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J27, a 32-year-old male orca named Blackberry, cruises off the Seattle waterfront in October 2012. Blackberry’s community, the endangered Southern Resident killer whales, are impaired by a high rate of inbreeding. Photo: National Marine Fisheries Service, taken under permit #16163

Inbreeding hinders population recovery among endangered Southern Resident killer whales

While a scarcity of Chinook salmon and other environmental factors may be pushing the Southern Resident killer whales toward extinction, a new genetics study has revealed that inbreeding has been exerting a powerful, overriding influence upon the small, genetically isolated population.

The weakened genetic condition of the Southern Resident orcas, which frequent Puget Sound, could help explain why their numbers have generally declined over the past 25 years, while other orca populations in Alaska and British Columbia have been growing at remarkable rates.

Experts have long suspected that inbreeding could be a factor in the Southern Resident population’s struggle to recover, but this new study by an international team of scientists has quantified how “inbreeding depression” may be suppressing population growth by increasing early mortality of the whales at all ages.

The study compared the entire genome of 100 living and dead whales from the Southern Resident population to those of four other orca populations in the North Pacific. The Southern Residents had the lowest level of genetic variation and the highest level of inbreeding — meaning that more of the whales were born to closely related parents. In some cases, the parents were as close as a mother-and-son paring.

Southern Resident killer whales have the lowest level of genetic variation and the highest level of inbreeding among North Pacific orca groups involved in the study. Photo: National Marine Fisheries Service, taken under permit #16163

Decades of conservation efforts no doubt have helped all the killer whale populations, but they have not responded to the same degree, said Marty Kardos, a geneticist with NOAA’s Northwest Fisheries Science Center and lead author of the report.

“Other killer whale populations … have rebounded rapidly,” Kardos said. “But the Southern Residents are an outlier in that respect. The effect of inbreeding is really quite large.”

Effects of genetic isolation

Inbreeding is known to reduce fitness at the individual level, which becomes reflected in reduced fitness of the population as a whole. Exactly how genetic defects contribute to premature deaths in the Southern Residents remains uncertain, but causes could involve losses in physical condition, metabolic function or disease-fighting capabilities.

Through careful genetic analysis and modeling, Kardos and his colleagues concluded that none of the fish-eating Southern Residents in the study were born of parents outside the three (J, K and L) pods, now totaling 73 animals. Those findings are consistent with observations of researchers who monitor the whales’ behaviors, even though the Southern Residents sometimes share the waters with fish-eating Northern Residents off Vancouver Island and frequently cross paths with transient (Biggs) killer whales, which prey upon marine mammals.

Based upon estimates of gene flow, it appears the Southern Residents have been genetically isolated for more than 20 generations, or roughly 500 years, according to a report of the study published today in the journal Nature Ecology & Evolution. It also appears that the most inbred individuals have been dying at a substantially younger age than less inbred whales.

For the most inbred females, the chances of living through their reproductive years (ending about age 40) is estimated to be 64 percent lower than the least inbred individuals, thus decreasing their reproductive potential by about 41 percent, according to the report. For males, the likelihood of living to age 40 is estimated to be 78 percent lower.

“These analyses probably underestimated the effects of inbreeding on mortality because we have no data on these effects in the earliest life stages (before or shortly after birth) when inbreeding depression is often strongest,” states the report.

Understanding the physical conditions of the Southern Residents, including pregnancies, has been advanced with the help of noninvasive drone photography, as in this photo of L pod taken in the San Juan Islands in November. Photo: Holly Fearnbach /John Durban of SR3 — SeaLife Response, Rehabilitation and Research — under NMFS permit #22306

Hormone studies of the whales, confirmed by aerial drone studies, have shown that only about a third of the Southern Resident pregnancies result in a live birth. Although early studies suggested that the miscarriages and post-natal mortalities could be directly linked to a shortage of Chinook salmon, those conclusions are being reconsidered, according to Eric Ward, also with NOAA’s Northwest Fisheries Science Center and another author of the new study.

Factors other than an abundance of salmon were suspected of having an effect on the population. Such factors might include foraging strategies, social behavior, noise, and disturbance from boats, as well as inbreeding effects and perhaps other unknown conditions. (See the 2021 study from researchers at the University of British Columbia.)

Even before the Southern Residents were placed on the federal Endangered Species List in 2005, the primary threats to the orcas were believed to be lack of food, toxic chemicals in their systems and human disturbance that could affect foraging and reproduction. Now the calculated effects of inbreeding must be considered more strongly than ever, according to Ward.

Previous estimates of recovery times for the Southern Resident orca population must be reevaluated with this new understanding about how genetic defects contribute to the increased death rate, Ward said. Some analyses have used traditional models of population dynamics with only environmental changes being considered.

In some places where terrestrial populations have been identified with high rates of inbreeding, wildlife managers have chosen to introduce animals of the same species from outside areas, according to Kardos. For example, so-called “genetic rescues” have been successful in helping genetically isolated populations of Florida panthers in 1995 (Science, 2010), bighorn sheep in 1985 (Proceedings, Royal Society 2006) and greater prairie chickens in 1992 (Science 1998).

Human intervention to improve the genetic condition of the Southern Residents is pretty much out of the question, according to Ward. The risks of capture and relocation or artificial insemination would be high with uncertainty of success. Disruption of the close-knit family structure of the orca communities would be a major concern.

One might hope for the remote chance that one or more Northern Resident males might mate with Southern Resident females, thus infusing new genes into the Southern Resident population. But the new genetic study shows that this has never happened among the 100 whales included in the genetic analysis.

The problem may be exacerbated by the limited number of males involved in producing offspring. The latest data show that among the 51 Southern Resident whales whose parents are identified, 44 came from one of two fathers. Some 23 offspring were sired by Ruffles (J1), whose birth is estimated in 1951. Another 21 were sired by Mega (L41), who was born in 1977. Ruffles died in 2010, and Mega died in 2020. Since then, considering the low birthrate among Southern Residents, it may be too early to say if one or more new males will dominate.

Similar studies of inbreeding among the Northern Resident orcas are being conducted by marine mammal biologists with Canada’s Department of Fisheries and Oceans. Scientists are eager to learn whether Northern Residents are as genetically isolated as Southern Residents or if they have maintained a greater genetic diversity, perhaps because of proximity to Alaska’s resident orca population.

Meanwhile, the new genetic study should not be taken as a prediction that the Southern Resident orcas are doomed to extinction, Kardos said. It does show that recovery may be more difficult for Southern Residents than for other killer whale populations and that greater recovery efforts may be needed to meet the challenge.

Genetic origins of inbreeding

Defective genes generally begin as a mutation occurring in a strand of DNA on one of the killer whale’s chromosomes. To code for each gene, an individual has two corresponding strands of DNA, one inherited from each parent. Most genetic defects are recessive, meaning that if the mutation occurs in one strand, the other strand can make up for the loss. This way, the gene coded by the piece of DNA can still function without impairment in the individual.

With inbreeding, two closely related parents may each contribute identical, defective strands of DNA to their offspring. Without a normal gene to compensate, the individual may lose whatever function is provided by that gene, whether physical, metabolic, immune or reproductive. The closer the relationship between the parents, the more defects are likely to be expressed in their offspring.

By sequencing the entire genome of each killer whale in the study, Kardos and his colleagues were able to measure how much each strand of DNA was alike and how much was different from its counterpart. When genes on both strands are the same, they are called homozygous; when different, they are called heterozygous. The more that the two strands are different, the less inbreeding is taking place, and this measure of “heterozygosity” can be compared among populations.

This new study involved comparing the genomes of the 100 Southern Residents to 24 Alaska Residents, 14 transients, seven offshore and two Northern Residents. The Southern Residents had the lowest heterozygosity of all the groups, and the transients had the highest. This is largely related to the size of the breeding population.

The study found a quantitative relationship between measurements of inbreeding and the probability of survival. It turns out that the least inbred animals in the Southern Resident population have an inbreeding rate typical of the Alaska Residents, which numbered about 700 among the groups included in the study. That population is believed to have more than doubled from 1984 to 2010.

Likewise, the Northern Resident population has more than doubled from an estimate of 122 in 1974 to 302 in 2018. Transients are estimated at 243 with a rapid growth period from the 1970s into the 1990s. The offshores, another distinct population, appears to comprise more than 300 animals with no identified growth trend.

From the genetic data, one can estimate an effective population size, which is somewhat akin to the breeding population and always lower than the census population. It appears that both the ancestral populations of Alaska Resident and Southern Resident orcas were much larger in the distant past before declining about 700 years ago, according to the study. Since then, the effective population of the Southern Residents ranged from about 61 to 76 — translated to roughly 200 living animals. It appears that genetic isolation took place about 20 generations ago — or roughly 500 years in the past.

With no improvement in environmental conditions, inbreeding depression can be expected to continue a population decline for the Southern Resident orcas,  as compared to projected population trends if the whales were not genetically impaired. Graph: Study in Nature Ecology & Evolution

Those numbers exclude recent decades when killer whales were sometimes shot with guns on sight and later captured for aquariums and marine parks. When the captures ended in 1976, the Southern Residents were counted during boat surveys and estimated to be 71, a number low enough to increase the likelihood of inbreeding as a result of human actions.

The new study developed numerous simulations of population growth over the next 100 years for the Southern Residents with and without inbreeding depression, assuming no change in today’s environmental conditions.  As shown in the graph on this page, continual inbreeding is projected to reduce the number of animals to very low levels within 100 years without an influx of new genes or else major changes to external conditions.

In addition to Kardos and Ward, researchers working on the study included geneticists Kim Parsons and Michael Ford and research biologists Brad Hanson and Candice Emmons, all with the Northwest Fisheries Science Center; and Craig Matkin, founder of Alaska’s North Gulf Oceanic Society. Genetic sequencing was conducted by scientists with BGI Group, a Chinese company specializing in genomics, with author credit going to Yaolei Zhang, Yunga A, Xun Xu, Xin Liu and Guangyi Fan. Two other Chinese authors, Hui Kang and Peijun Zhang, are affiliated with the Chinese Academy of Sciences.  

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