First comprehensive study on otters reveals low genetic diversity

A simple blood sample has led to the discovery that sea otters have low genetic diversity, which may threaten the species’ health in the future.

The sample was taken from Gidget, who was a sea otter at the Monterey Bay Aquarium, and aided in a UCLA-led study that resulted in the first comprehensive genomic analysis of otters.

Gidget’s genome was sequenced because she was the first otter at the aquarium to have a full veterinary examination. The veterinarian drew some extra blood, which was used for sequencing.

Annabel Beichman, the study’s lead author and a UCLA ecology and evolutionary biology graduate student, said the sequencing process began by deriving the genome from the sample and then breaking it up into tiny pieces.

“Then you sequence all those tiny pieces and put them back together,” Beichman said.

With 2.5 billion DNA letters making up the genome, the sequencing was a large computational undertaking, Beichman said.

The researchers found that sea otters have little genetic diversity, which refers to differences across a genome or the variation in genetic traits within a population of animals. It can be compared to M&M’s in a jar, Beichman said.

A larger population of individuals would have a greater variety of genetic traits among individuals. This would lead to a higher level of genetic diversity – more M&M colors in the jar, she said.

On the other hand, a smaller population could be compared to a handful of M&M’s from the jar, with the loss of certain colors representing the loss of certain genetic traits, Beichman said.

“(If) you reach in and grab a really small handful, you’re probably not going to get all the colors,” Beichman said. “You’ll just get one or two, and the one or two that you pull out are probably going to be the most common ones. There will not be as many green and orange or pink M&M’s, you’ll probably mostly get the red and the blue and you’ll lose everything else.”

Beichman said that the lower genetic diversity of a smaller population or “loss of colors” did not necessarily have to be good or bad. However, problems can arise when a smaller group has to breed and expand a species’ population.

“All the future diversity has to come from just that small, little handful,” Beichman said. “It can be bad if a disease comes through, and some of the individuals in the large, big population maybe would have been resistant to that.”

Klaus Koepfli, one of the study’s co-authors and a research scientist at the Smithsonian Conservation Biology Institute’s Center for Species Survival, said species with a higher genetic diversity are thought of as more healthy.

“(Species with) lower genetic diversity might have challenges associated with environmental changes that might be happening in the future,” Koepfli said. “If you have more diversity, you’re more likely to be able to have the resources, are committed to resources or capacity to adapt to those changes in the future.”

Sea otters were nearly hunted to extinction during the 18th century and are currently a threatened species under the Endangered Species Act. Their population in California has started to recover but is not at an optimal level yet, Beichman said.

“They’re only at about 3,000 individuals instead of 20,000,” Beichman said.

Nevertheless, the sea otter is faring comparatively better than animals with similar levels of genetic diversity.

For instance, gray wolves on Isle Royale, a biosphere reserve in Michigan, have a low level of diversity due to inbreeding. This led to harmful changes in genes, said Kirk Lohmueller, co-senior author of the study and UCLA associate professor of ecology and evolutionary biology.

Species with low diversity coming from a larger population, like the Isle Royale wolves, may have more problems. However, if a species has always had a small population size and low diversity and survives, as in the case of sea otters, it can probably keep persisting, Lohmueller said.

Despite this, Beichman said that low diversity cannot be discounted as a threat to sea otters.

“It’s sort of a red flag that they’re all pretty similar to each other,” Beichman said. “We need to monitor the genetic diversity going forward, to sort of think about the impact it will have on them going forward.”

The study also found evidence of genetic changes vital in otter evolution.

“It’ll sound like a long time, but (sea otters are) newcomers to the marine mammal world,” Beichman said. “They only entered the ocean maybe 3 to 5 million years ago, which on an evolutionary scale is actually very recent. … If you think of a dolphin or whale or seal, they evolved in the ocean 30 to 50 million years ago, 10 times longer than sea otters.”

Despite the fact that sea otters are newer to the marine environment, they are remarkably well-adapted to it, Beichman said.

“(They have) the densest fur of any mammal,” Beichman said. “And they have dense and thick limb bones that enable them to dive really easily.”

Researchers found evidence of genetic signals that resulted in the development of otters’ dense bone structure and thick fur, among other traits, Beichman said.

The researchers also found that the otter’s sense of smell has changed over time due to changes in the mammals’ olfactory receptor genes. Sea otters have fewer of these genes than other aquatic species, Lohmueller said.

Beichman said sea otters and giant otters have lost 200 to 300 of these genes, compared to their aquatic neighbors, which have lost more.

“(Their genes are) not yet as depleted as a seal or dolphin, which have been in the water for way longer,” Beichman said. “They’re recently kind of intermediate aquatic animals that are just sort of breaking into the water and their olfaction profile reflects that they’re somewhat evolved.”

Beichman said the team was excited by these signals of evolution given the relatively recent time scale.

Work has already begun on a larger follow-up study, wherein genes will be sequenced from around 135 sea otter populations from the north Pacific Rim, spanning the Kuril Islands of Japan to Baja California, Mexico.