Reduced genetic diversity: another challenge facing the Southern Resident killer whales?

As charismatic mega-predators, killer whales have no equal. Historically feared, respected, in some cultures revered, we now know them to be intelligent and highly social. They also have  fascinatingly strong ideas about what constitutes food, with different populations having vastly different preferred prey. 

Not surprisingly, then, the plight of the critically endangered salmon-eating Southern Resident killer whales of southern British Columbia and northern Washington state has attracted great public attention in recent years. The birth of a new calf or the death of a Southern Resident is front page news in Vancouver, Victoria, and Seattle, and the US and Canadian governments have spent millions of dollars in the last few years on efforts to conserve the population and allow it to recover.

Recently-improved practices for shipping, fishing, discharging pollutants, whale watching and the protection of  salmon-spawning habitats have not yet led to an overall increase in Southern Resident numbers. That said, however, the population has held the line at  73-75 members for five years, after a decline from an already low 98 members in 1995. It  would have likely continued to decline without these efforts, but still it’s tempting to think that researchers (me included) have missed one or more factors that are holding it back. 

Enter the world of genetics. Twenty years ago we learned Southern Residents were inbred relative to other killer whale populations — their genetic diversity was low. This finding was an incidental part of my PhD research at the University of British Columbia, and it didn’t make a splash, or even a ripple, at the time. I’ve wondered ever since, however, if inbreeding depression–reduced fitness of the offspring of closely-related parents could be playing a role. 

An important new study published by Washington-based researchers suggests that this may indeed be the case. Dr. Marty Kardos and colleagues took advantage of incredibly powerful new DNA analysis technology to sequence the entire genomes of 100 Southern Residents and those of 47 other eastern Pacific killer whales. Their paper includes a much more comprehensive picture of patterns of genetic variation in the species than had existed before.

Firstly, the study confirmed that Southern Residents do indeed have low genetic diversity across their entire genome, as would be expected given their small population size.  Furthermore, their population size has likely been small for at least 30 generations. Fun genetic fact: deleterious mutations are more likely to be eliminated from small populations than large ones, and in fact Kardos’ team found that the Southern Residents had fewer potentially harmful mutations than a much larger population of Resident killer whales in Alaska. That said, of the mutations that remain in their population, Southern Residents are more likely to carry two copies —one from the mother and the other from the father—than the Alaskan whales. This means that despite having fewer deleterious mutations, they likely suffer greater inbreeding depression than their Alaskan counterparts.

The second part of the Kardos et al. paper presents direct evidence of inbreeding depression. Examining a 40 year record of births and deaths in the Southern Residents, the authors found a positive correlation between a genetic measure of inbreeding and the probability of mortality for members of the population. In plain speak, individuals with closely related parents had a higher chance of dying in any given period than individuals with less closely related parents. Unfortunately for the Southern Residents, all of its members are closely related. A model that  projects birth and death rates into the future paints a dire picture: inbreeding depression has made the population less resilient than it would otherwise be, and if conditions that have prevailed over the last 40 years continue, it is unlikely to persist for more than a half dozen generations.

Does this mean that the population is doomed? 

Not by any means. Two things could help the Southern Residents recover. First, conditions could improve, reducing the mortality risk for even inbred individuals. The data used to calculate mortality probabilities were collected during a time with high levels of ship and recreational vessel traffic, thousands of pollution sources, heavy fishing pressure, and when the population was reeling from the loss of many members caught for display in Oceanariums. In the face of this litany of impacts, the population has been remarkably resilient, inbreeding or not. The management and conservation measures I referred to above have, to at least some extent, reduced threats to the whales. Maintaining, improving, and adding to these measures is what we need to do for this population if it is to have any reasonable chance of surviving.  

The second thing that could help is called genetic rescue, which occurs when unrelated individuals from other populations join and breed with a small inbred population. Research in the last two decades has shown that this can and often does significantly reduce inbreeding depression, even when immigration rates are very low. Previous genetic studies suggest that there has been very little if any gene flow into the population in the last few decades. But the Kardos et al. study does not rule out occasional immigration in the past, and it is at least possible that, given enough time, one or more immigration events will assist the population’s recovery.  The fact that the range of Northern Resident population overlaps part of that of the Southern Residents makes this more likely.  

Take home message

Researchers, marine wildlife managers, and the interested general public have known for many years that the Southern Resident killer whales are culturally and genetically unique. We know that as predators near the top of the food chain they are both ecologically important and serve as sentinels of ecosystem health. They are culturally important for First Nations and iconic for millions of others in British Columbia and Washington. They are worth saving.

The important message from this new genetics study is that the Southern Residents are more vulnerable than other killer whale populations, and saving them will be even more challenging.  This means that we need to redouble our efforts to reduce known threats. We need to build and expand recent efforts to reduce underwater noise and direct disturbance by vessels. We need to  make every effort to ensure that they have adequate prey, i.e Chinook and chum salmon, and that those prey are in turn healthy and contaminant free. We need to learn from species recovery success stories; populations that have declined to sufficiently low numbers to reduce genetic diversity and still recovered. Species in this category include sea otters, northern elephant seals and Eurasian beavers.

Finally,  we need to keep studying the species,as non-invasively as possible, to identify additional threats so that they can be mitigated as quickly as possible.  If we do all these things there is a fighting chance that our great grandchildren will, like us, have the privilege of  sharing the world with Southern Resident killer whales. 

You can help

Raincoast’s in-house scientists, collaborating graduate students, postdoctoral fellows, and professors make us unique among conservation groups. We work with First Nations, academic institutions, government, and other NGOs to build support and inform decisions that protect aquatic and terrestrial ecosystems, and the wildlife that depend on them. We conduct ethically applied, process-oriented, and hypothesis-driven research that has immediate and relevant utility for conservation deliberations and the collective body of scientific knowledge.

We investigate to understand coastal species and processes. We inform by bringing science to decision-makers and communities. We inspire action to protect wildlife and wildlife habitats.