Surprising genetic differences found in Iliamna Lake harbor seals

In Alaska, harbor seals thrive in the chilled water of Iliamna Lake, sliding their blubbery bodies onto floating pieces of ice for a winter rest. This group of round-eyed water dwellers has remained a mystery for years, but now, in partnership with local Indigenous communities, scientists have found surprising genetic differences in the seals. 

Results of their study, published in the journal Biology Letters, reveal that the seals in Iliamna Lake are notably different at multiple genetic markers from the seals found not only in waters that flow from the lake downstream to Bristol Bay but also in the broader Pacific Ocean. Findings indicate that Iliamna seals are likely evolutionarily, reproductively and demographically discrete from other seal populations in the Pacific and could be a unique endemic form of harbor seal.

The study was conducted by scientists from Florida Atlantic University, the University of Alaska Fairbanks, the University of Washington and the National Oceanographic and Atmospheric Administration. 

Donna Hauser, research associate professor at the UAF International Arctic Research Center, began studying the Iliamna Lake seals as an undergraduate student at UW. She’s still passionate about the work 25 years later and co-authored the research paper.

“Iliamna seals are super interesting and unique,” Hauser said. “There are only five different populations of seals who live year-round in freshwater across the entire world, and some of those are recognized as different species and subspecies. Iliamna seals have received relatively little scientific study.” 

That’s partly because their remote location makes the elusive seals difficult to research. A long-standing question has been whether the seals in Iliamna Lake are genetically different from those in Bristol Bay, the nearest marine population.

Iliamna seals have long been known to the Dena’ina Athabascan and Central Yupik peoples of southwestern Alaska, who have deep cultural and dietary ties to the creature. The initial critical samples for this research came from Alaska subsistence hunters, providing early hints that seal movements between Iliamna Lake and Bristol Bay might be limited. 

The rest of the samples came from seal scat that Hauser gathered upon revisiting Iliamna Lake in 2015 and 2017. 

“The scats did indeed produce viable DNA for extraction and greatly bolstered the sample size to be able to conduct more detailed genetic analyses,” said Hauser. 

The research team conducted a genetic study of Iliamna Lake seals and compared them to seals across almost the entire Pacific range.

The seals in Iliamna Lake were significantly differentiated from seals sampled at several regions across the Pacific, including Japan, the Commander Islands in Russia, other locations in Alaska, and California. They had lower levels of variation at the selectively neutral markers investigated and somewhat higher estimates of inbreeding compared to the marine populations.

“Our findings are both striking and unexpected,” said Greg O’Corry Crowe, senior author, program lead and a research professor at FAU Harbor Branch Oceanographic Institute. “Indigenous knowledge and early Russian explorers’ accounts suggest that the seals have been in Iliamna Lake for at least 200 years. However, it’s still uncertain whether they have been there for a longer period or if the observed differences might indicate that the Iliamna seals represent a separate subspecies, similar to other freshwater seal populations.”

The team is planning more research on Iliamna seals, which will include the addition of genomic analyses to further resolve their relationships with other seal populations and, more broadly, reveal how genetic diversity is generated, lost or maintained in small, isolated populations and how typically marine species adapt to freshwater habitats.

Concern for Iliamna Lake, its flora and its fauna has increased recently with the growing interest in mineral exploration and development in the region. Detailed scientific data is needed to inform species management and conservation. The authors hope findings from this study could inform comanagement of seals and assist NOAA, the federal agency that manages harbor seals, with decision-making.

Hauser is excited their research was able to address a key question about this unique population. “I hope it sparks new research, and especially collaborations with local communities and Indigenous knowledge holders around the lake,” she said.