Inbreeding a Factor in Decline of Endangered Orcas, NOAA Study Concludes

Fisheries scientists, using a combination of modern genomics and field observations, have determined that the small population and isolation of endangered Southern Resident killer whales in the Pacific Northwest has led to inbreeding—a contributing factor to their demise.

The study by researchers at NOAA Fisheries’ Northwest Fisheries Science Center in Seattle was published in mid-March in the online journal Nature Ecology and Evolution.

It adds new data to the question of why this group of 73 orcas is declining, and whether the major factor in the problem is solely the lack of a sufficient amount of Chinook salmon. The researchers also attempted to find out if several other factors have contributed.

The Washington state-based environmental group Wild Fish Conservancy is suing in federal court to halt the Southeast Alaska summer and winter troll salmon fishery, contending that if that commercial fishery stops there would be more fish for the endangered orcas, which are already competing for the Chinooks with hungry seals, other sea life and humans.

The trollers, backed by scientific studies, state and federal lawmakers in Alaska, contend that halting the multi-million-dollar fishery wouldn’t provide more fish for the endangered orcas, but would have a dramatic, adverse impact on the Southeast Alaska economy.

The international team of researchers at the science center came to their conclusions about inbreeding among this isolated population of whales after seeing the results of newly sequenced genomes from the endangered population.

Such sequencing is the process of determining nearly the entirety, or more, of the DNA sequence of an organism’s genome—in other words its blueprint, the set of instructions dictating its biological traits.

This entails sequencing all of an organism’s chromosomal DNA, as well as DNA contained in the mitochondria, small structures in a cell found in the cytoplasm, the fluid surround the cell nucleus.

But there are other well-known factors contributing to the whales’ decline, including disturbance, contaminants and possible prey limitations, according to the study.

Researchers said that without a genetic influx from other populations or some other major improvement in environmental conditions, inbreeding is likely to continue.

“This is hard news for everyone who cares about this unique population of killer whales so closely tied to the Northwest,” said Marty Kardos, a research geneticist at the science center and a lead author of the new research.

“At the same time,” Kardos continued, “this begins to answer long-standing questions about why substantial recovery efforts have not produced the results we hoped for, and what the future options might be.”

Historically, researchers have focused on three major threats to the Southern Resident population: fluctuation in salmon prey, toxic pollutants and disturbance and noise from ships and other vessels.

The study includes the first major findings from sequencing of the Southern resident genome that began in 2018, undertaken in collaboration with genomics company BGI and the Nature Conservancy. The project has decoded the DNA of some 100 Southern Resident orcas, including some that have died in recent years.

The research also looked at whales in other populations in the northeast Pacific Ocean.

Earlier genetic research, led by senior scientist Michael Ford, also of the Northwest Fisheries Science Center, and co-author of the current study, showed that Southern Resident orcas often mate within their family groups.

In fact, a 2018 analysis found that two male whales had fathered over half of the calves born since 1990 from which scientists have samples. Such dominant roles of a few whales prevent genetic mixing that could otherwise help adaptations to environmental changes.

“For a long time, we’ve struggled to understand why this population has consistently lower survival and birth rates than other killer whales in the region, and this research highlights a strong link between inbred individuals and increased risk of death,” said Eric Ward, a statistician at the science center and another study co-author. “It’s a view we’ve never had before, and it begins to fill a gap in our understanding.”

Still, Ward said, it would be a mistake to consider inbreeding as the primary cause of the population decline.

“Over the last 50 years, this population has been impacted by multiple stressors, and the relative impact of various threats on the Southern Resident population has fluctuated through time,” he remarked.

“These combined impacts,” he added, “coupled with the mating system of killer whales—where only a few males are contributing to the gene pool—may have made inbreeding a more significant threat in recent years.”