[Reading time: 2 minutes 33 seconds] Robert Audcent is a Zoologist who has been working in the Vertebrate Fauna team…
[Reading time 3 minutes 29 seconds]
Dr Joel Huey is a Geneticist who has been working at Biologic for six years. Since 2023 he has been leading the Molecular Systematics team, who provide molecular support across the company. His team’s latest project is the development of an environmental DNA assay for the sunset frog (Spicospina flammocaerulea), a species unique to Western Australia.
The evolutionary uniqueness of the sunset frog makes it almost like a relic in the landscape, in this exceptional habitat too.
Joel discusses what goes into developing an assay below.
The sunset frog is small with a dark purple-black back and a bright orange underbelly, hence the name. It is restricted to a small area around Walpole, in the Southwest of Western Australia, where it primarily inhabits swamplands. It is listed as vulnerable at both state and federal levels.
From an evolutionary point of view, the sunset frog is very interesting. It is the only species in its genus. Its closest relative sits in a different genus within the same family, an ancient relationship. This combined with its unique habitat makes it an iconic species and one we want to preserve for future generations.
The sunset frog (Spicospina flammocaerulea)
For the sunset frog we want to supplement existing survey methods that rely on the mating calls of males and are therefore restricted to mating season in late spring. There is a possibility we are missing populations where males are not calling, so eDNA adds another layer to complement our traditional survey methods.
Developing an assay starts with understanding the genetic variation of the target species, and of closely related species that are likely to occur in the same area, so we can distinguish between them. We used existing DNA sequence data and obtained tissue extractions of the sunset frog and related species in the area to assist in developing the assay.
From there we optimise and test the assay against non-target DNA to make sure we are not accidentally amplifying things we aren’t interested in, then verify it against environmental samples from locations where we know sunset frog populations exist. We have also been getting the assay externally validated by Associate Professor Dr Shane Tobe at Murdoch University. Whilst this is not a requirement, this process is recommended throughout eDNA literature to demonstrate that the assay is robust, repeatable, and fit for purpose.
All that rigor matters as we need to minimise false positives and false negatives.
The Walpole peatlands, habitat to the sunset frog
The real challenge with the sunset frog is not so much about its restricted range but that it is cryptic in the landscape. These are tiny frogs in huge, complex marshy environments, so they can be incredibly difficult to find. Species that are cryptic in the landscape need multiple complementary survey methods. eDNA can tell you if a species is present, but it is not good at telling you how many individuals there are. So, if we find a new population using eDNA, we would follow up with direct survey methods to confirm the detection and determine abundance.
One of the most powerful things about eDNA is that field sampling can be taught to anybody with a small amount of training on correct sampling methodology. That makes it perfect for citizen science, meaning we are not restricted to small windows of time to collect samples. Members of the public can survey large areas and monitor the species at a lower cost. Then it is off to the experts behind the microscope for analysis and interpretation.
Publishing this work is important, too. Most consultancies apply the same industry-standard methods year in year out. Biologic is constantly seeking better scientific outcomes; we are always testing and learning, working in a space traditionally reserved for university and research partnerships. In the consulting space, we sit at the interface between the researcher driving innovation and stakeholders who use these tools to make decisions. Engaging in this research and having our assay independently validated is how we demonstrate that these tools are fit for purpose, giving stakeholders confidence these tools will answer the questions they need answering.
Working in molecular science at Biologic means constantly finding new applications for our methods. The field has expanded massively over the last few decades, but we’re only just beginning to scratch the surface of its true potential. We are always working at the coalface of discovery; it is exciting to trial new ways in which this science can be applied.
As for the frog itself, I have a small confession. I have never actually seen a sunset frog in real life, only its DNA on a computer screen. That is the cross the molecular biologist must bear. I am hoping to one day jump on one of the monitoring trips and finally see one in the flesh.
