Key points
- The Spotted Handfish lives in a few remaining pockets of Tasmania’s south-east coast.
- Using advanced long-read DNA sequencing, we’ve published the first fully annotated Spotted Handfish genome.
- The genome will help ongoing efforts to boost population numbers and monitor genetic diversity.
The Spotted Handfish (Brachionichthys hirsutus) is a fish as beloved as it is bizarre. The marine species can be found scuttling along the sands of the Derwent River estuary on its hand-like pectoral fins.
Once plentiful around Tasmania’s south-east coast, Spotted Handfish numbers have dwindled alarmingly. In 1996, it became the first marine fish to be listed as critically endangered.
It’s hard to know for sure, but our scientists estimate fewer than 2000 individuals remain in the wild. That’s why it’s crucial to find out all we can, to help keep these fabulous fish from extinction.
Holding on by its fin-gertips
Since 1997, our scientists have been monitoring the Spotted Handfish, focusing on nine localised populations within the Derwent Estuary.
Researchers trace the decline of the Spotted Handfish back to earlier fishing practices. Historically, fisheries would dredge near the shoreline for scallops, changing the habitat and scooping up handfish as by-catch.
Coastal developments drove populations down further, as did the arrival of the Northern Pacific Seastar. This large, aggressive, invasive species preys on natives including stalked ascidians – a filter-feeder rooted in the riverbed. The Spotted Handfish relies on these ascidians for reproduction, laying its eggs around their cylindrical bases to anchor them against the pull of the tides.
Without a swim bladder, the Spotted Handfish moves infrequently and doesn’t travel far. This makes the small remaining populations even more vulnerable to encroaching human activity in the estuary. Additionally, climate change continues to exert pressure on their numbers, compounding the challenges they face.
Working hand-in-handfish
One way our scientists are working to save the Spotted Handfish is through the power of genomics. Our Applied Genomics Initiative (AGI) recently seized a rare opportunity to sequence the first ever full genome of the Spotted Handfish.
When a Spotted Handfish passed away of natural causes in captivity, the specimen was quickly preserved in ethanol and chilled to -20 degrees Celsius.
Working collaboratively with partners and colleagues, the AGI used state-of-the-art machinery to analyse a sample of tissue from the organism, effectively ‘reading’ its DNA. They assembled all of the genes which make up the organism’s DNA into a single sequence, known as a genome. This was then annotated (identifying where the genes are) in collaboration with the National Center for Biotechnology Information in the USA.
Senior Research Scientist Gunjan Pandey led the efforts. He knows from experience that marine species like the Spotted Handfish can be difficult to work with.
“The DNA degrades rapidly and becomes contaminated with microorganisms. This makes assembling a pure genome extremely challenging,” he said.
In collaboration with the Biomolecular Resource Facility at the Australian National University, the team was able to sequence the complete genome from a small amount of degraded DNA, using what’s called a low-input protocol.
“We are one of only three teams globally using this protocol,” Gunjan said.
“We customised the entire process – from the set-up of the lab to the bioinformatics software – to sequence a high-quality genome from poor-quality DNA,” he said.
“What used to take six to twelve months, we can now accomplish in days.”
Survival of the species
The genome is a critical tool for conservation scientists. It can assist with species detection, help monitor populations, and even estimate the fish’s lifespan. It helps us understand how the Spotted Handfish functions in daily life, while also offering insights into its evolutionary history.
Principal Research Scientist Toby Patterson specialises in the conservation and management of threatened species. Toby believes the genome will help inform conservation strategy over the long term.
“The Spotted Handfish is a threatened species in an urban context. We have to learn how to manage species in environments that humans have impacted, to prevent further loss of biodiversity,” he said.
Climate change is adding to the stressors faced by threatened species.
Conservationists need to be able to understand different species’ capacity to adapt. It also helps to be able to measure the size and genetic diversity of their populations, and how we can maintain or even enhance that. That’s where having rich genetic information comes in handy.
Genome sequencing technology holds huge promise for our understanding and conservation of many threatened species across Australia, and around the world.
A helping handfish
Our multi-pronged approach to conserving the Spotted Handfish includes a captive breeding program and innovative approaches to habitat restoration.
Principal Investigator Carlie Devine has worked with us on Spotted Handfish conservation since 2014.
“We aim to release Spotted Handfish bred in captivity into wild populations, to help boost their genetic diversity,” Carlie said.
“We have also planted artificial spawning habitat in the form of beautiful ceramic sticks made by Tasmanian artist Jane Bamford.”
From artisanal ceramics to artificial intelligence, the team is also experimenting with machine learning.
We are developing software that can learn to detect the fish from footage captured by an underwater operated vehicle. This could offer a more cost-effective way to monitor populations than sending out teams of divers.
Our Australian National Fish Collection also contributed research expertise to help sequence the genome.
Sharon Appleyard is the Director and worked on the only population genomics study of the Spotted Handfish.
“Previous research has told us that the clusters of Spotted Handfish in the Derwent Estuary don’t interbreed much,” Sharon said.
This means each cluster might need its own conservation approach.
“The Spotted Handfish is a Tasmanian icon. The new whole genome sequence will give our researchers, and the National Handfish Recovery Team, a crucial new tool. With it, we can assess and manage the conservation of one of the world’s rarest marine fish into the future.”