For decades, researchers stared at the same puzzle. In waters off North America, thorny skates came in two starkly different sizes—some topping out around 72 centimeters, others stretching over a meter. No obvious differences in sex, age, or environment explained it. But that didn’t stop their numbers from crashing. Fisheries imposed strict protections. Yet unlike their cousin, the barndoor skate, thorny skate populations never bounced back.

Conservationists couldn’t solve what they couldn’t explain. And until recently, the DNA of these bottom-dwelling fish offered few answers.

Photo: Wikimedia Commons / Biodiversity Heritage Library, License: CC BY 2.0

Thorny skates appear in two dramatically different sizes.

The COVID Pivot That Sparked Discovery

The breakthrough didn’t come in a planned experiment. It came from a pivot. As the pandemic halted lab operations, scientists at the Florida Museum of Natural History changed tactics. Rather than pursue their labor-intensive plan to analyze gene sequences from hundreds of thorny skates, they opted for full-genome sequencing of just a few individuals, Earth.com reports.

What they uncovered was a 31-megabase region on chromosome 2 that acted nothing like the rest of the genome. Initially flagged as an error, this segment turned out to be an inversion—DNA flipped in the opposite direction. This “supergene” was only found in the larger skates. It was the key genetic difference they’d missed all along.

The Supergene That Shapes Size

The size disparity, it turns out, is linked to two distinct alleles: HB and HS. Skates carrying two copies of the HB allele grow significantly larger—up to 67 centimeters on average—compared to those with two HS alleles, which tend to max out around 51 centimeters, according to the study, published in Nature Communications. Those with one of each fall somewhere in between.

The implications are huge. Until now, conservation assessments lumped all thorny skates together. But if skates with different genotypes follow different growth and maturity patterns, they may need separate management approaches.

Photo: Wikimedia Commons / Biodiversity Heritage Library, License: CC BY 2.0

Skate populations crashed despite protective measures.

Where It Came From—and Why It Matters

This wasn’t just a spontaneous mutation. Genetic comparisons suggest the HB allele didn’t originate in Amblyraja radiata at all. Instead, it was likely inherited from a related species, probably Amblyraja hyperborea, through a process called introgression—a kind of ancient gene transfer between species, reports SciTechDaily.

Introgressed supergenes like this are rare and fascinating. They act as a bundle of linked traits passed down together. Because they don’t recombine like typical genes, they can quickly spread and influence complex characteristics, like body size.

Why the Gulf of Maine Is Still Struggling

One discovery rattled conservationists: In the Gulf of Maine, there’s an extreme shortage of heterozygotes—skates with one HB and one HS allele. Instead, the population is split between large and small morphs, with little crossover. That suggests skates are mating with partners of similar size—a pattern known as positive assortative mating.

This mating pattern can drive inbreeding and reduce genetic diversity, especially in smaller populations. And that, researchers believe, might explain why Gulf of Maine skates haven’t recovered despite two decades of protection, ScienceBlog reports.

Canadian populations, in contrast, show a healthy mix of genotypes. That balance may be buffering them from the same genetic bottleneck.

Photo: Wikimedia Commons / Viktor V. Grøtan, License: CC BY 4.0

Only large skates carry two copies of the HB allele.

Modern Genetics Rewriting Management Playbooks

Scientists like John Denton and Shannon Corrigan, also at the Florida Museum, are already using newer DNA sequencing methods to explore other questions. As Florida Museum reports, they’re targeting specific genome regions to determine whether North Atlantic thorny skates represent one population or several, and if distinct conservation plans are needed for each.

Their work goes beyond the thorny skate. It shows how modern genomics can reveal hidden differences invisible to the eye.

Next Steps for Science—and Survival

Unraveling the genetics was step one. Step two is figuring out how these differences affect survival and reproduction. Without that, stock assessments will continue to paint with too broad a brush.

And there’s urgency. Climate change is heating the Gulf of Maine faster than almost any other ocean region. That environmental stress, paired with a fragmented gene pool, could push the population closer to collapse, Phys.org reports.

For a species already fighting to recover, the discovery of a supergene offers more than scientific insight. It may be their best shot at survival.