Study: Inbreeding contributes to the demise of Southern Resident orcas

Mating habits of endangered orcas are one of many factors under consideration

A new federal fisheries study concludes that the small size and isolation of endangered Southern Resident Killer Whales in the Pacific Northwest has led to high levels of inbreeding, which continues to contribute to their decline while other surrounding killer whale populations expand.

Researchers from NOAA Fisheries’ Northwest Fisheries Science Center in Seattle combined modern genomics with decades of field observations in an effort to fill a major gap in understanding why the Southern Resident Killer Whale population is failing to thrive. The groundbreaking study was published on March 20 in the online journal Nature Ecology and Evolution.

According to the study, newly sequenced genomes from a population of 73 whales indicate that inbreeding is a major issue, in addition to human impacts including marine park captures decades ago.  Other well-known factors contributing to the decline of these orcas include disturbance, contaminants, and possible prey limitations, the study said.

Without a genetic influx from other populations, or some other major improvement in environmental conditions, inbreeding is likely to continue the decline of these endangered orcas, researchers said.

Marty Kardos, a research geneticist at the Northwest Fisheries Science Center and a lead author of the study, said these findings are hard news for everyone who cares about this unique population of killer whales so closely tied to the Northwest.

“At the same time, 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,” Kardos said.


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

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

Researchers have historically focused on three main threats to the Southern Resident population, including fluctuations in salmon prey, toxic pollutants, and disturbance and noise from ships and other vessels. NOAA Fisheries’ 2008 Recovery Plan cited inbreeding as a concern, but it was only recently that scientists had the technology to measure the effects of inbreeding on this population of orcas.

Brad Hanson, a research scientist at the Northwest Fisheries Science Center, said the whales are not necessarily dying of inbreeding itself, but that inbreeding has set them up to be more vulnerable to diseases or other problems.

Killer whales first reproduce at about age 10, and reach their reproductive prime in their early 20s. The study found that highly inbred Southern Residents had less than half the chance of surviving through those prime years to reach 40 years of age, compared to the least inbred individuals. Female whales with low levels of inbreeding live long enough to produce an average of 2.6 offspring over their lifetimes, while those with high levels of inbreeding produce an average of 1.6 offspring due to shorter lives.

Animal populations must produce at least two surviving offspring per female to remain stable or increase in number, the researchers said.

Wildlife managers often address inbreeding in small populations by captive breeding in zoos or aquariums, or by adding genetic diversity through introduction of animals from other areas. This method is unlikely to help Southern Resident orcas, who choose not to breed with other killer whales and only reproduce within their own population, the study said.

Back in the 1960s and 1970s, marine parks extracted some 50 orcas from the Salish Sea, mostly Southern Resident orcas, which reduced the genetic diversity of what was already an isolated population. Researchers said this could have also put that whale population at a competitive disadvantage while other fish-eating killer whales in the northeast Pacific Ocean tripled in number.

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

A 2018 analysis found that two male whales had sired over half of the calves born since 1990 from which scientists have samples. That dominant role of a few whales prevents genetic mixing that could otherwise help avoid inbreeding and adopt to environmental changes the study said.

With only about 26 of the 76 endangered whales breeding at the time, the potential for inbreeding was a factor. Reduced survival has contributed to a lack of consistent population growth, including a decline from a high of nearly 100 whales in the mid-1990s down to 73 at the time of the study.

It would be a mistake, however, to see this as inbreeding alone causing the decline, said Eric Ward, a statistician at the science center and coauthor of the research. Ward noted that over the past 50 years this population has been hit by multiple stressors and that the relative impact of these threats has fluctuated through time. Still, the combined factors coupled with the mating habits of this population may have made inbreeding a more significant threat in recent years, he said.