Unravelling the genetic secrets of an ice age relic

The deepwater sculpin thrives in deep lakes and cold temperatures. Researchers are now sequencing its genome to unravel the genetic secrets of this iconic Canadian fish

  • Published Jul 25, 2022
  • Updated Jun 02, 2023
  • 869 words
  • 4 minutes
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Sifting through the scarce benthos in the frigid oligotrophic depths of Canada’s deepest lakes, a seemingly humble fish is busy making a living. It’s been living this way since the end of the last ice age. 

Described as a glacial relic, the deepwater sculpin is more than meets the eye. Lacking in scales, elongated in the body and with eyes sitting atop a dark grey-brown head, this freshwater fish’s backstory spans the length and breadth of Canada. And now, along with another 149 iconic Canadian animals, scientists are working on revealing its secrets — by sequencing the deepwater sculpin’s entire genome.

“One of the reasons this fish is special is its origin,” says Nathan Lovejoy, professor in biology at University of Toronto Scarborough and lead on the genome sequencing project. “If you look at most North American fishes, their closest relative is another local fish. In the case of the deepwater sculpin, its closest relative is an Arctic marine fish called the fourhorn sculpin.”

The fish’s Arctic heritage, proclivity for cold water as deep as 350 metres, and largely Canadian distribution all give weight to its status as a Canadian icon. It’s only fitting, therefore, that the funding behind Lovejoy’s and University of Toronto Scarborough post-doctoral fellow Alexander Van Nynatten’s efforts to sequence the genome comes from the CanSeq150 initiative. Aiming to sequence the genome of 150 iconic Canadian genomes, 104 are currently being worked on as part of the initiative — with the deepwater sculpin 91 on the list.

Van Nynatten has looked into the deepwater sculpin’s genetics before and found interesting adaptations in the fish’s genes that make it more sensitive to blue-green light — the type of light that best transmits in deep lakes such as Lake Superior and Lake Huron. 

“Looking at the entire genome will allow us to look across a multitude of other genes and get much higher resolution data on its adaptations,” says Van Nynatten. 

As well as being wide, apart from a couple of U.S. populations, the deepwater sculpin’s range is almost entirely Canadian. It extends from the Mont-Laurier region of Quebec through the Laurentian Great Lakes, continuing through Manitoba, Saskatchewan and Alberta, and northwest to Great Slave and Great Bear lakes in the Northwest Territories. 

So how does a fish whose closest relation resides in relatively shallow marine Arctic waters end up inhabiting Canada’s deepest freshwater lakes? In 2008, Lovejoy co-authored a study investigating the deepwater sculpin’s biogeography. He and his colleagues found that the deepwater sculpin’s distribution matches the location of giant lakes, called proglacial lakes, that formed around 10,000 years ago at the foot of melting glaciers retreating north. “That’s most likely how they initially moved between lakes to establish their current geographical position,” says Lovejoy.

North America's proglacial lakes closely match the current distribution of the deepwater sculpin. (Map: Chris Brackley/Can Geo; Glacial, lake, ocean and land extents based on data by Arthur S. Dyke)
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The deepwater sculpin now provides an important link in Great Lake food chains. It mostly feeds on small crustaceans called amphipods — interestingly, also considered glacial relics — and is in turn preyed on by fish such as lake trout and burbot. Lake trout, especially, are considered commercially important for the regions they inhabit. The deepwater sculpin’s success therefore contributes to maintaining these regions economically. However, it faces numerous challenges. 

“It has this ancestral need for very cold temperatures and highly oxygenated water,” says Lovejoy. “Because of this, it is a fish susceptible to changes in temperature and oxygen — and those are things that will change as lakes warm and become eutrophied.”

The deepwater sculpin is facing mouting pressure due to climate change and invasive species. (Photo: courtesy of Brian Weidel, United States Geological Survey)
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Another threat is that, due to an invasion by filter-feeding zebra mussels, the Great Lakes are actually getting clearer, says Van Nynatten. This has allowed some species to migrate deeper than they typically would, meaning increased competition — including from other species of sculpin — and predation for the deepwater sculpin.

In 2006, the Great Lakes-Western St. Lawrence populations of the deepwater sculpin were listed as a species of special concern under the Species at Risk Act. This was re-examined and confirmed in 2017. By sequencing the genome now, Lovejoy and Van Nynatten say they are taking a “biodiversity snapshot, freezing it in time.” 

Sequencing a genome is a huge undertaking — “500 million little nucleotides all strung together that need to be assembled into what makes up the chromosome of this fish,” says Van Nynatten — and as such, the project is still in its early stages.

Still, Lovejoy has clear goals for the future, including sequencing the genome of the fourhorn sculpin — the close Arctic relative. After that, other populations of fourhorn sculpins that have made the marine to freshwater transition — populations he describes as “little independent, natural experiments.” 

Comparing these genomes with that of the deepwater sculpin would undoubtedly reveal more about this unassuming fish turned iconic Canadian species. As would comparing this genomic “snapshot” with future iterations. 

“Who knows? Maybe in 50, 100 years, people will look back on our genome and compare it to more genomes they’ve collected over the years to see what’s changed,” says Lovejoy. “I think that’s pretty cool.”

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