DNA twist reveals why some thorny skates grow twice as large

For more than 20 years, scientists have puzzled over an unusual trait in thorny skates in the North Atlantic.

In some parts of their range, these fish appear in two distinctly different sizes, regardless of their sex. Researchers were unable to determine the cause of this phenomenon – until now.

A new study led by Jeff Kneebone and a team from the Florida Museum of Natural History has finally solved the mystery, thanks in part to unexpected disruptions caused by the COVID-19 pandemic.

A longstanding conservation puzzle

The size discrepancy among thorny skates has been noted for nearly a century, but the issue became especially significant in the 1970s when their populations began to plummet. Suspecting overfishing as the main culprit, authorities implemented a strict fishing ban on thorny skates and barndoor skates in 2003.

“The barndoor skate rebounded to the point where they’re now allowed to be harvested again, but for whatever reason, the thorny skate has remained low, despite 20 years of protection,” said Kneebone, a senior scientist at the Anderson Cabot Center for Ocean Life at the New England Aquarium.

Data from the National Oceanic and Atmospheric Administration indicates that thorny skate populations have declined by 80% to 95% in some regions, particularly in the Gulf of Maine and Canadian waters off the Scotian Shelf.

The mystery of thorny skates

Thorny skates have an extensive distribution, ranging from South Carolina to the Arctic Circle and across to Europe and Russia. However, the size variation appears to be unique to North American waters; in the Arctic and Europe, thorny skates only appear in one size.

“No one could understand what the deal was with these skates,” said study co-author Gavin Naylor, director of the Florida Program for Shark Research at the Florida Museum of Natural History.

Researchers had previously analyzed thorny skate DNA, searching for genetic differences between the two size variants, but found nothing. 

“The big forms are twice the size, and it takes them 11 years to reach adulthood. The small forms are mature by the time they’re six years old. There’s got to be genetic differences.”

Naylor believed a more detailed genetic analysis could uncover the answer.

Samples from hundreds of thorny skates

Previous attempts to solve the mystery involved sequencing short DNA fragments from a small number of individuals. 

While a reasonable approach, Naylor suspected it had failed because not enough of the genome had been examined. Instead, he proposed a gene capture method, an intensive approach that collects DNA sequences from thousands of genes across an organism’s genome. 

This would require analyzing samples from hundreds of thorny skates to gather a comprehensive dataset.

Researchers from around the world responded to Naylor’s request for samples, providing more than 600 tissue specimens spanning much of the Northern Hemisphere and helping him prepare for an extensive lab analysis.

Then, the COVID-19 pandemic shut down lab operations, halting their work indefinitely.

At that point, postdoctoral researcher Shannon Corrigan devised an alternative plan. Instead of conducting a labor-intensive gene capture study on hundreds of skates, they would sequence the full genome of just a handful – four or five individuals. While less comprehensive, it would still allow them to search for significant genetic differences.

It was a gamble. If the genome sequencing approach failed, the team would have used up their funding with no results.

“It was a Hail Mary,” Naylor said. But it paid off. In fact, had they stuck with the original plan, “we would have missed it entirely.”

A key genetic difference

The breakthrough came when lead author Pierre Lesturgie analyzed the genome – comprising 2.5 billion base pairs. As he sifted through the data, he noticed something unusual.

“There was a large region on chromosome two that we thought was weird. Since it was behaving in a way we didn’t understand, we considered removing it from the analysis,” Lesturgie said.

Initially, he suspected the anomaly was a sequencing error and worried it might skew their results. But before discarding it, Naylor recognized a pattern – it resembled a gene inversion, where a segment of DNA is flipped in the opposite direction.

Gene inversions are common across many species, including humans, but they rarely result in such dramatic physical differences. Still, the team decided to check if this inverted DNA sequence was present in both small and large thorny skates.

It wasn’t. Only the larger skates had the inversion. They had finally uncovered the genetic basis for the size difference.

Implications for conservation

Now that scientists understand why thorny skates appear in two distinct sizes, Kneebone believes they can develop more effective conservation strategies. 

The next step is to study the skates’ life histories more closely – something that has been challenging due to the difficulty of distinguishing between the two types.

“We could identify the large males and females because they’re bigger than anything else,” Naylor said. Both large and small males develop distinctive long claspers on either side of their tails when they reach maturity. 

“So when you’ve got a small male with large claspers, we know it’s an adult. But we can’t do anything with the small females because we don’t know whether they’re just babies on their way to getting big.”

This has complicated research on the species. “The big question has always been, what do the life histories of the two morphs look like? Currently, they’re not discriminated in the stock assessment, so a thorny skate is a thorny skate is a thorny skate,” Kneebone said.

The role of climate change

Even with this discovery, thorny skates are still struggling in parts of their range, particularly in the Gulf of Maine. One potential factor is climate change.

Current evidence suggests that the two size variants may have difficulty interbreeding in areas where populations are declining. Warming ocean temperatures could be exacerbating this natural reproductive barrier.

The Gulf of Maine has experienced some of the fastest ocean warming on the planet, with sea surface temperatures rising at a rate faster than 99% of the world’s oceans. This has already led to significant ecological changes, such as the collapse of cod fisheries.

Scientists are now investigating whether climate change is disproportionately affecting thorny skates compared to other skate species in the region.

“We’re trying to use the best available science to make decisions about how to best manage and sustain populations,” Kneebone concluded.

The study is published in the journal Nature Communications.

Image Credit: Illustration by Jorge Machuski

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