Researchers can now determine the age and sex of living beluga whales in Alaska’s Cook Inlet thanks to a new DNA-based technique that uses information from small samples of skin tissue.
Accurate age estimates are vital to conservation efforts for Cook Inlet belugas, which were listed as endangered following a significant population decline in the 1990s. Previously, researchers could only determine the age of beluga whales by studying the teeth of dead animals.
The new aging method uses DNA methylation data and machine learning to develop a model that captures the relationship between methylation and age. This relationship provides an epigenetic clock for beluga whales.
Epigenetics broadly refers to non-heritable molecular modifications of DNA that change the way genes function. Methylation is one form of epigenetics; it is a biological process by which methyl groups are added to the DNA molecule. In mammals, there are places along the genome that become more methylated as an animal ages.
The new method for determining Cook Inlet beluga whales’ age represents a significant advance in understanding the life history of the species and will have applications to other whale species. The method also can be used to identify an animal’s sex.
“The development of this tool and the use of the epigenetic clock is a major advance in the science of aging,” said Eleanor Bors, the study’s lead author. Bors worked on the project as a post-doctoral fellow at Oregon State University’s Marine Mammal Institute. “We have the technology now to do this easily and it can become a routine part of research on beluga whales.”
The researchers’ findings were just published in the journal Evolutionary Applications. Co-authors include Scott Baker, associate director of OSU’s Marine Mammal Institute; Paul Wade of NOAA’s Alaska Fisheries Science Center; and Steve Horvath of the University of California, Los Angeles.
Beluga whales are known for their distinctive white color and rounded heads. They average 13 feet in length and 3,150 pounds, and have a lifespan of up to 80 years. They are found in Alaska and throughout the Arctic.
Cook Inlet beluga whales are a geographically and genetically distinct population that does not migrate. The population had numbered more than 1,000 in 1979 but declined sharply from 653 to 347 between 1994 and 1998, in part due to unregulated hunting.
Hunting regulations were implemented in 2000 but the population has not rebounded. Today there are an estimated 279 beluga whales in the population, and they have been designated one of NOAA’s “Species in the Spotlight,” an initiative to bring greater attention and resources to species most highly at risk of extinction.
A NOAA species recovery plan issued in 2016 highlighted the need to determine the age structure of the Cook Inlet beluga population to better understand growth, reproduction and survival rates.
In toothed whales and dolphins, age is typically determined by examining teeth, which record age in growth layers similar to tree rings. But that option is only available once an animal has died. Using genomic information, which can be collected with a small biopsy dart, is an important development in the study of living whales and dolphins.
Researchers were able to develop the DNA methylation technique in part because the beluga whale’s genome had already been sequenced, Baker said.
Working with tissue samples from 67 dead whales, the researchers measured methylation levels across tens of thousands of sites in the genome and determined that an effective clock model could be built using just 23 sites related to aging.
The researchers used machine learning to develop an epigenetic age profile for the species based on their findings. Finally, researchers calibrated their findings against age information determined by teeth recovered from the same animals.
“With all of that information, we were able to accurately model the relationship between methylation and age,” Bors said.
Once the profile was built, researchers analyzed skin samples collected between 2016 and 2018 from 38 living whales. They were able to estimate ages and identify the sex of the animals using DNA methylation.
The new aging method gives researchers an important piece of data to use in their work to understand and, they hope, identify ways to reverse the population decline, Wade said. For example, while belugas in other populations reach sexual maturity at about age 8 or 9, the researchers have found that among the Cook Inlet whales tested so far, just one between ages 10 and 19 was pregnant.
“If reproduction is substantially delayed like that, it’s a signal that is surprising. That is an area we can explore further,” said Wade. “We want to keep adding data to see what else we can learn. We see this aging technique as something we want to do routinely now.”
As additional samples are collected, the age profile for the species should continue to calibrate and refine itself, Baker added.
One question for future research is whether this process for determining age is applicable to other beluga whale populations, or more broadly to other whales, dolphins and porpoises, the researchers said. Genetic information collected in the database also can be mined for other biological changes.
“There is a lot of interest in methylation as an indicator of stress, for example,” Baker said. “I’m also interested in kinship relationships within the population, which will now be easier to determine by knowing the age of individuals.”
The research was supported by a grant from the North Pacific Research Board and the Paul G. Allen Frontiers Group. The study this release is based on can be found at: https://onlinelibrary.wiley.com/doi/10.1111/eva.13195