As of late November 2023, UAMN has more than two dozen university graduate and undergraduate students working with and within the museum collections. That’s two dozen not including all the students that work for the exhibits, operations, visitor services, and education departments. This week, we highlight a discussion with Maggie Harings, master's student in fisheries, and Andres Lopez, museum Curator of Fishes and UAF Associate Professor at the College of Fisheries and Ocean Sciences. They sat with Roger Topp, Director of Exhibits, Design, and Digital Media to talk about Maggie’s research into Chinook Salmon environmental DNA.
Salmon eDNA Project Website
https://sites.google.com/alaska.edu/salmon-edna-yukon-river-basin/home
The More You Look is a production of the UA Museum of the North, on the campus of the University of Alaska Fairbanks and the ancestral lands of the Dena people of the lower Tanana River. UAMN illuminates the natural history and cultural heritage of Alaska and the North through collections, research, education, and partnerships, and by creating a singular museum experience that honors diverse knowledge and respect for the land and its peoples.
As of late November 2023, UAMN has more than two dozen university graduate and undergraduate students working with and within the museum collections. That’s two dozen not including all the students that work for the exhibits, operations, visitor services, and education departments. This week, we highlight a discussion with Maggie Harings, master's student in fisheries, and Andres Lopez, museum Curator of Fishes and UAF Associate Professor at the College of Fisheries and Ocean Sciences. They sat with Roger Topp, Director of Exhibits, Design, and Digital Media to talk about Maggie’s research into Chinook Salmon environmental DNA.
Salmon eDNA Project Website
https://sites.google.com/alaska.edu/salmon-edna-yukon-river-basin/home
The More You Look is a production of the UA Museum of the North, on the campus of the University of Alaska Fairbanks and the ancestral lands of the Dena people of the lower Tanana River. UAMN illuminates the natural history and cultural heritage of Alaska and the North through collections, research, education, and partnerships, and by creating a singular museum experience that honors diverse knowledge and respect for the land and its peoples.
Every time someone says they work on fish, I say,"Do you fish? Do you like fishing?"
Andres Lopez:I don't.
Roger Topp:Hello, and welcome to The More You Look, your behind the scenes journey into museum collections, research, exhibition, and public programming from Fairbanks, Alaska. I'm Roger Topp, Director of exhibits design and digital media at the UA Museum at the North and host for today's episode. As of late November 2023, UAMN has more than two dozen university graduate and undergraduate students working with and within the museum collections. That's two dozen not including the students that work for the exhibits, operations, visitors services, and education departments. So, I want to begin to dedicate some time some episodes and look at this wealth of student research. And this week, we have Maggie Harings, master's student in fisheries, and Andres Lopez, museum Curator of Fishes and UAF Associate Professor at the College of Fisheries and Ocean Sciences. They sat with me to talk about Maggie's research into Chinook salmon, and environmental DNA.
Maggie Harings:My name is Maggie Harings. I'm a second year graduate student in the College of Fisheries and Ocean Sciences here at UAF. I am originally from Wisconsin. I've spent the last 12 years kind of touring around outWest doing different fisheries projects and diving into other fields as well, and have since found my way to Alaska and been here for about seven years and joined the environmental DNA team here at UAF a couple of years ago. And here we are now.
Andres Lopez:And my name is Andres Lopez, I'm Curator of Fishes at the museum. And I'm also an associate professor in the Department of Fisheries in the College of Fisheries and Ocean Sciences. I've been in Alaska for 18 years now, something like that--15 years. Yeah, and I always loved working on fish research, fish biology, fish diversity, and with an emphasis on molecular tools to learn about fish biology and fish diversity. So there are different types of fish biologists and there are fish ecologists that tend to fish a lot and enjoy fishing. Evolutionary biologists tend not to, especially, the biologists folks that work in fish taxonomy and fish systematics are not commonly as avid fishermen as your regular fish biologist.
Roger Topp:So, Maggie?
Maggie Harings:I am. Yeah. I grew up fishing quite a bit with my family back home in northern Minnesota. And so it's kind of stayed stayed with me. But up here, I found that I don't, I don't fish as much I've I found that I you know, I've leaned more toward fish as a source of food now. And instead of, I've kind of moved away from catch and release. So, I don't fish as much anymore.
Roger Topp:There you go.
Maggie Harings:Yeah.
Roger Topp:Okay, let's get into what your research is all about. You mentioned the eDNA team here at UAF. So maybe on a larger scale, tell us about what eDNA is, and just what's happening here at the university, and then we'll get down to the specifics of what you're working on.
Maggie Harings:Sure. So environmental DNA is what eDNA stands for. I think there're--I've heard a couple different versions of that some people think it stands for
Andres Lopez:Electronic DNA.
Maggie Harings:Electronic DNA.
Andres Lopez:Which it's not. Definiterly not that.
Maggie Harings:Yeah. This is real, real DNA in the wild. And, you know, for instance, if if I were to take my finger here and place it on the table in front of me, and then remove my finger, I've left DNA on the surface. And I like to explain that especially to kids, I think it translates really well. The same thing with animals in the wild, right? So for instance, you think about salmon, when they're swimming through the water, they're physically moving, their tail's, you know, moving around and there's DNA shedding, right, through that process. Same goes for you know, reproductive processes, eDNA or DNA shed into the environment through those processes. Fecal matter is another source of environmental DNA, really, really any way for animals to shed tissue into their environment.
Andres Lopez:There is a growing number of people, both at UAF and everywhere in the world interested in using different ways of measuring environmental DNA to learn things about nature. And here are UAF we have at least three or four labs that are getting involved in environmental DNA. The particular team that we're talking about here includes Jessica Glass, who's another professor in the Department of Fisheries, Erik Schoen, who is a professor in IARC. So, the team is a nebulous configuration that keeps growing. More and more people are interested in using this tool to ask different sorts of questions in fish ecology, fish biology.
Maggie Harings:Salmon, yeah, so obviously, you know, I grew up in central Wisconsin, not really something that we had there. But when I moved out west, I really started to, to dive into kind of the world of salmon. And I realized the--you know, several years ago, even, you know, the, the decline they were having out there in abundance. So when I moved up here, to some extent, depending on where you're living, some of the rivers up here, I kind of feel like are still, you know, they're still in pretty good shape. Unfortunately, this system that we're focusing on is the Yukon River Basin. And, you know, if you're living in Alaska, most people are pretty aware of the declines that that system has been experiencing over the last several years, particularly in the last couple. And so right now, we are looking at Chinook and Chum, which are unfortunately doing particularly poorly right now in the Yukon. And we are using some--we were working with a couple different agencies, Fish and Game, Fish and Wildlife Service, as well as Tanana Chiefs Conference. And all of these different agencies and organizations are out there every summer monitoring salmon runs. So, we've partnered with them, they, in combination between the three organizations, they're monitoring salmon on five different rivers that were collecting eDNA at their sites from, so so they have their technicians that go out in the field, they're counting. So they're living out there at these weirs or sonar sites. They're counting salmon every day. What they were doing as well in 2021, and 2022, for us, were taking environmental DNA samples every morning. And really all that means is they're filtering water. And so they, by the end of the sampling event, they end up with a couple different filters that in theory have any kind of DNA or as well as any other sediment or particles in the water that they filtered. And we're able to quantify the amount of DNA on those filters. The--and then in turn, so now, you know, we have these eDNA samples, and then we have these known salmon counts at the same locations, right? And so in turn, very, very simply put, we can do a bunch of fancy statistics and modeling, to say, Okay, if we have, you know, for instance, and these are very theoretical numbers, but if we, for instance, have, we find, you know, 30 DNA copies of DNA on one filter, and that happens to consistently correspond with maybe 100, fish passing, right, you're able to make that correlation. And so, and this has been done a couple other areas throughout the state as well. And so you can actually use the environmental DNA, or the copy number, in that filter as kind of a proxy for the daily salmon count. Does that make sense?
Roger Topp:Yeah.
Maggie Harings:Okay.
Roger Topp:I've been, I've been your website.
Maggie Harings:Sure.
Roger Topp:And you mentioned the age of DNA in the water. Yes. So you kind of have an idea of that. You have a regular sampling at a particular location once a day. And then you have multiple sites along the river. And from that you can filter out material coming downstream.
Maggie Harings:Yeah. So that's actually the second chapter of my my work, I think, is what you're getting at. So this other project that we're working on is on the Chena. And we've, yep, just like you said, we've collected three different times throughout the summer. Last year, we collected eDNA samples with the intent of kind of collecting samples before the salmon came, during the peak of the run, and then after, and we're going to be looking at how DNA concentrations change throughout the period of of the salmon run. Maybe, you know, make observations based on DNA, potentially DNA transport rates, DNA degradation, things like that. Because there's a lot of different things that affect how long eDNA can stay or remain in a system. You know, for instance, it can get hung up and vegetation it can adhere to biofilm. It can get resuspended you know, in a really turbulent area, it can get resuspended. And then things like you know, environmental conditions, water temperature, all those things can affect how long DNA is present or at least detectable in your system.
Roger Topp:So I haven't heard much about eDNA on the front page of the newspaper. Right? But what I have heard recently, of course, is a study of COVID use--measuring COVID effluent from cities. Is that very similar process to this?
Andres Lopez:Exactly the same process, yeah. So what you're talking about is using--sampling sewage, and counting how many particles of COVID genomes are there. And there's a very clear correlation between that measurement and the prevalence of COVID in a given region, the catchment whatever that sewage system is draining. So the technology that Maggie's using in her research is identical. There are obviously specific reagents that tell us things about Chinook DNA, or Chum DNA. But in every other respect, it is the same approach the same tools in the lab.
Roger Topp:Of course, it's very, very small amounts of the DNA in the water. Use a technique, qPCR. Yeah, to amplify the signal. Talk a bit about that.
Maggie Harings:Yeah, that's exactly right. And for those listening, qPCR just stands for quantitative PCR. So we're quantifying we're using PCR, and we're quantifying the amount of DNA in our samples. But yeah, that's a that's a really good point. Like I mentioned before, you know, Yukon River salmon aren't doing so well. And so this was kind of a pilot project per se, to, to look at, you know how well we're able to detect DNA in systems that don't have--may not have a lot of DNA, just simply due to the fact that there aren't a lot of fish. So qPCR is quantitative polymerase chain reaction.
Andres Lopez:And people are probably familiar, because one of the tests that people would get, if they thought they had COVID would be a PCR test. So is the same PCR the same polymers, yeah. But that would be more or of a lab-- That's when you go to a lab and they then they take a sample, and then they run the exact same thing that I was doing with water samples, they did it with your saliva sample. So polymerase chain reaction, and the value there is that you are taking advantage of something that happens in all your tissues, all your cells, when when a cell has to divide and has to copy the full genome. So that there's two versions of it to for the daughter cells to inherit. So there is a synthesis of genomes, the model of DNA sequences, the polymerase chain reaction captures that biological process that takes place in your cells and puts it in a test tube and speeds it up. So that you have this chain reaction where you make a copy and then the products of the copy get copied themselves and again, and again through a chain reaction. And very quickly, you can go from having a single copy of your target Chinook DNA molecule, to having billions in your little test tube. And the reason we need to do that is because there are no cheap instruments that will allow you to detect a single copy of DNA. But it's very easy to detect 10s and 1000s of copies of DNA. So we need to have that multiplication step before doing the detection.
Roger Topp:And the pre trick is figuring out what reagent multiplies that particular part of the genome. Yes, you get salmon multiplied and not grayling.
Maggie Harings:Yes, exactly. And I think, you know that that's something that's not always very well understood. And that's, that really is key to this whole project. The kind of the, the mixture of different reagents that we use, it's called an assay. You can think of it as kind of a recipe, right? And this recipe is really specific to the single species that you're after. So So in other words, a well designed assays are well designed to kind of recipe if you will, should not--you're not going to be getting any data that's reflective of any other species. The results are only representative of the species that you're after. But that's a great question. Yeah.
Roger Topp:Salmon is interesting to every Alaskan.
Maggie Harings:Yeah.
Roger Topp:Right? And it probably is also interesting to people outside of Alaska. I don't--I mean, when I think of commercial species of salmon, I think of Sockeye and pinks, right, which I forget what pink's are. What are they called?
Maggie Harings:Humpies.
Roger Topp:And but the King, are they a commercial species, and are Chums?
Andres Lopez:There used to be, when there were enough of them.
Maggie Harings:Yep, yep. I can't remember the year that they--commercial fishing was shut down. But I believe there was a small commercial fishery on the Yukon.
Roger Topp:But at one point, kings were a commercial species at some level, and they're not today, because--
Andres Lopez:There's just not enough, there's not enough Kings to go around.
Roger Topp:Now we're worried about kings being viable for subsistence purposes?
Andres Lopez:They've already been closed off.
Maggie Harings:And that's the other thing I was gonna add. That's, I think, is really critical, a critical aspect of this whole project is, you know, we, it's, it's really, I guess, it's really sad to see numbers get so low to the point where subsistence users aren't even able to harvest, you know, what they've been harvesting and their cultures based around and has been for, you know, eternity, right? So, environmental DNA is a relatively in the grand scheme of things. It's a relatively new field, right, or subfield? And--which is really exciting. But what that also means is, there seems to be, you know, a broadening of, you know, different types of applications every day, right? It's, it's people are finding new ways to use eDNA to quantify or, you know, do presense non detection, biodiversity assessments, although certain different types of studies. So, in Alaska, there's potential to use eDNA not just in the way that we're using it, right. This is all very theoretical, but it's, it's quite possible that it might be able to be used, for instance, when biologists are grounded, when they're trying to go out and do an aerial surveying, the weather's too poor, they there is a possibility that, you know, maybe in turn, they could, you know, contract someone in a more remote community, and that person could go out during days when they're not able to fly and collect DNA samples instead. Again, these are things that we haven't gotten to the point of testing or anything like that. But the future is bright, yeah.
Andres Lopez:So, people are thinking that it may be a new tool that has some advantages over existing tools, like Maggie was saying, to, to show that there's a given species in a given location, you have to go there and catch it. And that takes time, logistically in Alaska, tends to be very challenging. And because it's challenging, it's expensive. So the thought is that maybe eDNA based approaches can be cheaper and easier to implement more broadly. Because if you feel need to be at a remote site for as long as it takes to run your net through the water until you catch that fish, if all you need to do is land, or maybe send the drone to collect a little bit of water and bring it back, then it could be made along the surveys and the monitoring of different species can be done a lot more cheaply. So we're hoping to show that, based on in this particular study, we're hoping to show that this is a great new tool that makes things cheaper, easier, or maybe just add extra eyes on the situation.
Roger Topp:And in the case with every new technology that the more uses you find for it, the more people using it, whether it's tracking viruses or salmon or who knows what are their uses, it will become cheaper to do the to do the the lab work.
Maggie Harings:Yeah, absolutely. And, you know, the way that we the way that we were running this project is, you know, filters are collected during the summer, and then in the winter, they're processed in the lab here. You know, what would be great in the future, with with, you know, more research and, and whatnot is, if communities, there's there's right, right now there's these,--and I haven't played around with them yet. So maybe we don't, I don't know.
Andres Lopez:Yeah.
Maggie Harings:But there's these devices that you can take out into the field and run qPCR I believe right there in the field with you. So there would be much less of a delay in receiving those results from us versus if you're able to do that in the field.
Andres Lopez:Like Maggie said, this is a relatively new technology. It's about 12 years old. So in 2008, there was a group that decided to see if they could find Asian Carp invading, Midwestern train urges or dispersing across Midwestern drainages. This is an introduced species that has some ecological impact. And they showed that you could look at DNA in the water and find the species so that that is pretty much the birth of eDNA as a monitoring tool for animals. People before,you know, before that people knew that you could look at the DNA in the water to look at the bacteria that were there. But this was kind of the eureka moment where if there is DNA in the water, and we can somehow pull it out and detect it, we can learn things about the organisms that are living in that environment.
Roger Topp:And I'm guessing the bacteria were there at much higher numbers, and so it was maybe easier to spot them. Maybe? But I love the idea that you could you could test the drainage regularly and almost get an idea of what's there.
Maggie Harings:Yeah, absolutely. And one thing I I'll add to that, too, is something that I that I'm particularly interested in, maybe after grad school and looking more into is, you know, there's a lot of--Alaska is a massive state, obviously. There's, there are tons of tributaries to mainstem rivers that bring in, you know, or foster, you know, great spawning habitat for salmon that are never mon--, that've never been monitored before, right. And so one thing that I think would be really cool is to go out into some of these tributaries use environmental DNA to track relative changes in some of these salmon runs in these tributaries that have never been studied before. You wouldn't necessarily be able to get, you know, salmon counts, per se, but you could, you could, you might be able to get in theory to a point where you can say, Okay, this was probably a good year, or this year, ooh, not so great.
Roger Topp:So, one presense, and two, relative year to year change.
Maggie Harings:Yeah. Yeah.
Roger Topp:It feels like it could be, but you just gotta That's fantastic.
Andres Lopez:And that's the big selling point with Maggie study, not just knowing that the Chinook are coming through, but getting a sense of how many are there. And whether it's bigger find out.
Maggie Harings:Yeah, and I, I mentioned, I think I mentioned earlier, too, that this has been done fairly successfully in a pools of spawning fish versus one year versus the next or the timing of the arrival. The that's really the key new insight that Maggie's work will generate. We know, we as in humanity knows that your DNA is there, that you can detect it,that you can--that it makes sense, the species, you detect are the species that should live in that river. But now the cool extension is to figure out if there's a quantitative relationship between the number of individual fish and the amount of eDNA, because if, if that relation doesn't exist, then it's still a useful tool for detecting and surveying biodiversity. But it's not a counting tool. Hopefully, we'll find that it is a counting tool. couple areas of Alaska. Those systems in particular, were smaller in size and river volume. And they had a higher density of salmon. And so, you know, just hearing those two, like things combined, you start to think, okay, there's probably a lot more DNA, right, it's probably a lot easier to capture DNA and those systems. So I guess it isn't entirely surprising that, you know, they, those researchers were had successful projects, right. And so it'll be interesting to see. It'll be interesting to see what we find with our system. And I'm excited.
Roger Topp:So, you are in a master's program here at UAF?
Maggie Harings:Yeah, yep.
Roger Topp:So where are you in your in your project?
Maggie Harings:Most of them are, the processing involved with the filters themselves and the DNA extractions are done. So we're moving on to the step where we're actually starting to quantify environmental DNA. What I'm finding is that during the the very, very beginning of for instance, the Chum run in the Chena, I'm not necessarily--I'm finding that there isn't necessarily enough DNA for us to, without going into too much detail ,for us to use those data. We have had samples, though, during more toward the peak of the run, that are producing results that we would be able to use.
Roger Topp:So, pure science technology of doing this research, everything being done with it is valuable to, kind of, advance a part of the science, and then is the extra hope that it is actually applicable, and we can learn-- A tool to use in Alaska.
Andres Lopez:Right. And I think the goal is to ground truth, the technology in a study and if it works, then that the work of deploying it and using it regularly on different locations for different Chinook runs, falls to the folks that are most closely tied to that particular run, right? So it stops being the job of the university or the museum to do once we show that okay, if you follow these steps, you can quantify the size of your run using this eDNA approach. That's where we step back and if folks want to just implement a routine monitoring study, they can do it outside of our participation.
Maggie Harings:And I'll add on to that, too. I think another kind of cool aspect of this project is the fact that the the folks, the technicians, the fisheries technicians that were hired by the agencies and organizations that we partnered with, a lot of them were in the grand scheme of like, relatively quite young, you know, think 18 to 22 range on average. And, and the reason I bring that up is because it means that they, they really haven't had a lot of training, if any, right in environmental DNA sampling techniques. And so we were able to come in, provide a couple, couple hours of in depth training on environmental DNA sampling and proper techniques and whatnot, avoiding contamination, et cetera. And they were able to, you know, successfully go out into the field and collect daily samples for several months at a time. And that isn't necessarily something that applies to every sampling technique out there in fisheries, right? So I think that that's a really, it's, it's, you know, the some of the maybe science some, some folks might get a little bit intimidated by like, maybe some of the, you know, molecular bio---you know, by-- molecular biology, like terms and phrases surrounding this technique, but but the, the process of actually filtering in the field is very easy, which is, I think, makes it a pretty powerful technique to use.
Roger Topp:It sounds on the one hand that, you know, the process will be pretty delicate, in a matter of collecting the material. But in other hand, when you talk about contamination, what I'm asking, is there a control for that? But secondly, what is the likelihood that someone's going to contaminate with too much King Salmon?
Andres Lopez:A good question.
Maggie Harings:Are you asking? So, you're saying in yours where there is a lot of salmon.
Roger Topp:Say, I'm out in the field? And I don't know.
Maggie Harings:Yeah, okay. Okay.
Roger Topp:Just job to collect some water? Yep. What if I put some human DNA in there is that gonna matter? Or is that put my lunch in there, is that going to be more of a problem if it was King--
Andres Lopez:Depends somewhat on what you have for lunch? if you had King--
Maggie Harings:You're not allowed to bring salmon to the field with you.
Andres Lopez:So a little a little side story, I was recently in a field experience with a team that was collecting eDNA samples. And as part of their data sheet that went along with each sample that was collected, they had to write down what fish they had eaten for lunch. So that it was clear that if that fish showed up in the result, then it made sense, right? So--
Roger Topp:Is that that part of control, so you can control for that, like--
Andres Lopez:Just noted, so that you have that information? And if some the result is unexpected, then you have a possible source of explanation.
Maggie Harings:Yeah, and when you ask about controls to or field blanks is what we call them. They depends on kind of your your sampling scheme. But, we did ask the technicians to every every few days, they would collect their two replicates. So there are two they they collect their two filters, eDNA filters. And then at the very end of that process, they would they would collect a third filter where they'd filter just distilled, in theory, uncontaminated water. And so that's kind of a check for us in the lab, when we analyze that, that lab or that field blank, to say, okay, this, in theory should not have any DNA in it. But if it does, then there might be a bit of an issue. And there's there's ways to kind of determine, you know, whether or not it may have been isolated just to that, that sample or if there was a bigger issue. So.
Andres Lopez:Another thing to think about, specifically with this project, many of the technicians that were in the field collecting samples were at weirs where fish were being counted and handled. So if the technician was not careful, and they were handling fish, Chinook, that day, the day that they filter water, it's possible to introduce contamination and that's why a well designed environmental DNA survey includes contamination controls at every step of the process, not just in the field like Maggie described having blanks that are collected in the field using the same setup, everything the same except the source of the sample is something you know should not have any any river DNA. But then when those samples get to a lab we introduced blanks at every step, the idea is to track if we at the end end up with results that make no sense whatsoever. Hopefully we can track it down to a specific point in the process where some mistake took place and DNA that wasn't supposed to be there and that up where-- with our samples.
Roger Topp:Thank you for mentioning wiers again for like the third time, because I keep on envisioning you some on a gravel bar somewhere with no one else insight getting your sample out of the river. Of course, Yukon's pretty large. I'm seeing a nice little scene, a river runs through it. And that notices your tests are being done where there are people, there are activities happening.They are near villages, settlements. So.
Maggie Harings:Yeah.
Andres Lopez:Well, the key thing is that the samples come from--Maggie's work is going to depend on having eyes on fish, that's one count. And then the count of amount of DNA. And if the two things move up and down with each other, we're super happy and we report great success and fun papers. If they don't dance with each other, then we show that in under some situations, like this particular site, the tool is not very sensitive. So those are possible outcomes.
Roger Topp:So, in terms of--in terms of this research, or other research within the museum, we have quite extensive collections here within the building. So I'm interested in knowing how much our collections have benefited this research and vice versa.
Maggie Harings:Sure, yeah. So I'll start kind of, again, kind of at the beginning, but when the samples come into the lab, we cut the filters in half and one half of the filter remains--gets set aside for for research purposes, for my project. The other half of the filter gets archived. And ultimately, it will be stored with a fancy barcode that, you know, someone can look up in the future if they need, if they say, oh, you know, I, I'm really interested in learning more about what may or may not have been in the Salcha River in 2021. They can come to the museum, talk with folks here, and they can get connected with some of these filter halves that came directly from this project. And this isn't necessarily, you know, specific to my project. This applies to any, you know, any eDNA filters stored from from other projects, as well. And kind of the, the unique thing is that these filters don't just have salmon DNA on them, right. So there's DNA from anything in, in theory, anything near where that sampling location was, there'll be DNA there, on those filters from any species in the in the water. And so, you know, someone, for instance, looking at invertebrates could come in and use this filter, not just for salmon, but to look at, you know, maybe invertebrate presence / absence or something like that. We were also able to use some specimens from the museum collections to, you know, when we were talking about, you know, how specific is, is our mixture or our recipe right to the salmon that we're looking at, we were able to run what's called a specificity test. It it basically just says, is our is our recipe specific only to the species that we want it to be right. And so we're able to use some specimens from the museum to test for that. So, we were able to pull specimens from the museum that corresponded to species found in our study rivers, and test whether or not our recipe if you will, we're detecting DNA from the species as well. Luckily, we found very little, what's called cross amplification, where you have DNA that amplifies from a species that you don't want. And so our recipe, if you will, you know, it seems to be working very well, is really only targeting the species that we are after. So oftentimes, when I'm presenting at conferences, the same question comes up from folks, and they're curious about what happens if you have, let's say, theoretically, you go out to a stream. And without knowing it, you're collecting an eDNA sample looking for Chinook but there just aren't any in the system, right. The question is always well, what if a bird came along, for instance, and pooped upriver, and the bird had eaten a Chinook and now you're sampling DNA from that that fecal matter? And I guess my my response is that they which is a good concern to have, I think that's a very valid question. So So with eDNA or environmental DNA, there's something and qPCR there's something called the limit of detection. And the as well as limit of quantification. These are just different thresholds that say, okay, for instance, you need x number of molecules of DNA in your sample, before you can legitimately actually detect say, Yes, I can 100 You know, I can confirm that I have to DNA from this one species and then one level up would be the limit of quantification. Okay, I need even more DNA in my sample to say, Yes, I can adequately quantify the amount of DNA in that sample. And so the more I read about this, it just does not seem likely that you're ever going to get enough DNA from a fecal sample that if you even happen to capture in your filter floating downstream, there's a very low chance of there being enough DNA in that sample, for you to detect it. Above your limit of quantification.
Andres Lopez:The other way of thinking about this same idea is that we are hoping that this approach captures the average of what's happening in that river. So that mixture of all the contributors and little things like that happen, little weird events, like a Chinook got injured and lost the fin and or it's bleeding all over the place. We're hoping that those little bumps in DNA concentrations will not drive the signal. So if--
Roger Topp:The outliers dont--
Maggie Harings:Yeah.
Andres Lopez:So if this technique is so sensitive that some random event throws the signal off and off of an on what Maggie will see, instead of this, trends of DNA concentrations moving with the pulse of fish moving, she'll just see noise, right? Like one day, there's a million copies and the other day, there's zero, and then two minutes later, there's a million again. And if that's why we see just a very noisy line over time, that has no relationship with the known number of fish that move through that spot in the river, then we'll throw that technique away as this doesn't work in this river. We know it works in other places for other species. But if, if that line is just noise, then it is noise, and there's nothing to do about it. But if the line has nice behaviors, then we don't care about the fact that there's possible sources of variation. Because we see that that variation gets controlled by the dynamics of the river mixing everything and making everything a nice little low, some volume of DNA that is matching the amount of the source of the DNA,
Maggie Harings:Other juvenile fish in the system too, things
Andres Lopez:Oh yeah. Those are really cool questions. One of like that. the next steps in eDNA applications in these kinds of settings is at some point, those fish are going to move past the sampling site, finder spawning beds on spawn, and they're going to be releasing gametes, and they're going to be falling apart. And there's going to be all kinds of things happening. And folks are already developing specialized assays that will, will give you a little flag that says spawning is happening now. Because the signal now just changes in intensity. But you could, for example, if the species you're interested in has sex determination genes, and or some other marker that is more prevalent in sperm, for example, then you could develop one of
Roger Topp:In which case, can't count fish anymore. Yoiu get a these recipes that very specifically says something is weird here. This signature is changing. And it's indicative of the presence of a lot of gametes in the water. lot of a huge--
Andres Lopez:Exactly. Yeah. But it could tell you, Okay, this is the date of spawning in this river, which is important information for fish biology, especially now that we're thinking about climate change and how changing environmental regimes are altering the biology of species. One of the things that folks really want to know is whether that has an effect on the timing of key events in life history, spawning being one of them, and all of these other things. So, there's other ways--there's so many ways in which eDNA can be deployed to ask questions that are different from from the questions that Maggie is asking.
Maggie Harings:You know, I think moving forward, I am hoping to stick around in either Alaska or spend some additional time down in Idaho. Kind of, regardless of where I ended up, I'm hoping to obviously remain in fisheries and, and secure a position with hopefully the federal government, which would be great. And, yeah, also make sure that I make some time for some fun things like packrafting and rafting and splitboarding and all those classic Alaska activities
Roger Topp:Rivers, rivers are key.
Maggie Harings:Rivers are key. Rivers have always been a huge player in my my upbringing as well and remain remain a very, very important kind of aspect in my work life and personal. And so it's the work I'm doing I think is extra meaningful because of that.
Roger Topp:I wish you luck with that, because I always thought I'd be involved with coast, coastlines.
Andres Lopez:Are here you are.
Roger Topp:I've failed miserably for 30 years.
Andres Lopez:The most important question, Have you fallen in love with molecular biology? This is a question coming from from your advisor, who is very invested in molecular biology.
Roger Topp:You answers here will be judged.
Andres Lopez:I will judge you very harshly, if the answer is incorrect,
Maggie Harings:I see myself sticking with environmental DNA.
Andres Lopez:Wow, that was a very neutral, not in love with molecular biology--
Roger Topp:She also likes fish.
Andres Lopez:Yeah. Okay. Yeah, I guess.
Roger Topp:Well, thank you both for sticking with us for the last hour. That's fascinating.
Maggie Harings:Yeah. Thank you.
Roger Topp:See you around.
Andres Lopez:Yeah.
Maggie Harings:Thanks.
Andres Lopez:Thanks, Roger.
Roger Topp:Thank you to Maggie and Andreas for sharing their stories and thoughts on his ongoing research. The museum and the University of Alaska could not conduct this work and provide these opportunities to students without public and private sector partnerships, and without individual gifts and state and national funding. Be sure to explore the museum's website for insights into all 10 of the museum's research collections, and the vast and all encompassing work of faculty, staff, and student researchers. Just as I did, you too can visit Maggie's salmon and eDNA Project website. Find it and learn more. We put the link in the show notes. The More You Look is a the production of the UA museum of the North on the campus of the University of Alaska Fairbanks and the ancestral lands of the Dene people with the Lower Tanana River. UAMN illuminates the natural history and cultural heritage of Alaska and the North through collections, research, education, and partnerships, and by creating a singular museum experience that honors diverse knowledge and respect for the land and its peoples. Thank you for listening. Please subscribe, share and rate the program. This helps other listeners discover more about not only the work of this museum, but quite possibly other museums and their neighborhoods. The more you look, the more you find.