Blood, bone and brainpower: A deep dive into sea otter DNA

Being a sea otter might sound simple: swim, snack, nap, repeat. Glorious.

Gidget is the face of the sea otter genome.

But the task before Annabel Beichman, a PhD candidate now in her fifth year at UCLA’s Department of Ecology and Evolutionary Biology, is monstrously complex. Annabel is investigating everything that makes up a sea otter, down to its DNA. She hopes what she learns will contribute to recovery of a species that plays a critical role in the health of coastal ecosystems.

Annabel’s effort to sequence the southern sea otter genome (which she wrote about for us last year) is tied to the Monterey Bay Aquarium by one of our exhibit otters, a 9-year-old female with a blonde, gray-streaked face, named Gidget. Through the DNA that Annabel has been laboring to sequence, assemble and annotate, Gidget will become the embodiment of the sea otter genome. And the work is nearly complete.

‘A reference point for generations’

“Gidget is going to be a reference point for future genetic studies of southern sea otters for years to come,” Annabel says. That research stands to help a species that has been listed as threatened for decades. So, she says, “Gidget’s contributing to the conservation of her entire species.”

A remnant colony of sea otters was rediscovered off the Big Sur coast in the 1930s. Photo © William L. Morgan/California Views Photo Archives

A century ago, the fur trade had nearly wiped out sea otters in California; only a few dozen survivors remained along a rugged and isolated stretch of the Big Sur coast. Since then, conservation efforts have helped the population rebound.

“All otters that exist in California today, maybe around 3,000, descend from that tiny group,” Annabel says.

What genetic diversity remains, of a population that numbered more than 10,000 animals before the fur trade, flows from those few Big Sur otters.

In the effort to better understand the impacts of that “population bottleneck” and what it will take to help southern sea otters return to their historical numbers and range, Gidget’s contribution is foundational.

Piecing the puzzle together

The process began with a routine exam at the Aquarium. Our veterinary staff took samples of Gidget’s blood and quickly froze it to keep its long strands of DNA from breaking down. It was then shipped overnight on dry ice to Annabel’s UCLA lab, where she set about translating its genetic code into a mountain of digital puzzle pieces.

Annabel Beichman and the DNA sequencing team at UCLA. Photo courtesy Annabel Beichman

Printed out, the complete genome might fill a stack of phonebooks three stories high, making sifting through it all and teasing out patterns a colossal challenge. Annabel says that’s compounded by the possibility that much of it is “junk DNA” that doesn’t code for anything meaningful.

The more relevant DNA passages contain blueprints for specific sea otter building blocks: the proteins that comprise a whisker, for instance, or part of a paw or a furry belly.

It’s possible to recognize some of these sections, thanks to earlier work sequencing mammals with similar DNA—particularly ferrets, otters’ mustelid cousins.

Earlier work sequencing the DNA of other mustelids, like these domesticated ferrets, will help researchers identify similar code in sea otter DNA.

“Something that codes for an important protein isn’t going to necessarily change much from an otter to a ferret,” Annabel explains. From an evolutionary standpoint, otters have more in common with ferrets, weasels and badgers than with other marine mammals, like seals.

Still, deciphering how a complete genome fits together requires considerable computational firepower. “Picture 50 computers all working together for weeks on end, devoting all their energies to this,” she says.

A section of DNA code that, in its entirety, maps the sea otter genome.

Once that “de novo genome” assembly is finished, and she has mapped which parts of the DNA code for proteins, it paves the way for much easier comparison among other sea otter specimens.

“Instead of having to sequence the entire thing again, we can pull out the sections we’re interested in—maybe 3 to 5 percent of the genome,” Annabel says.

Growth in numbers, range

Andy Johnson, who’s managed the Aquarium’s sea otter program for about 20 years, says the recovery of wild sea otters in California seems to have hit a wall in recent years.

California sea otters’ current range along the Central Coast is a fraction of the area they historically inhabited.

To grow their numbers, they need to expand farther up and down the coast, back into what are now otter-free portions of their historical range. Sea otters can currently be found only from Point Conception to around Half Moon Bay.

“If the otters aren’t able to expand their range, what are the implications, and is there anything we can do about it?” Andy asks. “Some of Annabel’s work will help us understand this better,” particularly where it involves looking back at ancient DNA samples and seeing what traits might’ve been lost from the era when otters were more abundant, before the population bottleneck.

DNA extracted from teeth in this jawbone found in a Native American midden sheds light on the genetic diversity that existed before otters were decimated by fur hunters. Photo courtesy Annabel Beichman

Annabel can track qualities that have gone missing from the modern-day sea otter population by comparing present-day DNA against ancient samples, called aDNA, dating back more than 2,000 years, when Native Americans hunted otters for food or pelts, and left behind their bones. Those bone piles, called middens, can be excavated and dated. Sometimes they contain hidden troves of aDNA, often inside teeth.

Ecosystem engineers

Sea otters contribute a cascading benefit to coastal ecosystem diversity, Andy says; he contrasts the example of the Aquarium’s iconic kelp forest exhibit with what he calls “urchin barrens.” Otters gladly dine on sea urchins; in their absence, an unchecked urchin population can devastate a kelp forest, undermining an important nursery habitat for many other species.

By eating sea urchins and other grazing animals, sea otters allow kelp forests to thrive. Photo by Neil Fisher

That outsize role as “ecosystem engineers” is what makes Annabel’s research into the genetic history and traits of sea otters so vital, Andy says.

“Animals like Gidget are cute and fuzzy but also kinda snarly, and much more complex than people imagine,” he says. “Our ability to learn from them while they’re at the Aquarium is an opportunity we don’t want to let slip by. A project like Annabel’s allows us understand them in ways that will help us take care of the wild population.”

For Annabel’s part, she’s “charmed” to have Gidget as an ambassador to the public.

“Having dedicated so much time to studying her genetic code in black and white on my computer screen,” she says, “it’s pretty awe-inspiring when I get to see her on exhibit.”

—Daniel Potter

Learn more about our work to recover California’s threatened sea otters.

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