By Charlotte Fielding
Photography by Andrew Morris
Featured in Capital #91
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Shaun Wilkinson and his crew are like Sherlock Holmes, but for critters. Instead of dusting for fingerprints, they’re decoding DNA from water samples, revealing who’s who in New Zealand’s river party. From troublemaking clams to shy native fish, Wilderlab’s on a mission to keep nature’s balance in check.
Shaun Wilkinson describes the environmental DNA work his lab does as resembling crime scene investigation, but for species rather than offenders. Instead of analysing blood or hair from a human, they take a sample of water from one of Aotearoa’s rivers, and sequence the DNA from it. Then instead of matching it against a database of crime suspects or known perpetrators, run it against a database of species that people have uploaded over time.
That’s how Wilderlab, the lab Wilkinson founded and runs, can tell which critters are found in the environment the sample was taken from. This is a simplified version, of course.
The work Wilkinson’s team does at Wilderlab in Miramar falls into three broad categories. First there’s biosecurity surveillance, which is important for protecting New Zealand’s unique ecosystems by detecting invasive organisms before they have had a chance to establish themselves and get out of control. Recently a new clam has been causing mayhem in the Waikato river. This invasive clam from Asia is clogging up the hydroelectric power plant by breeding prolifically on the power turbines, stirring up a whole lot of sediment and causing a decline in water quality. It will eventually compete with the native mussels. What they know so far is that the clam hasn’t yet made it beyond the Waikato river to cause damage in any of the lakes.
Another aspect of Wilderlab’s work is searching for threatened species, such as Hochstetter’s Frog, or rare native fish. Understanding where the species is makes it easier to target protective measures. Take the native galaxiid fish, which has about 20 species ranging from threatened to critically endangered. Some have the same threat ranking as Kākāpō, because of predation by trout and habitat degradation. “There’s a huge push to try and protect these little guys before they go extinct,” Wilkinson says. “We work quite closely with the Department of Conservation, carrying out an environmental DNA monitoring programme for them. And they’ve managed to find new populations of these little galaxiids that we’ve never known about before. Clutha flatheads are in the Clutha river, and they’ve been able to find little hidden populations, which they would probably not have been able to find with visual surveys, because they’re quite cryptic.” Finding this species of galaxiid in Central Otago means DOC are now putting in measures to protect this rare fish, like installing trap areas to remove the trout.
The third category of work for Wilderlab’s eDNA technology is looking at overall ecological health, using the samples to generate a time series on each waterway to figure out if it’s declining, improving, or staying the same. On the basis of this information, management actions can be taken – “particularly if things are getting worse,” says Wilkinson. Mitigation measures might involve, for example, “keeping stock out of the river or doing some riparian planting.”
Sometimes the samples turn up surprising results, such as marine fish in samples from the freshwater reservoir at Zealandia. It turned out that the shags would fly to the south coast, eat a bunch of marine fish, and fly back to roost in the macrocarpa at Zealandia. Their poo would end up in the water and show up in the eDNA samples. Another time, kangaroo DNA at Breaker Bay had the scientists stumped, until dog poo was sighted; the dog had been eating kangaroo meat. “We’re picking up the DNA that’s in the water, not necessarily living organisms that are there,” Wilkinson says. “Most of the time, it overlaps. But occasionally, there’s a little divergence in the Venn diagram there.”
Science was not Wilkinson’s first career. After spending some years as a chef then working as an account manager, he attended Te Herenga Waka, Victoria University of Wellington as a mature student. A BSc with first class honours was followed by a PhD, a postdoc, and a teaching fellowship.
The technology has been around for a while, but Wilkinson and his team scaled eDNA testing, and made it more accessible. He developed a sampling kit that anyone can use, including school groups. “Our mission was to unlock its potential as a monitoring tool for positive conservation impacts,” he says. The price per sample has now been reduced by 90 percent. Sampling is now also less time-consuming, and carries less risk of contamination.
Wilderlab currently processes around 15,000 samples a year, and is building a larger lab as it has outgrown its original premises. They’re also doing more work internationally. Wilkinson recently returned from a workshop in Suva, where he undertook eDNA sampling with village representatives from various islands in Fiji. “We’ve been processing their samples which look absolutely amazing,” Wilkinson says. “Just so many fish. I’ve never seen so many different fish in a single cup of water before”. They are excited to expand into the Pacific countries, and hope to add value to big infrastructure projects by providing a baseline and an ongoing environmental impact monitoring tools.
One of Wilkinson’s current projects is developing an index to distil all the data collected down to a single number, giving a river health score. “I’m really motivated to see this technology being used and unlocked to help improve things around rivers in New Zealand,” he says. The index is already in use by the Ministry for the Environment, local councils and other groups.
“I’m interested in helping others to help improve the environment,” says Wilkinson. The hope is to establish “an uncontestable metric” for progress and setting targets: being able to say “We want to get our river to a score of 100, within the next five years” would be, he suggests, “quite a powerful motivator, and we can build up a really nice national picture of river health across the country.”
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