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March 10, 2022 — Show notes: Dr. Kelly Diehl talks with Dr. Aryn Wilder of the San Diego Zoo Wildlife Alliance about her work with the Pacific pocket mouse. Although the species is recovering, Dr. Wilder discusses some of the challenges that come with saving a species when only a few individuals are left.


0:00:05.3 Kelly Diehl: Welcome to Fresh Scoop, Episode 42. What happens when a species has only a few animals left? I'm your host, Dr. Kelly Diehl, Morris Animal Foundation, Senior Director of Science and Communication. And today we'll talk to Dr. Aryn Wilder. Dr. Wilder is a senior researcher in conservation genetics at the San Diego Zoo Wildlife Alliance. Welcome, Aryn.

0:00:28.0 Aryn Wilder: Thank you.

0:00:30.7 KD: Before we get started, I always ask everyone to tell us a little bit about yourself, and then what led you to study wildlife genetics.

0:00:38.5 AW: Yeah. So, I've always been passionate about the natural world and about conservation and how we can sort of conserve the natural world as we have it. And I actually started out in my graduate studies studying disease ecology, and so how diseases move around and spread in wildlife. And in that context, the spread of disease, it's really useful to know how organisms are moving about the landscape and how different populations are connected with one another. And so, I got into genetics as a tool to understand how species were moving across the landscape. And the more and more I learned about genetics, the more I realized that it's a huge source of information on how species work, and different ways to understand that species, its life history, its natural history, as well as how best to conserve it. And so, I was often running as a geneticist at that point.

0:01:58.2 KD: Sounds great. I wanted to start to talk a little bit about your foundation-funded study, because I know you've worked with lots of different species. And for everyone listening, I will post some links in our show notes because Aryn works with the Pacific pocket mouse, which is adorable. It looks like a gerbil, but it's not a gerbil. So, tell us more about what exactly is this Pacific pocket mouse and what happened to make it become endangered?

0:02:31.1 AW: Yeah, so Pacific pocket mice are actually really interesting and unique and charismatic species, I think a lot more than their name would suggest. [chuckle] So, they're actually a Heteromyidae rodent, which means they're part of the family Heteromyidae, and that family includes pocket mice and kangaroo rats, and they're actually really distinct from mice and rats, like the house mice that you might see in your barn or, hopefully not in your kitchen, but they're actually... Heteromyidae are actually more closely related to beavers than they are to house mice and rats. So, they're a really unique group. And most Heteromyidae live in deserts and grasslands of Western North America. But the Pacific pocket mouse is a coastal species, so it's uniquely adapted and found only in the coastal sage scrub habitat of Southern California. So, it's only found within six kilometers of the coast. It's really uniquely adapted to the sandy soils found there. So, it historically ranged from as far north as Los Angeles in Southern California, down to the Mexican border, and it was known in a number of locations across that coastal range before the 1930s. But like so many species, it really suffered from the impacts of habitat loss, and after large-scale coastal development began in the 1930s in Southern California, it disappeared in the following decades and was actually thought to be extinct for several decades.

0:04:22.1 KD: And then... Yeah. So anyway, developers versus Pacific pocket mouse. They have the prime real estate.

0:04:31.6 AW: Exactly.

0:04:31.7 KD: Unfortunately... So, tell the story, because this is really interesting because obviously they weren't extinct. What happened... How did people find these? And how did... What did the San Diego Zoo Wildlife Alliance research team...? What did you guys do to save it?

0:04:51.6 AW: Yeah, so after a few decades where it was thought to be extinct, it was re-discovered in 1992 in Dana Point in this tiny peninsula of land, and then once it was re-discovered there, then there was a much larger effort to survey for it in that region. And the following year, it was discovered in three other locations in San Diego County. And unfortunately, it has since disappeared from one of those locations. So, it now persists in these three small, isolated populations in Dana Point, so that's in Orange County, and then two populations in San Diego County on Camp Pendleton. And in 1993, it was emergency listed under the US Endangered Species Act. So, after that, continued declines prompted the establishment of a captive breeding program at the San Diego Zoo, and the purpose of the breeding program was to serve as an insurance population against extinction, but also to provide a source of individuals for reintroduction into unoccupied parts of their historic range, so places where they used to exist, but they're no longer found. And so, the reintroduction of new populations was part of the overall recovery strategy for that species. So, the conservation breeding program was really supposed to be the source of that and has been the source of that.

0:06:34.7 KD: Right. And you bring up an interesting point, Aryn, when you first were telling the story, which is that even though they were found and protected, they still were struggling. Correct?

0:06:48.2 AW: Yeah, exactly. They're definitely struggling from continued encroachment and habitat loss and habitat shifts. But there are also genetic components to the survival and persistence of a species once it becomes really small and rare.

0:07:13.1 KD: Right. And for everyone listening, this is really... We're getting to the meat of part of why I wanted Aryn to come on today. Because I think a lot of us go, "Hurray! Look, we've found this species, and they're not extinct, and good for us." But there are other problems, that's not the solution, is, "Okay, we'll just try to protect them." And so, Aryn, talk a little bit about the problems, specifically genetic problems, that arise when you only have a few individuals remaining in a group of animals.

0:07:47.8 AW: Yeah. So, there are a number of problems that arise. So small populations... First and foremost, I think small populations tend to lose genetic diversity. And the smaller the population, the more quickly they lose the unique genetic diversity that they harbor. And genetic diversity is really the source of adaptive innovation for a species, and it's the arsenal that the species has to help it respond to future environmental changes, so things like new diseases that emerge and climate change. And there's lots of evidence for a strong link between genetic diversity and survival of individuals, so how fit an individual is, as well as the risk of extinction of a population or species. And importantly, once genetic diversity is lost, so in a short bottleneck or a short decline in populations just for a few years, can lead to the loss of genetic diversity that then can take thousands of years to be restored.

0:09:02.9 AW: And then secondly, small populations also tend to accumulate harmful mutations in the genome, and those harmful mutations are... The sum total of harmful mutations in the genome is called genetic load. And all species carry harmful mutations in the genome, and these harmful mutations are constantly arising at random. But natural selection acts to weed out those mutations and keep them rare in the population so that they're often masked in a state where there's another copy of... Another good copy of that gene that can sort of rescue that mutation. And the problem is natural selection doesn't operate very well when populations are small, and the result is that there's this overall decrease in survival and reproduction across individuals of that population, and that's called inbreeding depression.

0:10:07.4 KD: And I think we can see that in a bigger population. I think a lot of folks know we're doing the Golden Retriever Lifetime Study. And we did... One of the papers that spun out early was on inbreeding depression. And that's a big population, goldens are popular. So, I can imagine when you're dealing with a really tiny population that doesn't have the ability to select mates very well, right? I mean, I think that's part of it. And so that's really interesting. The other thing, Aryn, I think you reminded me that I tend to forget, maybe other people do, or maybe they don't, is that evolution continues. I think we go to the museum, and we see, "Look, here's what a horse looks like now," and we forget it's still going on even now. It's not like we're like, "Ta da!" we're done, and that when you have these small populations, that doesn't happen.

0:11:06.1 AW: Absolutely. And especially now, we're in a period of really rapid environmental changes because of climate change, because we're moving diseases around the globe, and actually we're putting a lot of additional pressure on species to change really quickly, and small populations have a much harder time of doing that.

0:11:31.4 KD: Okay. And actually, Aryn and I talked a little bit about this before we jumped on today, which is the term bottleneck, which Aryn has brought up. And I think a lot of us hear that term. But just for everyone so we're all on the same page, can you define what a bottleneck actually is?

0:11:51.3 AW: Yeah. Yeah, as you mentioned, bottlenecks are a term that you hear a lot when it comes to endangered species. And bottleneck is just when a population substantially decreases in size for a period of time. That's referred to as a bottleneck, because if you were to sort of draw a picture of that population over time, it would sort of look like a bottleneck. And the longer the bottleneck lasts and the smaller the population becomes during the bottleneck, the more genetic diversity is lost from the population. And even if the number of individuals in that population increases so you're able to increase the total number of individuals in the population, the genetic diversity doesn't increase right away, and it can actually take thousands of years for that genetic diversity to recover.

0:12:48.1 KD: Right. We're going to circle back to your foundation study, because I think discussing a little bit about your methodology with the Pacific pocket mouse can maybe help people understand what you're trying to do to address this. So, again, kind of walk us through what you're doing.

0:13:09.2 AW: Yeah, so one way that we can restore genetic diversity that's been lost from a population is to introduce migrants from outside populations that actually carry unique genetic diversity. So, this helps to both restore the genetic diversity that has been lost, and then also can help mask those harmful mutations in a recessive state. And this strategy is called genetic rescue. So, the genetic rescue can ameliorate inbreeding depression, but it also poses potential risks. And those risks are mainly outbreeding depression. And so outbreeding depression is a decrease in survival and reproduction as a result of the introduction of new genetic diversity from an outside population. And it's been studied for a number of years. Yeah, so there are potential risks of genetic rescue. And those risks are higher when the donor population, so the source of migrants, is very distinct from the receiver population or the population that you're trying to rescue. So, the longer they've been diverging and the longer they've been isolated, the more likely you are to have some sort of incompatibility when you interbreed them. And also, if there are differences in the number of chromosomes, so you can end up with these reproductive incompatibilities or genetic incompatibilities.

0:14:50.8 AW: So, our study in Pacific pocket mice aims to examine the risks of a genetic rescue strategy for the species by looking at fitness of Pacific pocket mice in the conservation breeding program. So, the breeding program, the conservation breeding program started from about 10 to 15 founders from each of the wild populations. So, 10 to 15 founders from each population were brought into the San Diego Zoo and allowed to interbreed for the next 10 years. And in the next 10 years, actually, there was a huge growth in the population of the breeding program. And as I mentioned before, it provided the source for reintroductions back into the wild. But it also provides a source of information that we can use on fitness of individuals with different genetic backgrounds. So, Pocket mice that are pure, single population ancestry compared to pocket mice that have multiple ancestries, so our crosses between different wild populations. And so, we can use this information to measure the effects of inbreeding depression versus outbreeding depression and explore its genomic underpinnings. So, what mechanisms actually might be controlling inbreeding and outbreeding depression. And this can help us to design optimal management strategies for the wild populations.

0:16:37.6 AW: So, what we've done is we've now sequenced the genomes of hundreds of pocket mice from both the conservation breeding program and the wild populations. And we've measured things like genetic diversity in the genome, levels of inbreeding. We've looked at the number of harmful mutations in the genomes, as well as chromosomal differences across individuals and how each of those genetic factors correlates with reproductive success in the breeding program.

0:17:14.4 KD: Okay, and what did you find? And did anything surprise you when you were working on your project?

0:17:23.1 AW: Yeah, so one thing actually that did surprise us is that we could actually measure... We could see in real time in our data, the increase in levels of inbreeding over the past two decades in two of the three wild populations, and especially in the Dana Point population. I wasn't expecting to have that kind of... I guess that level of detail in the data. And I think a lot of why we were able to see that is just the increasing sophistication of genomic tools that we can apply to these conservation questions. So that was both sad to see, but also heartening that we can use these methods as a tool when we don't have this information already on the ground. We also found and were slightly surprised to find that the Dana Point population, so that's the smallest and most inbred of all the wild populations, was more distinct than we expected from the other two populations. So, it was both really highly genetically differentiated but we were also able to confirm that it has a distinct number of chromosomes, so actually different numbers of chromosomes between Dana Point and the other two populations. The Dana Point population also had higher levels of genetic load, some more harmful mutations as we expect, given that it's the smallest and most inbred.

0:19:09.0 AW: But after running all of our analyses and looking at the trade-offs between inbreeding depression and the potential risks of outbreeding depression, our analyses actually suggested that inbreeding depression has the stronger influence, negative influence on the species. So really, the introduction of new genetic diversity is beneficial, despite the potential negative impacts of outbreeding depression. So at least in the short term, the introduction of new diversity is really warranted.

0:19:46.1 KD: Okay. So, I had a question, and I hadn't written this down ahead of time, but have you guys re-introduced, into the wild, the populations that were raised up in San Diego?

0:20:02.5 AW: Yeah. So, in one location, we've re-introduced new individuals, so in the Laguna Coast Wilderness Preserve. But that is an unoccupied site, so those animals, those pocket mice are not interbreeding with the wild population.

0:20:22.8 KD: Right. Okay.

0:20:24.2 AW: But really, a question that remains in my mind is whether we should be trans-locating or introducing migrants into the wild populations. And so far, we've not done that, and that is still... The Pacific pocket mouse is being managed by a number of government and non-profit and local organizations, so it's this huge collaboration with a lot of stakeholders and a lot of actors. And we're going through the process of deciding what is the next conservation strategy for the species.

0:21:12.1 KD: Okay.

0:21:12.8 AW: So, it does take some time.

0:21:13.7 KD: Yeah. Well, thanks for reminding me. I forgot you had talked about its range and putting these new individuals not like, "Hey Dana Point, here's a bunch of new guys," but to actually introduce them into an area that they used to be in, and that's really interesting. The other thing I was going to ask you though, you sort of talked about this, but just for the audience's sake, is because they're not really mice, it sounds like that's why they never sort of bred with the local gals or whatever, right? They can't really intermix. We've done studies on wolves. And as you know, getting a grip on wolf genetics is tough, because they'll breed with coyotes and other species, so they're complicated.

0:22:02.3 AW: Right. Right. Yes, so Pacific pocket mice are very different from mice and other rodents that they might come into contact with. But actually, now that you mention dogs and wolves, in our study we found that the Dana Point population is actually as distinct from the other two pocket mouse populations as dogs are from wolves.

0:22:28.0 KD: Wow!

0:22:30.3 AW: So, there's sort of a similar level of distinction there.

0:22:33.6 KD: Wow! Was that surprising to you?

0:22:36.6 AW: Yes, it was a little surprising to me. Yeah, I mean, we knew... We had smaller scale genetic data before that suggested they were different, but I was surprised when we sequenced the whole genomes just how different they were.

0:22:51.8 KD: Wow! because I think I've seen pictures, and they're... Yeah. If we think about a wolf and a dog, sure, they look alike, but you can definitely see some differences. But these guys look phenotypically quite similar, right?

0:23:05.7 AW: Yeah. Though dogs are kind of a unique case, because different breeds of dogs don't... Genetically, they're very, very, very similar, but they look genetically different, if you think of a Great Dane versus a chihuahua. So, genetics don't always tell you how different the species will look for sure.

0:23:25.4 KD: Right, that's true. Thanks, that's kind of interesting. I think people think that if from the outside, you look different, you must genetically be very different. And that's a good reminder, not always, and that you can look similar and be genetically very different. Based on this outcome and what you find, what are you guys doing next?

0:23:52.0 AW: Yeah, so our analysis, we're still working on it of course. And we've also recently collected samples from the wild. We have more Dana Point samples that were recently collected that we'll... Once we get a handle on the more recent patterns of genetic diversity and inbreeding in that population, we can sort of gauge how important it is that we act right away or if we still have a few more years to run some experiments to measure risks about breeding depression. So, we're also now looking at historical samples. Because, as I mentioned, the species used to have a much wider distribution than it does now, and so that will help us understand how much diversity has actually been lost and what is remaining and also how connected these populations used to be. So, the other thing is we now know that there are fixed differences in the number of chromosomes across these different populations, and we can actually now look in the historical data to see if that was always the case. It's possible that these populations used to have individuals that carried multiple different chromosome numbers, but because of the loss of diversity, they now only have the single number of chromosomes that they have now so that may not have always been the case.

0:25:49.2 KD: Wow. That's kind of interesting, the different number of chromosomes.

0:25:56.7 AW: Yeah.

0:25:57.5 KD: Do we see that a lot in other species?

0:26:00.8 AW: You know, it's actually more common than you would think, having different numbers of chromosomes. There are many species that have very... So, it's called the carrier types, how your genome is structured into chromosomes. And there are species that have wildly variable carrier types that get along just fine, that have no problem with that. But from what we know in humans, that is kind of surprising because humans are much more consistent in their numbers of chromosomes.

0:26:37.9 KD: Right. Right. And I think we often associate changes in number of chromosomes in people with some pretty serious problems.

0:26:45.4 AW: Exactly. Yes, but that's not always the case in other spaces.

0:26:50.4 KD: Wow, that's fascinating. So, as we wind up, Aryn, what's kind of your take home message for people who are listening, they're thinking about conservation, they are thinking about small populations that we're trying to rescue. Where do you think we're going or what would you say to them?

0:27:11.0 AW: Yeah, I think one take home message is just generally about the loss of genetic diversity, that when a population becomes small, even if you recover it numbers-wise, there's really no going back as far as diversity, genetic diversity goes. Once genetic diversity is lost, it takes a really long time to come back, much longer than the scales that we're used to thinking about. And so, it's really important that we conserve populations in their current size, that we maintain large populations or grow them when we can. The other thing is that I think I've sort of made the case for it, that the conservation involves risks, both risks and benefits. And one of those risks is inaction, so just assuming that introducing migrants or bringing animals into a conservation breeding program and reintroducing them, there are risks to those actions, but another risk is inaction and doing nothing and allowing these populations to continue to decline.

0:28:37.7 AW: And I think as conservationists and managers in general, we've often erred on the side of inaction to avoid these risks of our different management strategies. And I think that the Pacific pocket mouse is a really great model system for other endangered species because we actually have this great... This wealth of information from 10 years of the conservation breeding program that we can use to measure the trade-offs between these risks and benefits. And it can really provide a source of insight that is not available for most species. So, I think besides the Pacific pocket mouse just being a really cool or charismatic species on its own, it's also really helpful for other endangered species.

0:29:33.1 KD: Right, and for folks who are listening, that was I think something that was really attractive to the foundation with Aryn's proposal was the broader... We often ask our researchers to say, well, what's the broader implication, because these things are as cute as little buttons, but in addition to saving them, it really was a wonderful system to study for, because there's a lot of populations, I think we all realize, that are out there that are getting down to very, very few individuals, and this is going to be a big problem.

0:30:10.8 AW: Right, yes.

0:30:13.6 KD: Well, anyway, that does it for this episode of Fresh Scoop. So once again, thank you so much, Dr. Aryn Wilder for joining us today and putting up with all my questions, because this was a tough one for me intellectually to wrap my head around. It's a topic I don't know, so thank you, Aryn, so much.

0:30:32.0 AW: Aw, thank you so much for the great questions and the opportunity to talk about such a cool species.

0:30:38.2 KD: For sure. So, we'll be back with another episode next month as always, that we hope you'll find just as informative because we know the science of animal health is ever-changing and we need cutting-edge research information to give our patients, for those of us who are veterinarians and for those of us who are just animal lovers the best possible care, and that's why we're here. You can find us on iTunes, Spotify, Google Podcasts and Stitcher. And if you liked today's episode, we sure appreciate it if you could take a moment to rate us because that will help others find our podcast and this is probably the last time I'll say this, but big thanks to everyone who have been listening and recommending us to your friends, because our podcast just celebrated our third anniversary. We are among the top 25% of podcasts in the world. So, hurray, we need more science podcasts out there. To learn more about Morris Animal Foundation's work, again, go to There you'll see just how we bridge science and resources to advance the health of animals. You can also follow us on Facebook, Twitter and Instagram, and I'm Dr. Kelly Diehl and we'll talk soon.