For nearly a century, scientists have been puzzled by the thorny skates of the North Atlantic. These creatures, found in waters from South Carolina to the Arctic Circle, exhibit a peculiar trait: in some areas, particularly along the North American coast, they come in two distinct sizes. This mystery, which intensified as skate populations plummeted, has finally been solved, thanks to a serendipitous turn of events during the COVID-19 pandemic.
“People have known about the size discrepancy in thorny skates for nearly a century,” explained Jeff Kneebone, a senior scientist at the Anderson Cabot Center for Ocean Life at the New England Aquarium. The puzzle grew more urgent in the 1970s, when thorny skate numbers began to decline sharply, prompting a 2003 fishing moratorium in the U.S. While the barndoor skate, another species under the same protection, rebounded, thorny skates remained stubbornly low, especially in the Gulf of Maine.
The key to understanding this discrepancy lay in their genes. “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,” said Gavin Naylor, director of the Florida Program for Shark Research at the Florida Museum of Natural History and co-author of the new study published in Nature Communications.
Naylor and his team initially planned a gene capture approach, a method to analyze thousands of DNA sequences. However, the COVID-19 pandemic disrupted their plans. Shannon Corrigan, a postdoctoral researcher at the time, suggested a risky alternative: whole-genome sequencing of a few individuals. “It was a Hail Mary,” Naylor admitted, but it paid off. “Had they used the original gene capture idea, ‘we would have missed it entirely.’”
The genome sequencing revealed a 31-megabase region on chromosome 2 that behaved strangely. “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,” said Pierre Lesturgie, the study’s first author. But Naylor recognized it as a potential gene inversion, a flipped DNA sequence. Further investigation confirmed that this inversion, a “supergene,” was present only in the larger thorny skates.
This supergene, the researchers discovered, was likely acquired through introgression, a transfer from another species, potentially Amblyraja hyperborea. The study revealed that “a ~ 31 megabase bi-allelic supergene associated with the size polymorphism, with the larger size allele having introgressed in the last ~160,000 years B.P.” This genetic twist explained the size differences observed in North American thorny skates.
Further analysis revealed a crucial detail: the Gulf of Maine population showed a significant deficit of heterozygotes, individuals with two different versions of the supergene. “This suggests inbreeding driven by assortative mating for size in GoM but not in CAN,” the study noted, contrasting it with the Canadian population, which had a more balanced genotype distribution.
This inbreeding, driven by skates mating with others of similar size, could be hindering the population’s recovery. “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,” Kneebone said, highlighting the stark contrast in recovery rates.
The study also delved into the thorny skate’s demographic history, revealing a range expansion originating near Greenland and Iceland. “Consistently with the RE evidence, we found larger ROH in areas away from the putative center of origin,” the researchers stated, referring to Runs of Homozygosity, indicators of inbreeding.
Now that the genetic basis for the size difference is understood, researchers can focus on conservation efforts. “The big question has always been, what do the life histories of the two morphs look like?” Kneebone said. “Currently, they’re not discriminated in the stock assessment, so a thorny skate is a thorny skate is a thorny skate.”
The researchers are also investigating why thorny skates continue to decline in certain areas, particularly the Gulf of Maine, where sea surface temperatures have risen rapidly. “We’re trying to use the best available science to make decisions about how to best manage and sustain populations,” Kneebone concluded, emphasizing the importance of understanding the complex interplay between genetics, environment, and behavior in conservation.
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