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Dive In with NOAA Fisheries
NOAA Fisheries conducts world-class science to support sustainable marine life and habitats. We manage millions of square miles of ocean (almost 100,000 miles of coastline), support a $244 billion fishing industry, and protect and rebuild endangered marine species and habitats. It’s a huge job. Our podcast is about the work we do and the people behind it.
Join our host, John Sheehan, for new episodes every other Thursday.
Transcripts available at https://www.fisheries.noaa.gov/podcast/dive-in-with-noaa-fisheries
Podcast Transcript
0:00:00.4 John Sheehan: On the West Coast, particularly in the waters of Puget Sound and the Salish Sea, killer whales, or orcas, are iconic and beloved.
0:00:09.1 S?: Majestic moments like this pod swimming at the surface in West Seattle.
0:00:13.0 S?: A super pod orca sighting, today's group even delayed ferries between Seattle and Vashon Island.
0:00:18.1 S?: They've just been a magical thing ever since I was a kid.
0:00:22.8 JS: But a small population of them, the southern resident killer whales, are endangered and despite conservation efforts have so far failed to recover.
0:00:31.1 Mike Ford: From the mid-1960s up through the '70s, this population was particularly hard hit by captures for the aquaria trade. They were protected, like all marine mammals, by the Marine Mammal Protection Act and did actually start to recover. So by the mid-1990s, there were almost 100. And then since then, they've kind of started to decline again and now we're back to about 73.
0:00:52.6 JS: Now, a new study, one that combines cutting edge gene sequencing techniques and traditional field work, is giving scientists a clearer picture of the challenges facing the southern residents. This is Dive In With NOAA Fisheries. I'm John Sheehan, and today I'm speaking with a senior author of the study, Dr. Mike Ford, a senior scientist at the Northwest Fisheries Science Center.
0:01:14.1 MF: This is one of the very first times that we've collected whole genome sequence data from nearly every member of an endangered population.
0:01:21.9 JS: Before we talk about this new analysis and its conclusions, let's remind ourselves a little bit about the southern residents, which have been listed as endangered since 2005, thought to be largely due to things like reduced prey and toxins in their environment.
0:01:36.3 MF: So if you go back to the time that they were listed and then the publication of their recovery plan, the primary factors that were identified were some of the ones you mentioned: Disturbance, they partially live in a fairly urban environment where there's a lot of both large and small boat traffic; contaminants, there's been numerous studies that show that killer whales in general and the southern residents in particular are quite contaminated with both legacy contaminants from decades ago and also more recent toxins; and the lack of prey. They specialize on salmon and, of course, the Pacific northwest salmon themselves are listed as threatened or endangered or many populations are under the Endangered Species Act. And so that's been another potential problem for the whales.
0:02:22.2 JS: Yeah. And that's what brings us to the study, which introduces another wrinkle into the story of southern resident killer whales. Can you give us an overview of what the study is, what it was looking at?
0:02:36.0 MF: We were interested in evaluating the effects of inbreeding in the population. Inbreeding is just the mating of close relatives. And this has been known to be a potential problem for the population going all the way back to the time that they were listed in the early 2000s. Not surprisingly, because there's not very many whales. Of those 70-some odd whales, only about a quarter of them are of breeding age and it's therefore not surprising that you could have some interbreeding between relatives. And so we have tried to look at that over the years but it's a tricky problem to study. And what this recent study did was use more modern technology, basically the sequencing of the entire genome of every whale that we had a sample for, to look at the degree of inbreeding of each whale in the population. And then we can ask, Is there any relationship between how inbred an animal is and how long it survives and, basically, how well it's doing? And what we found is that there is that kind of relationship, that the more inbred an animal is, the less likely it is to survive for a long period of time.
0:03:47.3 JS: And before we get to the results of the degree of inbreeding, can we talk about what does it mean to sequence a genome?
0:03:54.9 MF: Sure. So all of us, humans, killer whales, dogs, cats, have a genome, which is our genetic material. It's what we inherit from our parents, and it's the code that helps the developing animal develop into what it's supposed to be. And you get half of your genome from your dad and half of your genome from your mom. And it consists of a series of chemicals which we use shorthand, the letters A, G, C, T. In the case of mammals, there is a couple billion of these letters in the genome. And so to sequence the whole genome means to go in and look at that sequence of a couple billion letters for an individual animal.
0:04:39.4 JS: And so the results indicated that in the case of the southern resident killer whales, there is a lot of inbreeding.
0:04:47.8 MF: Yeah. So, as I mentioned, when you get half of your genome from your dad and half of your genome from your mom, if your mom and your dad are unrelated then the odds are that you're gonna have a lot of variability between those two halves of the genome. If it happens to be the case, however, that your mom and your dad are closely related, then their own genomes are gonna be very similar to each other. And so you can think of this like in the extreme case of, say, identical twins. They have identical genomes. And if you are siblings, your genomes are expected to also be quite similar. So in the case of a small population like the southern resident killer whales, when you have relatives that are mating together, you can end up with individuals that have genomes that are less variable than you would if the parents were all unrelated. And that's what we see in the case of the southern resident killer whales. And we had the opportunity in the study to also look at some other killer whale populations around the Northeast Pacific, and of those groups the southern residents were the least variable and the most inbred of these Northeast Pacific killer whale populations.
0:05:53.9 JS: And I think we all know, beyond anthropomorphizing, it's really not good to have no genetic variation in a population. That's just not a sustainable trait.
0:06:07.4 MF: Yeah, it's bad for a couple of reasons. Genetic variation, in the very long term, is critical for evolution. It's what kind of keeps the species going. In the short term, it's also a problem because most individuals carry what we would call a deleterious variation in their genome, so these would be mutations in the genome that lead to some problem, some metabolic problem or physical problem. And we all carry these. You and I carry them, animals carry them. And for the most part, it's not too big a deal because you do get one copy from your dad, one copy from your mom. And as long as you have one good copy, everything is good. But when mom and dad are closely related, then the odds of getting two deleterious variants together or two bad copies of a gene together go up and that can lead to reduced survival, and that's what we're seeing in the case of the southern resident killer whales.
0:07:02.1 JS: And you've modeled their chances of survival. And what does that look like?
0:07:07.9 MF: Within the population, we see a range of inbreeding. So we have some individuals who are highly inbred and other individuals who are not. And one huge advantage of working with the southern resident killer whale population, and a really important reason why this is a useful study, is that we have detailed histories of every individual in the population. So we know when an individual was born and we know when they died. And this was due to pioneering work by folks like the late Ken Balcomb and other early researchers who have really studied these populations for decades.
0:07:42.1 MF: So because we have that really detailed information, we can ask, Did an individual who is more inbred, did they survive as long as an individual who is less inbred? And we can do that for lots of whales for most of the population. And what we found is that for those individuals that are highly inbred, they tend to not live as long as individuals who are less inbred. And if you take all that information and put it into a population model and ask what's gonna happen to the population in the future, we predict that with the current level of inbreeding the population will continue to decline in the future. If you kind of do the thought experiment and say what if every individual was like the least inbred individuals and had the survival rates of the least inbred individuals, then the model would predict that the population would grow. So we used this kind of result to conclude that inbreeding is a pretty big problem and is one of the reasons why the population is declining.
0:08:42.1 JS: So what are the implications for conservation actions? What does this mean? What does this study mean for next steps?
0:08:50.6 MF: Yeah. I think our results are not great news for the recovery of the southern residents. We have found one more problem that they're facing and this problem of inbreeding is one that may be difficult to directly address in management actions. So in that sense, it's not great news. It does kinda confirm some things that we already knew. Most recent analyses of the southern resident population have predicted that they will continue to decline, we just didn't really know why. And this study helps us understand the why a little bit better. I think it would be a mistake to think that our study suggests that we shouldn't be protecting them. It sort of reinforces that they are in quite a bit of trouble. On the other hand, I think that there is still some potential for optimism. The predicted decline is expected to occur over a pretty long period of time, decades to maybe even more than a century, and a lot can happen in 100 years, right? If you think about what's happened in the last 100 years, the world is a radically different place. And so even though we predict this future decline, there's some inherent uncertainty in what we think will happen in the future and there are some things that could happen that would help the population.
0:10:09.4 MF: For example, a little bit of interbreeding with other killer whale populations would probably help reduce the problems of inbreeding a lot. And even though we haven't observed that happening in the past, it's certainly possible that it could happen in the future. They overlap with other populations, particularly the northern resident killer whale population that's doing quite well, and it's not impossible that there could be some interbreeding with that population. It's also important to realize that we did all this modeling under what I would call typical environmental conditions, basically the way the environment's been for the last 50 years or so. It's not impossible that you could imagine improving the environment such that maybe the whales would do better. Of course, there are other reasons to expect that maybe the environment will not improve, climate change and so forth, but I think we have to recognize that we don't really know what's gonna happen in the future.
0:11:01.1 JS: Yeah. I think climate change is a great example of the inherent unpredictability of what we can say in the near term.
0:11:09.0 MF: Yeah, I think that's right. It's a little bit like the stock market. You can build a great model that explains the way the stock market behaved but past returns don't predict future returns. And so some of our predictions are inherently uncertain. But that being said, I think we do need to recognize that we have identified a problem for the population and I don't wanna sugarcoat that.
0:11:32.9 JS: But at the same time, and this is something that you and your colleagues have said, that while the implications aren't great for this population, the study was rather ground-breaking and a significant step forward for science. It was a great study.
0:11:51.5 MF: Yeah, no. It is a really exciting study. This is one of the very first times that we've collected whole genome sequence data from nearly every member of an endangered population and we've been able to combine it with these decades of really high quality field work done by our partners and the combination of the modern genetic science with old-fashioned careful dedicated field work is what allows us to make these fairly strong conclusions about the effects of inbreeding in the population. So in that respect, I think it is a really important study and I think it has implications beyond the southern residents. It shows that inbreeding can be a real problem in these small isolated populations and it's a little bit of a warning not to let things get to this state, that it's better to conserve populations when they're large and healthy than to try to recover them when they're small and struggling.
0:12:50.4 JS: And what I really like about... Or what I find so interesting about the results is that it does take these years, decades-long data sets and puts them through the filter of new technologies, and it seems like that has big implications for a lot of NOAA Fisheries work. A lot of the science centers have extremely long data sets that can be utilized in new ways.
0:13:15.9 MF: Yeah, I think that's a really great point. The Fisheries Service and Fish and Wildlife Service and others who do these really long-term monitoring projects, that's a really important service to the nation and to our understanding of the natural world. And you can learn things by studying a population for 50 years that you simply can't in a short couple of years' study.
0:13:37.7 JS: Is it right that Canada is in the process of trying to repeat this process for northern resident killer whales?
0:13:43.4 MF: Yeah, that's correct. So the northern residents are another group of fish-eating, salmon-eating killer whales that have an overlapping range with the southern residents but kind of extend further to the north into Canada. They've been studied for just as long as the southern residents so they have similar detailed field observations going back to the 1970s. It's a much larger population, over 300 whales, and it's one of these populations that's generally grown fairly strongly since the '70s, so it's gonna be a great comparison with our study. The Canadian Department of Fisheries and Oceans has obtained whole genome sequence data from, I think, nearly 150, maybe a little more, northern resident killer whales and it'll be an opportunity to basically repeat the experiment with a healthy population or a healthier population. And I expect we'll learn a great deal from that.
0:14:35.9 JS: And something you just touched on, I think a study's importance is also when it confirms something. That's as important as understanding the threats. You've answered a question with this study.
0:14:49.6 MF: Yeah, no. I think I feel really good about that. I think one of the hard parts about studying natural wild populations and especially something like a whale that's swimming around, not necessarily easy to observe and monitor, is that it's inherently difficult to understand what's driving their population increases and decreases. And one of the nice things about this study is that I do feel like we have come to a fairly strong conclusion that this particular factor, inbreeding depression, is clearly a problem for the population. And, yeah, it's useful and nice to understand that in that level of detail.
0:15:40.9 JS: Dr. Mike Ford, thanks so much.
0:15:42.5 MF: Yeah, of course, it's been a pleasure talking to you.
0:15:45.0 JS: Dr. Mike Ford is a senior research scientist at the Northwest Fisheries Science Center and senior author of the new analysis of the recently sequenced genome of the southern resident killer whales. The study is published in the journal, Nature Ecology and Evolution. To keep up with the latest about endangered species or regional news stories like this one, sign up for one of our newsletters at fisheries.noaa.gov. I'm John Sheehan and this has been Dive In with NOAA Fisheries.
0:00:09.1 S?: Majestic moments like this pod swimming at the surface in West Seattle.
0:00:13.0 S?: A super pod orca sighting, today's group even delayed ferries between Seattle and Vashon Island.
0:00:18.1 S?: They've just been a magical thing ever since I was a kid.
0:00:22.8 JS: But a small population of them, the southern resident killer whales, are endangered and despite conservation efforts have so far failed to recover.
0:00:31.1 Mike Ford: From the mid-1960s up through the '70s, this population was particularly hard hit by captures for the aquaria trade. They were protected, like all marine mammals, by the Marine Mammal Protection Act and did actually start to recover. So by the mid-1990s, there were almost 100. And then since then, they've kind of started to decline again and now we're back to about 73.
0:00:52.6 JS: Now, a new study, one that combines cutting edge gene sequencing techniques and traditional field work, is giving scientists a clearer picture of the challenges facing the southern residents. This is Dive In With NOAA Fisheries. I'm John Sheehan, and today I'm speaking with a senior author of the study, Dr. Mike Ford, a senior scientist at the Northwest Fisheries Science Center.
0:01:14.1 MF: This is one of the very first times that we've collected whole genome sequence data from nearly every member of an endangered population.
0:01:21.9 JS: Before we talk about this new analysis and its conclusions, let's remind ourselves a little bit about the southern residents, which have been listed as endangered since 2005, thought to be largely due to things like reduced prey and toxins in their environment.
0:01:36.3 MF: So if you go back to the time that they were listed and then the publication of their recovery plan, the primary factors that were identified were some of the ones you mentioned: Disturbance, they partially live in a fairly urban environment where there's a lot of both large and small boat traffic; contaminants, there's been numerous studies that show that killer whales in general and the southern residents in particular are quite contaminated with both legacy contaminants from decades ago and also more recent toxins; and the lack of prey. They specialize on salmon and, of course, the Pacific northwest salmon themselves are listed as threatened or endangered or many populations are under the Endangered Species Act. And so that's been another potential problem for the whales.
0:02:22.2 JS: Yeah. And that's what brings us to the study, which introduces another wrinkle into the story of southern resident killer whales. Can you give us an overview of what the study is, what it was looking at?
0:02:36.0 MF: We were interested in evaluating the effects of inbreeding in the population. Inbreeding is just the mating of close relatives. And this has been known to be a potential problem for the population going all the way back to the time that they were listed in the early 2000s. Not surprisingly, because there's not very many whales. Of those 70-some odd whales, only about a quarter of them are of breeding age and it's therefore not surprising that you could have some interbreeding between relatives. And so we have tried to look at that over the years but it's a tricky problem to study. And what this recent study did was use more modern technology, basically the sequencing of the entire genome of every whale that we had a sample for, to look at the degree of inbreeding of each whale in the population. And then we can ask, Is there any relationship between how inbred an animal is and how long it survives and, basically, how well it's doing? And what we found is that there is that kind of relationship, that the more inbred an animal is, the less likely it is to survive for a long period of time.
0:03:47.3 JS: And before we get to the results of the degree of inbreeding, can we talk about what does it mean to sequence a genome?
0:03:54.9 MF: Sure. So all of us, humans, killer whales, dogs, cats, have a genome, which is our genetic material. It's what we inherit from our parents, and it's the code that helps the developing animal develop into what it's supposed to be. And you get half of your genome from your dad and half of your genome from your mom. And it consists of a series of chemicals which we use shorthand, the letters A, G, C, T. In the case of mammals, there is a couple billion of these letters in the genome. And so to sequence the whole genome means to go in and look at that sequence of a couple billion letters for an individual animal.
0:04:39.4 JS: And so the results indicated that in the case of the southern resident killer whales, there is a lot of inbreeding.
0:04:47.8 MF: Yeah. So, as I mentioned, when you get half of your genome from your dad and half of your genome from your mom, if your mom and your dad are unrelated then the odds are that you're gonna have a lot of variability between those two halves of the genome. If it happens to be the case, however, that your mom and your dad are closely related, then their own genomes are gonna be very similar to each other. And so you can think of this like in the extreme case of, say, identical twins. They have identical genomes. And if you are siblings, your genomes are expected to also be quite similar. So in the case of a small population like the southern resident killer whales, when you have relatives that are mating together, you can end up with individuals that have genomes that are less variable than you would if the parents were all unrelated. And that's what we see in the case of the southern resident killer whales. And we had the opportunity in the study to also look at some other killer whale populations around the Northeast Pacific, and of those groups the southern residents were the least variable and the most inbred of these Northeast Pacific killer whale populations.
0:05:53.9 JS: And I think we all know, beyond anthropomorphizing, it's really not good to have no genetic variation in a population. That's just not a sustainable trait.
0:06:07.4 MF: Yeah, it's bad for a couple of reasons. Genetic variation, in the very long term, is critical for evolution. It's what kind of keeps the species going. In the short term, it's also a problem because most individuals carry what we would call a deleterious variation in their genome, so these would be mutations in the genome that lead to some problem, some metabolic problem or physical problem. And we all carry these. You and I carry them, animals carry them. And for the most part, it's not too big a deal because you do get one copy from your dad, one copy from your mom. And as long as you have one good copy, everything is good. But when mom and dad are closely related, then the odds of getting two deleterious variants together or two bad copies of a gene together go up and that can lead to reduced survival, and that's what we're seeing in the case of the southern resident killer whales.
0:07:02.1 JS: And you've modeled their chances of survival. And what does that look like?
0:07:07.9 MF: Within the population, we see a range of inbreeding. So we have some individuals who are highly inbred and other individuals who are not. And one huge advantage of working with the southern resident killer whale population, and a really important reason why this is a useful study, is that we have detailed histories of every individual in the population. So we know when an individual was born and we know when they died. And this was due to pioneering work by folks like the late Ken Balcomb and other early researchers who have really studied these populations for decades.
0:07:42.1 MF: So because we have that really detailed information, we can ask, Did an individual who is more inbred, did they survive as long as an individual who is less inbred? And we can do that for lots of whales for most of the population. And what we found is that for those individuals that are highly inbred, they tend to not live as long as individuals who are less inbred. And if you take all that information and put it into a population model and ask what's gonna happen to the population in the future, we predict that with the current level of inbreeding the population will continue to decline in the future. If you kind of do the thought experiment and say what if every individual was like the least inbred individuals and had the survival rates of the least inbred individuals, then the model would predict that the population would grow. So we used this kind of result to conclude that inbreeding is a pretty big problem and is one of the reasons why the population is declining.
0:08:42.1 JS: So what are the implications for conservation actions? What does this mean? What does this study mean for next steps?
0:08:50.6 MF: Yeah. I think our results are not great news for the recovery of the southern residents. We have found one more problem that they're facing and this problem of inbreeding is one that may be difficult to directly address in management actions. So in that sense, it's not great news. It does kinda confirm some things that we already knew. Most recent analyses of the southern resident population have predicted that they will continue to decline, we just didn't really know why. And this study helps us understand the why a little bit better. I think it would be a mistake to think that our study suggests that we shouldn't be protecting them. It sort of reinforces that they are in quite a bit of trouble. On the other hand, I think that there is still some potential for optimism. The predicted decline is expected to occur over a pretty long period of time, decades to maybe even more than a century, and a lot can happen in 100 years, right? If you think about what's happened in the last 100 years, the world is a radically different place. And so even though we predict this future decline, there's some inherent uncertainty in what we think will happen in the future and there are some things that could happen that would help the population.
0:10:09.4 MF: For example, a little bit of interbreeding with other killer whale populations would probably help reduce the problems of inbreeding a lot. And even though we haven't observed that happening in the past, it's certainly possible that it could happen in the future. They overlap with other populations, particularly the northern resident killer whale population that's doing quite well, and it's not impossible that there could be some interbreeding with that population. It's also important to realize that we did all this modeling under what I would call typical environmental conditions, basically the way the environment's been for the last 50 years or so. It's not impossible that you could imagine improving the environment such that maybe the whales would do better. Of course, there are other reasons to expect that maybe the environment will not improve, climate change and so forth, but I think we have to recognize that we don't really know what's gonna happen in the future.
0:11:01.1 JS: Yeah. I think climate change is a great example of the inherent unpredictability of what we can say in the near term.
0:11:09.0 MF: Yeah, I think that's right. It's a little bit like the stock market. You can build a great model that explains the way the stock market behaved but past returns don't predict future returns. And so some of our predictions are inherently uncertain. But that being said, I think we do need to recognize that we have identified a problem for the population and I don't wanna sugarcoat that.
0:11:32.9 JS: But at the same time, and this is something that you and your colleagues have said, that while the implications aren't great for this population, the study was rather ground-breaking and a significant step forward for science. It was a great study.
0:11:51.5 MF: Yeah, no. It is a really exciting study. This is one of the very first times that we've collected whole genome sequence data from nearly every member of an endangered population and we've been able to combine it with these decades of really high quality field work done by our partners and the combination of the modern genetic science with old-fashioned careful dedicated field work is what allows us to make these fairly strong conclusions about the effects of inbreeding in the population. So in that respect, I think it is a really important study and I think it has implications beyond the southern residents. It shows that inbreeding can be a real problem in these small isolated populations and it's a little bit of a warning not to let things get to this state, that it's better to conserve populations when they're large and healthy than to try to recover them when they're small and struggling.
0:12:50.4 JS: And what I really like about... Or what I find so interesting about the results is that it does take these years, decades-long data sets and puts them through the filter of new technologies, and it seems like that has big implications for a lot of NOAA Fisheries work. A lot of the science centers have extremely long data sets that can be utilized in new ways.
0:13:15.9 MF: Yeah, I think that's a really great point. The Fisheries Service and Fish and Wildlife Service and others who do these really long-term monitoring projects, that's a really important service to the nation and to our understanding of the natural world. And you can learn things by studying a population for 50 years that you simply can't in a short couple of years' study.
0:13:37.7 JS: Is it right that Canada is in the process of trying to repeat this process for northern resident killer whales?
0:13:43.4 MF: Yeah, that's correct. So the northern residents are another group of fish-eating, salmon-eating killer whales that have an overlapping range with the southern residents but kind of extend further to the north into Canada. They've been studied for just as long as the southern residents so they have similar detailed field observations going back to the 1970s. It's a much larger population, over 300 whales, and it's one of these populations that's generally grown fairly strongly since the '70s, so it's gonna be a great comparison with our study. The Canadian Department of Fisheries and Oceans has obtained whole genome sequence data from, I think, nearly 150, maybe a little more, northern resident killer whales and it'll be an opportunity to basically repeat the experiment with a healthy population or a healthier population. And I expect we'll learn a great deal from that.
0:14:35.9 JS: And something you just touched on, I think a study's importance is also when it confirms something. That's as important as understanding the threats. You've answered a question with this study.
0:14:49.6 MF: Yeah, no. I think I feel really good about that. I think one of the hard parts about studying natural wild populations and especially something like a whale that's swimming around, not necessarily easy to observe and monitor, is that it's inherently difficult to understand what's driving their population increases and decreases. And one of the nice things about this study is that I do feel like we have come to a fairly strong conclusion that this particular factor, inbreeding depression, is clearly a problem for the population. And, yeah, it's useful and nice to understand that in that level of detail.
0:15:40.9 JS: Dr. Mike Ford, thanks so much.
0:15:42.5 MF: Yeah, of course, it's been a pleasure talking to you.
0:15:45.0 JS: Dr. Mike Ford is a senior research scientist at the Northwest Fisheries Science Center and senior author of the new analysis of the recently sequenced genome of the southern resident killer whales. The study is published in the journal, Nature Ecology and Evolution. To keep up with the latest about endangered species or regional news stories like this one, sign up for one of our newsletters at fisheries.noaa.gov. I'm John Sheehan and this has been Dive In with NOAA Fisheries.
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New genome sequencing reveals the reason behind Southern Resident killer whales' failure to thrive.
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