The next step in Olympia oyster restoration? Genome sequencing.

To boost populations of the West Coast’s only native oyster, scientists and conservationists have been trying some familiar tactics: captive breeding, habitat restoration and close monitoring of numbers. 

But scientists from California Sea Grant are also using a less common tool to inform Olympia oyster restoration: genome sequencing. Scientists hope mapping the Olympia’s genome will help them get a better understanding of the species as a whole, and what steps may need to be taken to ensure a healthy recovery in the most impacted estuaries.

“Just like a thoroughbred horse breeder can use advanced genetics to get what they want, we can also use the same tools to achieve the restoration outcome we want,” says Luke Gardner, aquaculture specialist at California Sea Grant, who is co-leading a new Nature Conservancy-funded effort on the Olympia oyster. 

Tiny oyster, big challenges

Olympias are small oysters – about 2.5 - 3 inches in length – and historically were prevalent up and down the West Coast, from British Columbia to Baja California. They’re an important part of their ecosystems – like all oysters, they are prolific filterers, helping maintain water quality in their marine environments, and their hard shells create habitat for other marine creatures. But numbers of this native bivalve are small today compared to estimates of what they once were, a population decline that scientists say is due to overfishing, pollution (including agricultural runoff) and habitat loss. Their recovery so far, Gardner says, has been tricky.

“We don’t fully comprehend why they haven’t come back in some areas,” he says. It may have to do with human-caused changes to the environment, including pesticides, too much silt and habitat loss.

Scientists like Gardner and California Sea Grant extension specialist Kevin Marquez Johnson are hoping that the oyster’s numbers can be boosted by turning Olympias into sought-after molluscs for commercial aquaculture. Right now, the Olympia oyster aquaculture market is  niche, due to the oyster’s small size, low numbers and relatively slow growing time. 

But growers are starting to experiment with raising Olympia oysters on their farms. As of now, Olympias are being grown on three farms in California. One of these farms is Hog Island Oyster Company, which, with help from funding from the Supporting Oyster Aquaculture and Restoration initiative (SOAR), now has 350,000 young Olympia oysters in its care – up from the 50,000 or so Olympias it usually sells in a year. 

As oyster farms begin to raise native Olympia oysters, they have an opportunity to contribute to the species’ recovery. Olympia oysters take nearly three years to reach market size, but in optimal conditions, they can begin to reproduce within one year. So while the oysters are growing for market, they’re also helping grow the local population. 

How genome sequencing can help

Several distinct Olympia oyster populations in California have been identified by scientists as needing a boost in numbers from conservation aquaculture. However, Olympia oysters’ small population size makes for a small breeding pool for conservationists to pull from – which means more inbreeding among the oysters.

“Morally, that isn’t really an issue for oysters,” says Gardner. “But genetically, as animals that are very similar breed with each other, that genetic diversity goes down.”

Two things put low-genetic-diversity populations at risk: recessive traits, which are more likely to come out as a result of inbreeding, and lower resiliency to stressors. A population that’s genetically similar is more likely to respond similarly to negative impacts on the environment – meaning, for instance, that the entire population could be wiped out by one stressor or event, instead of only a percentage of a genetically healthier and diverse population. 

That’s where the Olympia’s genome comes in. By sequencing the oyster’s genome, Gardner and Johnson are hoping to give resource managers and other decision-makers more information about how similar Olympia oyster populations are. That data is key not only for questions of inbreeding, but for understanding the differences among subpopulations. Johnson and Gardner are also focusing on the Morro Bay population of Olympia oysters, a place where the population of Olympias was, for several years, assumed by scientists to be non-existent. But recently, scientists made an exciting discovery: about 500 Olympia oysters in Morro Bay. Johnson is now working on breeding them and sending them out to commercial aquaculture farms. 

“While we’re doing that, we’re looking at genome sequence data to better understand how unique the Morro Bay population is compared to Elkhorn Slough, Tomales Bay or some of our other areas in California,” Johnson says. “From there, we’re starting to look at questions about inbreeding, and whether it makes sense to bring oysters from another estuary in to breed with Morro Bay and Elkhorn Slough oysters.”

Some stakeholders may want to retain the genetic signatures of a particular population of oysters – a desire that will have to be balanced against the threat of inbreeding.

“That’s where that value judgment comes in,” Garder says. “Is it better to only have oysters from Elkhorn Slough or Morro Bay, which look like Elkhorn Slough or Morro Bay oysters, at the expense of them potentially having low genetic diversity and not being particularly resilient to things like climate change?”

With more data from the genome, stakeholders and decision-makers can better make that judgment call. 

This isn’t the first time a marine creature’s DNA has been sequenced to aid conservation efforts: It’s been done in abalone, too, and scientists are also looking into whether bits of DNA left behind by marine organisms can be used in population monitoring. Sequencing a genome is complicated – the process involves taking DNA from an individual organism, chopping up that DNA and using specialized instruments to sequence the pieces and supercomputers to reconstruct them – but research has shown the practice holds promise for ocean conservation. 

“By sequencing the genome, we have a really powerful tool to determine who’s related to who, and whether there are inbreeding problems,” Gardner says. 

Learn more about Olympia oysters and California Sea Grant’s and partners’ other efforts to restore this native species.