its prehistoric ancestors. It uses this saw-like body part to find prey and slashes it back and forth to impale, kill, cut and feed on small schooling fish and bottom-dwelling crustaceans and mollusks.
Researchers in northern Australia, one of the last places harboring a significant population of largetooth sawfish, are applying pioneering eDNA (environmental DNA) analysis to locate and help conserve these rare animals.
“The point of this work to date has been to work out if this is a valid way to survey sawfish,” said Colin Simpfendorfer, Director of Centre for Sustainable Tropical Fisheries and Aquaculture at James Cook University. “This is the first step in a much bigger project to go global. Sawfish are on the bridge of extinction, so we need to know where they still exist and how we work in those areas to conserve them.”
eDNA analysis for sawfish
As Barnes and Turner (2016) put it, “Environmental DNA (eDNA) refers to the genetic material that can be extracted from bulk environmental samples such as soil, water, and even air. The rapidly expanding study of eDNA has generated unprecedented ability to detect species and conduct genetic analyses for conservation, management, and research, particularly in scenarios where collection of whole organisms is impractical or impossible.”
Thomsen and Willerslev (2015) add that eDNA comes directly from the environment rather than from an evident biological source. They describe eDNA analysis as “an efficient, non-invasive and easy-to-standardize sampling approach” that has helped monitor biodiversity in aquatic and terrestrial ecosystems.
Simpfendorfer et al. (2016) applied the eDNA technique, made possible by big leaps in gathering and studying DNA, by collecting small samples of water and investigating them for sawfish DNA.
“All animals that live in water slowly leak DNA—skin sloughing off, excretion if they’re wounded, cells dying,” explained the lead author. “We sample that soup and see if we can find the signal for sawfish.”
Simpfendorfer and colleagues from James Cook University and Charles Darwin University had heard about researchers using eDNA to hunt for invasive tilapia in Queensland, so his team worked with them to modify the methodology for largetooth sawfish. Before testing the method in the field, the scientists sampled water from various aquaria and successfully determined which ones contained largetooth sawfish. Then they partnered with the Malak Malak indigenous people to take eDNA analysis to the Daly River, a prime sawfish habitat. They put water samples through filter papers to collect DNA and transported the filters to the lab for genetic analysis. They extracted the DNA and compared the extracts to known sawfish DNA sequences to positively identify them and confirm sawfish presence.
The Australian government’s National Environmental Research Program funded the project.
Traditional ways of looking for sawfish, such as fishing surveys in which scientists drop nets hoping to catch specimen in the murky water, can be costly, laborious and even dangerous to both the animals and humans. eDNA analysis, on the other hand, enables researchers to obtain similar results covering a much greater area faster with fewer people.
“This gives us the ability to fairly quickly and cheaply look if there’s sawfish in certain places,” said Simpfendorfer of the eDNA method. “This revolutionizes how we survey for these animals.”
Pilliod et al. (2012) at the US Geological Survey also pointed out the benefits of the eDNA approach for biodiversity inventorying, monitoring and understanding the status, distribution and habitat requirements of small, rare or elusive aquatic creatures.
“Increasing evidence demonstrates improved species detection and catch-per-unit effort compared with electrofishing, snorkeling, and other current field methods,” the factsheet states.
Yet eDNA analysis as a means of identifying sawfish has limitations. According to Simpfendorfer, you can end up with inaccurate data if you are not careful enough collecting and handling DNA samples and contaminate them. Another drawback is that the method can only detect sawfish occupancy; it doesn’t provide any other information, such as the number or size of the fish present, because it doesn’t involve actually catching animals. Additionally, the technique has not been effective in flowing rivers. But he believes they will clear this hurdle in time as they conduct more trials, examine how far DNA travels in flowing water, and refine the method accordingly.
A conservation crisis
The sawfish’s rostrum makes it particularly vulnerable to being entangled in fishing lines, gillnets, otter trawls and seines. As a result, it’s often trapped by commercial fishing as bycatch or gets deliberately targeted and overexploited by unregulated operations for its meat, highly valuable fins or saw, which people dry and sell as a curio, or for display in public aquaria. Degradation of its estuarine and freshwater habitat has also adversely affected sawfish populations; the conversion of mangrove forests and other shallow densely vegetated nursery grounds for beachfront development has reduced sawfish numbers. To make matters worse, the sawfish’s slow reproductive rate and high age of maturity means diminished populations cannot quickly recover.
The largetooth sawfish historically swam in warm-temperate oceans across the tropics. It inhabited the Atlantic from Florida to Brazil and Spain to Angola, the Indo Pacific by Southeast Asia and Australia, the Indian Ocean all the way to East Africa and the eastern Pacific from the Mexico to Ecuador. It also occurs in freshwater environments in Central and South America and West Africa and estuarine habitats and partly enclosed lagoons in North America. The ray’s once extensive range has shrunk dramatically and no longer includes the Mediterranean. Researchers say the species could now be extinct in 50 countries.
An advancing, versatile technology
“DNA technology is evolving very rapidly,” concluded Simpfendorfer. “There’s the possibility of getting this to the point where you can understand how abundant sawfish may be rather than if it’s present or not.”
He added that scientists hope that the technique will be completely field-based and not require laboratory analysis in five to ten years.
eDNA has conservation applications beyond sawfish for any aquatic species for which you can acquire a DNA primer. According to Pilliod et al. (2012), eDNA could also be an effective early detection and eradication confirmation tool for aquatic invasive species, such as Asian carp (Jerde et al., 2011) and American bullfrogs (Dejean et al., 2012), and possibly New Zealand mudsnails, zebra mussels and quagga mussels.
What’s more, Thomsen and Willerslev (2015) predict that eDNA-based approaches will eventually “move from single-marker analyses of species or communities to meta-genomic surveys of entire ecosystems to predict spatial and temporal biodiversity patterns.”
“Sawfish – National Wildlife Federation.” Sawfish – National Wildlife Federation. Web. 09 Sept. 2016.
“Largetooth Sawfish.” National Aquarium. Web. 09 Sept. 2016.
“Largetooth Sawfish (Pristis Pristis) :: NOAA Fisheries.” NOAA Fisheries. Web. 09 Sept. 2016.
“Largetooth Sawfish Photos and Facts.” ARKive. Web. 09 Sept. 2016.