Learning from Trout DNA, with Helen Neville.
Podcast Transcript:
Tom: Hi, and welcome to the "Orvis Fly-Fishing Podcast." This is your host, Tom Rosenbauer. And my guest this week is Helen Neville. Helen is a senior scientist for Trout Unlimited, and Helen also has a background in genetics. So, I wanted to talk to Helen about what we've learned with the recent breakthroughs in genetics, what we've learned about trout populations and about the interrelationship between trout populations and the different species. I think it's a fascinating discussion talking about, can you tell a hatchery fish from a wild fish by looking at their DNA? And how do they do this? How do they extract their DNA? And I gotta warn you, you may wanna go back and review a little bit of your high school biology because it does get a little scientific and geeky. But for those of you who are into this kind of stuff, I think you'll find it a fascinating interview.
And we're gonna do the Fly Box. But before we do, I got a product for you. One of my favorite products is the Mirage LT reels. These reels are made in New Hampshire, about an hour away from the Orvis rod shop. And they're 100% made in USA, in New Hampshire in the one shop. It's the same shop that makes the reel seats on our Recon and Helios rods and also makes the Orvis pliers. And I'm very, very fond of the products that come out of the shop. And the Mirage LT reel, particularly the LT II if you're a trout angler, is just an amazing reel. It's a beautiful piece of machinery. It has a very, very smooth drag, and yet it can be a strong drag.
You know, often when I'm fishing small streams where I know the fish isn't gonna take a lot of line, I'll use a CFO reel because I'm a traditionalist in trout fishing, and I just love the CFO reel because it's light and I like the sound of them and I like the looks of them. But if I'm going on a bigger river, you know, the Delaware, the Madison, the Henrys Fork, the Green, any of the bigger rivers where a fish might really take some line, and I want a little bit stronger drag to slow the fish down, but yet I want a smooth drag, I'm gonna go with the Mirage LT. And the LT II size will work on a size 2, 3, 4, or even 5-weight rod, 5-weight line with 100 yards of backing, which is plenty of backing for trout fishing. It's just such an elegant, smooth, beautiful piece of machinery. It's a pleasure to just see it hanging on your rod and to crank it and listen to it and enjoy it. Anyway, if you haven't tried a Mirage LT reel, I think you're in for a treat.
Okay. On to the Fly Box. And if you have a question for the Fly Box, you can send it to me at
"Yesterday, I had another guided trip in Estonia that was a complete opposite. At first, I asked him when he had been to that part of the river. He said in spring. The waders that he brought were leaking badly, so we had to buy new ones. Another thing that made me curious, he didn't even bring a net. When I asked him what to do when I hook a pike, he gave me a little stick and he told me to block his jaw with it. The guide was fishing for himself the whole time, and we had quite some distance from each other. The day went by fast, and I had not seen a single fish. In my opinion, he did a terrible job. I would never bring a client to a stretch of river where I haven't been for half a year. I think this was a big mistake. Overall, I was really disappointed with the experience. I think his bad preparation was the main reason we did not catch a fish. What do you think about it?"
Well, Michael, I don't think you need to ask me what I think about it. The first guide was a terrific guide. The second guide was awful. You know, it's rare these days when you hire a fly-fishing guide to have someone who is that bad. You know, before you hire a guide, you really should check references. Check with somebody that's fished with the guide before. This is the reason that many years ago, we started the Orvis Endorsed program because we wanted to make sure that when our customers went out to fish with a guide, that the guide was prepared, and was knowledgeable, and nice, and competent in first aid, competent in all kinds of safety, and just would give our customers a great day on the water.
Hiring a guide blind without a phone call beforehand is always a risky thing. But like I said, that's pretty rare, and you had an awful experience. But it's not something that's gonna happen very often. But do your homework first. Always talk to the guide over the phone and let them know your expectations before you take a trip.
Jared: Hey, Tom, this is Jared and Sage at The Chocolate Lab from Missoula, Montana. I got three questions for you. First question is in regards to fighting fish and whether you think the rod size or the tippet size is more the limiting factor for being able to fight big fish. I've got the Blackout 3-weight, 11-foot rod, and I find myself...it's a little difficult to fight some of the bigger fish with that rod, kind of gotta let them go where they want. And I'm typically fishing, it's a Euro setup with a 4-weight, pretty much a micro leader 4X tippet. I don't know if these fish is harder to fight them because I've got this lightweight tippet that I'm trying to not break or because the Blackout rod is pretty soft in the top half, and that's just harder to fight big fish.
So, I'm curious what you think about that. Second question is regards to taking photos. I know you've answered similar questions. People talked about, you know, I think taking a sharpie...or no, dying the net, I guess it was, to get rid of the net in the background to fish, but I had a really nice brown trout that I landed a week ago. And when I fish by myself, you know and I've got nobody to take a photo of me with the fish, I just end up taking a photo of it in the net and there's nothing to judge the size of it by. So, I'm curious when you're by yourself, do you try to do anything that helps you get a sense of scale for the size of the fish? Or what creative ways do you take pictures of fish when you're on your own?
And the third question is in relation to fall fishing. It seems like fall's a good time of year for catching good fish and mini fish. I don't know if that's partly because the weather is getting more conducive, cooling off, being cloudy, or if it's coinciding with, you know, brown trout spawning and such, or, I'm wondering if you think that trout are known to do hyperphagie, essentially the same type of thing that bears do before going into hibernation. I know that trout stay active during the winter, but I wonder if you know if they kinda try to bulk up a little bit while they still have some warmer temps before getting into winter. So, those are my questions. Thanks for all that you and Orvis do, and I hope this makes it onto the podcast.
Tom: So, Jared, regarding fighting fish, it's really both. You know, the rod size and the tippet size are both gonna be limiting factors. However, in your situation, that 3-weight rod, you would have trouble breaking a 4X tippet with a 3-weight rod. I think that what you need to do, particularly with a 4X tippet, and even a 5X tippet and a 6X tippet is really put the boots to that fish. That rod should bend around it in a pretty severe arc. And the rods will handle it. They'll handle the shock because they're so flexible. So, I think that you need to use the butt of the rod more. In other words, use side pressure and use your, use your body to fight the fish.
Use your lower legs and your core to fight the fish and try to get the bend of the rod into the butt section where that rod is gonna have a lot more beef. So, if you're just kind of playing the fish off the tip and not putting a lot of pressure on it, it's gonna take a while. But you can, again, with a three-weight rod like that, you can really, really put a lot of pressure on the fish to the point where you think you're putting too much pressure on it, but it'd be very, very difficult to break that rod and very difficult to break a 4X tippet. So, I would just really, really put it to the fish and get him in quickly.
Regarding taking photos by myself, I don't often take pictures of fish by myself. I usually wait until I'm with a buddy or a guide. But I do take a lot of pictures in the net. And, you know, when you take a picture of a fish in a net, you do have something to gauge the size by. But if you really wanna know how big that fish was, lay your rod and reel down next to the fish and then you can measure the rod later. I wouldn't worry about how big they are. Personally, I take pictures of fish because of their coloration. When I catch a particularly colorful or just beautiful fish with really clean fins, I do like to take a picture of them. But again, you shouldn't really worry about how big they are and gauging their size.
Regarding fall fishing, actually, fishing does get a little better in the fall because fish are moving, as you correctly assumed, and because the water temperature's cooler and they're probably gonna feed a little bit more actively. But actually, fish do not exhibit hyperphagie like bears, they don't fatten up for the winter. In fact, their growth rate slows down in the fall. So, you know, if you have similar water temperatures and a decent bug hatch in the fall versus the spring, the fish are gonna be a lot more actively feeding on those bugs or whatever they're eating in the spring than they're in the fall. Their growth rate just slows down as the water starts to cool. Generally, growth rate increases as the water temperature is increasing in the spring, but it does slow down. So, they're not trying to pack on pounds for the winter. They will feed, but they're not gonna feed as actively, and that's been proven by looking at their otoliths or their ear bone. It's like rings on a tree, they can tell how fast a fish is growing at various times of year, and they don't grow as fast in the fall, which means they're not eating as much. Okay.
Here's an email from Russ from Kentucky. "I was recently given an old Orvis impregnated bamboo Battenkill fly rod. It is a 7-foot rod with 2 tips and is a 2-piece model. The rod is marked HDH, which based on a quick Google search means it is rated for a modern 6-weight double taper fly line. My question for you is, would it be okay and/or advisable to underline the bamboo rod with a weight-forward-five or even a weight-forward-four line? I'm just curious to get your thoughts on the best line recommendation for this beautiful old fly rod. As a quick side note, the serial number on the rod dates it back to 1962. The rod is 23 years older than I am, and I'm only the third owner. I'm honored to have it and hope to pass it down to my children one day.
Well, Russ, I don't normally recommend underlining rods when I'm talking about graphite rods or even fiberglass rods. But the older bamboo rods bent a lot more. They flexed a lot more in the cast, and people were used to that and people would cast a lot more with their wrist in those days because they could get away with it. But yes, you can probably underline that rod with a weight-forward-five. It's going to feel a little bit crisper and maybe more like the action of a graphite rod when you underline it. I don't know about a four-weight line, you could probably use a four on it, but for sure you could use a five on it. And, you know, putting a six on it, well, it's gonna make it behave more like a bamboo rod, so it's gonna flex more, the action's gonna be slower. So, if you wanna speed it up a little bit and make it a little crisper, you can definitely put a five-weight line on that rod.
Here's an email from Buzz from New Mexico. "This summer, I fished with three old buddies in Colorado, and we planned the trip to give us access to four rivers. Two of our team went out with guides, and on 2 different rivers, the guides rigged a double dropper with a hookless strip of material tied into the tippet above the flies, followed by a bead-head fly for weight, and a small size 20 to 22 midge below that. The guides said the material at the top was an attractor imitating a worm, and it was the bottom small fly that was expected to catch the fish. One of the rigs had a hook tied 2 to 4 inches below the worm, similar to an egg-bead rig I once fished in Alaska. I always love to understand guide tricks, but I wasn't on these outings. So, can you explain this setup? Is the worm purely an attention grabber? And doesn't that bear hook below it constitute an effort to foul-hook the fish? What is the best method to use for the worm? And if it's anticipated that a worm will be attractive, why not just use a San Juan worm including a hook?
Well, I'm with you, Buzz. I know that pegging beads and things like that are a method that people use, and they generally hook fish on the outside of the mouth. And yeah, maybe that's a little bit better for the fish. I've spent my whole life trying not to foul-hook fish on the outside of the mouth and I'm not about to start. If I were in that situation, I wouldn't fish that rig. I'd ask the guide to let me rig it or re-rig it because I don't wanna hook a fish on the outside of the mouth. So, if I needed a worm as an attractor, I would just use a heavily weighted worm, you know, some kind of bead-head San Juan or tongue-head San Juan, and then put the small midge below it, or put a split shot above it for that matter just to get it down. But yeah, I'm with you. I mean, that's a perfectly legal method, but it's just not something I would care to do, and sounds like you wouldn't either.
Here's an email from Mike. "I'm writing you from Charleston, South Carolina, where I use a canoe on the flats targeting redfish. I just listened to your canoe episode and have a tip for paddle management while fishing spring clamps. I bought two rubber-coated spring clamps from Harbor Freight that I clamp onto the gunwale of my canoe. And when I transition from paddling, usually standing and using a kayak paddle, like a SUP paddle while solo, I place it along ways in the clamps to act as a sort of padded cradle. And while paddling, they work well for quick-access rod storage too." Well, thank you, Mike. That's that's a great tip. I think I'm gonna try that on my own canoe. It sounds like a really good solution to that.
Chase: Hey Tom, this is Chase out of Lehi, Utah. I primarily fish for trout, however, after your last episode with James, I'm considering spending more time on new species and urban fishing. I think species like bass are pretty straightforward, and I have a good handle on what I need in the equipment that I need to use, but carp seemed to elude me. After listening to your last podcast, I can definitely say that I'm using a leader that is too short. But, what size leader and tippet should I be using? What can I get away with without being too light and still getting a good presentation to the fish? My second question is, I run both a six and eight-weight. The eight-weight, I primarily use for trout streamers, big trout streamers. Which rod would you recommend for carp?
I know the six-weight's gonna give me a little bit better presentation, but the eight-weight's going to give a little bit better fighting ability. And I'm just kind of confused on which one would be the better option for the task. And as always, thanks for everything that you and Orvis do. I appreciate it.
Tom: Well, Chase, generally, you know, I think you need a strong tippet, but you need a little bit lighter tippet for carp. They are pretty picky. I typically use a 12-pound fluorocarbon tippet. I have a couple of buddies that use 10-pound. And I've been known to use 16-pound if I'm using a big, heavily weighted fly. But I generally go with a 12-pound tippet and, you know, a 12-foot leader. You don't want your leader too short. Carp are very, very spooky, and you wanna keep that fly line as far away from a carp as possible. So, it, I think at least 12-foot, 12-pound leader. And you're probably gonna have to, if you're using a full fluorocarbon leader, you're probably gonna have to add some material onto the butt section of an existing... I don't know if you can buy 12-foot fluorocarbon leaders.
You could also use a 12-foot nylon leader and just put a fluorocarbon tippet on it, but it's not gonna sink quite as quickly. And then regarding a six or an eight-weight, you know, people use sixes, sevens, and eights for carp. I have a friend who sometimes fishes a five-weight per carp, and it really depends on the size fish you're going to be targeting. You know, in some places, the carp aren't very big, they're gonna be, you know, up to maybe 8, 9 pounds, and in that case, a 6-weight's probably. But if you get into the bigger carp where they might be 10, 15, even 20 pounds, you're probably gonna want an 8-weight. And obviously, the eight-weight is gonna be a little less delicate than the six, so you wanna make sure that you have a long leader on the eight-weight.
I personally use a 7, most of the time, a 10-foot, 7-weight for carp. And I don't know why, just because I think it's a good all-round. So, you could use a six or an eight. I would find out how big those carp are. And also, the size of flies you're gonna fish. Sometimes you're fishing 10s and 12s, and even 14s for carp, and the 6-weight would be fine. Sometimes in deeper water, using bigger, heavily weighted flies, and then you want to go with the eight. So, you know, take a look at the fisheries you're gonna be hitting and that'll tell you whether you wanna take the six or the eight.
Here's an email from Doug. "Regarding the caller's question about drop-shotting. In many states, having weight below hooks is illegal in an effort to curb snagging. For example, drop-shotting would be illegal in California. And I recommend folks check their state and local regulations before using that method." And Doug sent a reference from the California Fish and Wildlife Department, which I'll read for you. "There is often confusion regarding this setup as it is very popular in other states," they're talking about drop-shotting, "Given the presentation. Not to mention, when the split-shot snag is on the bottom, the angler usually only loses the weights. Unfortunately, in California, if the weight is oriented below the flies, it would be illegal." So, word to the wise, if you're going to use a drop-shotting technique, check your local regulations. I didn't know that. So, glad to know that. And thank you, Doug, for letting us know about that issue.
Here's an email from John. "I'm hoping you can help me expand my stable of rods efficiently. Over the years, I built up a collection of rods that may not be well suited to the type of fishing I do these days. I live in Birmingham, Alabama, which puts me in close proximity to small streams where I can chase red-eye bass, thanks for that podcast, and plenty of ponds with panfish where I love to take my 5-year-old daughter. The Gulf Coast is just four and a half hours away, so I've started experimenting in salt water. Additionally, you piqued my interest on carp, so I've started scouting for carp spots near me. Lastly, I get to fish in the Northeast regularly. Every summer, I fit in some fly-fishing in northwest Maine during a family vacation. And last year, I had one of the most fun fishing trips in my life when I visited my cousin in Connecticut, who was a bit of a Euro-head."
"We aspire to make that trip an annual tradition. With budget in mind, I wanna refine my rod collection so it supports my current fishing goals and opportunities. Here's the current roster, 7.5 with 3-weight, which is new and a ton of fun, 9-foot, 5-weight, which is a stiff bargain rod I don't love. And an 8.5-foot, 6-weight of a Silver label gifted to me as a kid in 1998, and a 9-foot, 9-weight Orvis Clearwater. My three-weight is perfect for small Alabama streams and panfish. I think my Clearwater is suitable for anything I'd wanna do down at the Gulf, right? Could it also be a good carp rod? My biggest deficiency is in the five to six-weight range. I'd love a solid all-round rod that could upgrade my five and six-weights, as well as support my budding interest in Euro nymphing."
"What do you think of filling this spot with a new 10-foot, 5-weight Clearwater? I've started to think that rod could handle dries, nymphs, or streamers in a typical trout stream, and act as a serviceable Euro rod on those trips to Connecticut. While I know it would not be as sensitive as a dedicated Euro rod, I'm guessing the extra length means it would do the trick until I have the opportunity to Euro-nymph more than once or twice a year. Is that a terrible abuse of Orvis rod designers' intentions? What is that 10-foot, 5-weight intended for? Everyone says it because we mean it. Thanks to you and Orvis for your commitment to the sport and our shared environment."
So, John, you know, you can absolutely use a 10-foot, 5-weight for Euro nymphing. You're right, it's not gonna have the sensitive tip that the 10-foot, 3-weight or 2-weight, or 11-foot, 2 or 3-weight rod would have, but you've got the length there, 10-foot, rod is okay. What you wanna do with that 10-foot, 5-weight is to use a super, super long leader, like 25-foot leader or something like that. Build your own leader. There's lots of places on the web where you can see how to build a Euro leader. But that way, that five-weight line stays inside your guides because if you do have the five-weight line outside of the rod tip, it's gonna sag too much and you're not gonna be able to get a decent drift.
But I think, yeah, you can definitely euro nymph with a 10-foot, 5-weight. You might consider a 10-foot, 4-weight. Both of those rods are a great compromise rod. You know, the little bit of extra length gives you a little bit more reach, and mending ability, and the ability to hold more line off the water, and that's why they were designed. Some people like a longer rod for bigger water. And, you know, they're great lake rods as well. So, yeah, you can do it with your 10-foot, 5-weight. If you really get into that Euro-nymphing stuff, you're probably gonna wanna get a rod with a more sensitive tip. Also, those two and three-weight Euro rods are so flexible in the tip that they will actually cast the weighted flies that you're gonna be kind of lobbing with your Euro technique. So, it does help the more flexible tip on those two and three-weights does help you cast those flies because you don't have a fly line to bend your rod, but it helps to flick them out there. So, that is gonna be a little bit of a problem, but you can water-load and get away with it. So, I would say give it a try and see how it works.
Here's an email from Riley from New Hampshire. "Question about the PRO Zip waders. Should I be using lube on the zipper? The other T-zip products I have come with zipper lube and the waders did not. I'm in them four to five times a week and just wanted to get the most life out of them." Well, Ryan, that's a great question. We're gonna consider including a tube of the T-zip lube with our zippered waders in the future. But it is a good idea. You don't wanna put too much of that stuff on the zipper teeth. They recommend that you just put it on both ends of the zipper, so where it docks in the open position and where it docks in the closed position. And then as you use a zipper, that will distribute that lube on the zipper. But what you can do also is to make sure that you clean your zipper regularly. So, just use a fine brush and mild detergent in water and just clean out the zipper, particularly. if there's any debris in there. You don't wanna use any solvents or abrasives. And any debris that's caught between the teeth can have a negative impact on the ceiling lip. So, you know, just make sure that you keep the zippers clean. A little lube goes a long way. Just put the lube on the friction points where it's docking because those are the most important parts of the zipper to lube.
Here's an email from Carlos from Boulder, Colorado. "My questions to you are, one, I'm only 29, but I have horrible eyes. For this reason, I wear glasses. I know how important polarized sunglasses are when fishing. So, do you have any recommendations? Should I try to wear contacts and buy sunglasses, or should I save up and buy prescription sunglasses? Or do you think those clip-on sunglasses work well? I'm trying to find my best option. I wanna buy a new fly rod for fly-fishing for carp and tossing big streamers, but also using it for still water. So, do you think the Orvis Clearwater will provide for all those situations? Thanks for all your help and all your amazing work in fly-fishing." So, Carlos, clip-on sunglasses, they're just awful. Generally trying to find a pair that fit right, it's gonna be a problem.
The polarization in general in clip-on sunglasses isn't very good. The lenses aren't very good, they're usually fairly inexpensive plastic. They don't last very long. They scratch easily. You get a lot of light in between the clip-ons and the glasses unless you can get a pair of clip-ons that really fit your glasses perfectly, so I don't recommend them. You have two options, and you pretty much stated that. If you are comfortable wearing contact lenses and getting a good pair of sunglasses, that's a great option. The other option is to go with prescription sunglasses, and you can even get them in progressives now. I've had really good luck with both, Smith... Because I have pretty strong glasses as well, I either wear Smith's or Bajio.
I've had really good luck with prescription sunglasses from both of those companies. And yes, they're expensive, but they'll last you a long, long time. When you're fly-fishing, you don't wanna sacrifice either your safety or your visual acuity, and trying to make do with a pair of clip-ons, you're gonna suffer. And if it's that important to you, I would go the extra mile and either go with contacts and good sunglasses or a pair of prescription sunglasses. And again, Smith and Bajio are both companies that make excellent prescription polaroid sunglasses.
Dave: Hi, Tom, it's Dave calling from New Brunswick, Canada. I appreciate the podcast. I look forward to every week though, so thanks for that. Question on tippet size, I'm fishing brook trout in a small meadow stream in New Brunswick using a four-weight line on a four-weight, eight-and-a-half-size fly rod. What I typically do is I'll just tie either the four, five, or six-size tippet directly to the fly line. And my question is, tapered leaders, am I missing out by not utilizing a tapered leader or not tying on a heavier butt section and then working down to the tapered leader? My casts, based on the size of the brook, are not real long. So, I'm just wondering if there's any advantages to using a tippet leader versus just tying one tippet size directly onto the fly line.
Second question is around brook trout in these small meadow streams. I'm fortunate to have a property where we have about 400 feet of frontage on the brook, and that's typically my home water, if you will, and seem to have really good luck catching brookies there late in the day in the evening. I guess my question is, the brookies that I'm catching there, would they be there all year round? And so would they typically be the same brookies I'm catching time after time each time I go out there? Or do they move up and down through the river system? Just thought I'd ask that question. Just curious. Anyway, thanks very much for answering my questions.
Tom: Well, Dave, you know, if that's working for you in this small stream by just tying a tippet directly to the fly line... I'm wondering what knot you're using to tie your tippet to the fly line. I would imagine that's not a very strong connection. Light tippet isn't that strong with a perfection loop, which is what you probably loop your tippet with and then loop that to the fly line, is not a particularly strong knot, I find, in finer tippets. The fish probably aren't large, and so you don't really need to worry about the knot strength. But you're gonna sacrifice some casting ability. When you get into longer casts and, you know, slightly wider places, you're gonna find that your presentation without a tapered leader is gonna suffer a bit.
You're not gonna be able to get the fly exactly where you want to, whereas a tapered leader is gonna allow the whole arrangement to cast better. And again, particularly on longer casts or short cast in a small stream, it probably doesn't matter. I would try a tapered leader. I think you're gonna find your casting is going to be much better and much more accurate. Now, regarding brook trout and small meadow streams, they can move around or they may not. It all depends on the environment. If the water stays cold all summer long and there's enough depth and protection to allow them to evade predators, and they have decent spawning gravel in the immediate vicinity and with a fairly good amount of spring water mixed in, then they may not move much.
However, if the water temperatures fluctuate and/or the river gets too low in the summertime, then they're gonna move. Generally, the water temperature gets too warm, they're gonna move upstream to try to find cooler water if there's enough depth. And generally, if the river gets too low and there isn't enough depth to protect them, then they'll probably drop down. And if there isn't sufficient spawning gravel and spring water in the area, they're definitely gonna move starting in, probably late August and into October, November, probably after your season closes, but they're gonna move up because when brook trout spawn, they need a fairly substantial volume of groundwater, more so than browns or rainbows. So, they're gonna be close to sources of groundwater when they spawn. So, they may move or they may not. I really can't tell you, but brook trout will move. They certainly will move if they need to. All right. That is the Fly Box for this week. Let's go talk to Helen about trout DNA. My guest today is Helen Neville of Trout Unlimited. And Helen, what's your exact title with Trout Unlimited?
Helen: Senior Scientist.
Tom: Senior Scientist. And Trout Unlimited has a lot of scientists, one of the reasons I'm so high on TU because they're really a science-based organization. Do you know how many scientists are on your staff?
Helen: We have 10 in my national program currently and are expanding that imminently. And then we also have, you know, fair number of scientists who are hired under our state-based programs to focus on specific project-related work. But I run the national program which is somewhat anchored in Boise and somewhat distributed across the country now.
Tom: Well, that's amazing. I mean, employing 10 scientists full-time is pretty cool for a conservation organization. And today, your background is in genetics, right?
Helen: Mm-hmm. Conservation genetics.
Tom: Conservation genetics. I thought we'd talk about what we've learned in the past, I don't know, 20 years or so when we first started really analyzing the DNA of trout and you know, changed some of the relationships we always understood about trout and gave us some new insights on how they're related, how they're distributed and everything. So, let's talk a little bit about that. Talk about how you do it first of all, how do you actually do this analysis?
Helen: Oh, that's a good question. And that's changing a lot with the, you know, field of genomics that was kind of originally driven by the Human Genome Project. But in all of these realms, you basically take a small tissue sample from the trout. So, we often just cut off a little tiny corner of their fin, for instance out here in the West, in Maple, just to simply put that in a little coin envelope and let it dry. So, they're great, easy to store, bring them back to a lab, then we go through a first process of extracting the DNA from the cell.
So, you do these sort of chemical manipulations to break down the cellular walls, pull the DNA out and spin that down and let off all of the...other parts of the cell go off in the liquid matrix, spin down the DNA, and then you go through a process called polymerase chain reaction, which basically creates millions of copies of the DNA because you just don't have enough DNA in one cell, or, you know, in a group of cells to do the kind of analysis we do. So, you have to replicate the DNA, you know, millions of times. So, that involves these cool...some people may have heard about these enzymes that were discovered in the hot springs of Yellowstone, I believe originally that can function in hot temperatures. And so, that's the necessary thing for PCR, polymerase chain reaction, is to have these enzymes that can function in hot temperatures.
So, they use those and replicate the DNA through this process thousands, millions of times. And then you take that replicated DNA and typically for various needs, you have certain parts of the genome you're targeting, and we can talk about that a little bit. So, you have these specific primers or little pieces of DNA that match the section of DNA you're trying to target and they attach to it, and then we'll replicate that small segment that you're wanting to target. And then you can look at the variability within that segment. Then there's, you know, the sequencing, modern-day sequencing is somewhat different, but basically, you just break up the DNA, you have these primers, build libraries of them, replicate the DNA, and sequence those pieces of DNA to understand things about that individual fish.
Tom: Okay. So, I got a couple of questions already. First of all, do you examine the DNA under, like, an electron microscope? Is that how you look at it?
Helen: Not for what we do. The sequencing these days is actually literally reading the nucleotides, the ATGC code. And so, literally, you're just getting the sequence of that readout. What I was trained in was a marker called microsatellites, and they are small repeat segments of DNA where they mutate by adding or deleting repeats. So, it might be AT, AT, AT, and they mutate by adding or deleting those repeats. So, what we look at is the size of that marker. So, in those cases, you're actually running them out. It used to be on the big gels, you know, you may have seen people in labs. I did this in high school actually, running these out on gels and seeing they'd migrate farther if they're smaller in size through this gel.
You put an electrostatic charge across the gel and they're attracted to that, and they'll migrate farther if they're smaller in size. And so, you simply assort them by size. And those are the different variations or what we call alleles that an individual might have. It's kind of interesting. Now, they do that, if you're running those markers even today, they run them through these tiny little filaments that are filled with the gel and they migrate by size and then you are reading them by a fluorescent marker.
Tom: Okay. So, you're actually looking at a bunch of numbers on a program to see that?
Helen: Mm-hmm.
Tom: Oh, wow.
Helen: I mean, for the microsatellites, you get a readout of sort of what the size, you know, a typical locus or the place of DNA that you're looking at for that particular genetic marker, you might have say 5 or 6 alleles. And so, you get a readout that there's a 256 allele, you know, 287 or 288 allele if it's a dual repeat. So, you get the readout of the different sizes for each individual. So, it might be a 256, 256, which is an individual that has two copies of the same allele, or a 256 and a 278, which is an individual that would have different copies of the allele at that locus or case on the DNA.
But with sequencing, we use what's called single nucleotide polymorphism. So, it's just one change at one of those nucleotides. So, you're literally getting the readout of A or a T or, you know, G at that particular location. And you might have millions of those that represent the variability that you're looking at in an individual.
Tom: Wow. That's mind-boggling.
Helen: It's kind of complicated. It's changed so much since, you know, even when I was trained and graduated with this work, it's an entirely different field with the sequencing. And I don't actually do that lab work anymore in my position, obviously, but I collaborate with a lot of people who do. So, they know more of those details than I.
Tom: Okay. And then the second question is total curiosity, but the enzyme that they extracted from was bacteria in Yellowstone in the geothermal areas? Do you have to go back to these geothermal areas...
Helen: That's a great question.
Tom: ...to get more enzyme, or have you been able to recreate it in the lab?
Helen: No. They can replicate the bacteria in the lab to get that enzyme.
Tom: Just curious.
Helen: But, you know, I brought it up because it's just so fascinating. It's frankly a brilliant recognition by the scientist who connected this opportunity that, "Hey, we have these bacteria that are able to replicate in this hot environment, and we need the hot environment to be able to..." You know, there's things that you do about denaturing DNA and, you know, the chemical process that you need to replicate it involves high temperatures. And so, you need this enzyme that can function in high temperatures. So, to me, it's just such an interesting story because it was such a simple, but very smart connection that you could use those kind of, you know, creatures.
Tom: Yeah. It just makes you cognizant of the things we need to preserve in nature because we never know what we're gonna discover that's gonna be helpful.
Helen: Right. Exactly. Exactly.
Tom: All right. Let's talk about trout. You know, the first question I would have is, I always knew the rainbow trout when I was growing up and I was trained as a fish biologist many, many years ago, that rainbow trout was Salmo gairdneri. And then suddenly, somebody said, "Oh, no, they're not Salmo, they're not on that genus, they're Oncorhynchus." Is that how you pronounce it?
Helen: Mm-hmm. Oncorhynchus mykiss.
Tom: Okay. So, how did that change? Why did that change? And was it a result of DNA analysis?
Helen: Yes, I think largely so. I forget the timing of that particular decision, but yeah, that was moving the fish to an entirely different genus. So, not related to Salmo, which are more Eastern salmons, but putting it in the Western Pacific Oncorhynchus group. And that would've been done by probably some of the earlier DNA to be honest, I forget exactly when that change was made. I mean, some of that was quite some time ago. And a lot of this gets done through more symmetric measurements and looking at the fish, you know, physically, looking at different types of bony structures or things like that. And then gets complemented later if it's further down the road with some of the earlier genetics, you know, using Allzyme.
So, that was a process of looking at proteins and running them across gels, kind of similar to what I mentioned earlier about microsatellites. And now a much more sophisticated, you know, sequencing and analysis that are related to parts of the genome that get highly preserved, and so don't mutate readily over time. And so, they can look at these deeper relationships among lineages.
Tom: Okay. Well, what have we learned more recently about the relationships between various species and subspecies of trout and how they were distributed?
Helen: Well, you know, this is a field that's changing rapidly. I mean, there are just constant updates of different relationships. I'll say one area that I work in, and I don't follow all of this deeply anymore in my position, but one area that I do work in is with cutthroat trout. So, for instance, there was a large effort several years ago to update the systematic relationships of cutthroat trout, partly related to mykiss or rainbow trout for one, that looked at a lot of different information. There's a book that was published by the American Fisheries Society and has a lot of really interesting and deep information about just the geologic history of this range of cutthroat trout out West, you know, the uplifts of the terrain out here, the geology and geomorphology of different rivers, systems and how they moved over time and, you know, some headwater captures and things like that. It's really pretty fascinating, and a lot of information from the fossil record.
So, for instance, there was an ancestor that was found outside of Reno, actually Reno, Nevada, that has been dated to about 10 million years old, that has now been really confirmed to be the ancestor of cutthroat trout. So, previously we thought that split between mykiss or rainbow trout and cutthroat trout was much earlier than that, you know, more recent, but that pushed that date back tremendously. And so, then there was this interest in pulling together all of the considerable genetic data that have been collected through these various approaches and bringing all of that together in one resource.
And it really emphasized the deeper lineages among the cutthroat trout. And to me, it gives us a much greater appreciation for what we have on the landscape, and therefore, what we stand to lose in terms of this true heritage of these fish.
Tom: You said 10 million years?
Helen: Mm-hmm.
Tom: I thought trout were much younger than... How old are the trout that we recognize today as trout? How far back?
Helen: Well, was the true ancestor, but, you know, I think some of the more recent splits from these different lineages are from, you know, two million years to several hundred thousand years old.
Tom: Okay. Two million to several hundred thousand. Still a long time to adapt to environments.
Helen: Yeah. Lineages within. And I'll let you know, every time we do these newer genetic studies and apply the more modern techniques, I mean, part of it is not even the modern techniques, it's having a representation of all of the fish from across the landscape to evaluate at once. So, often people will do an individual study that looks at the relationship among these several species, but not the whole. And so, the really interesting part about this book was trying to bring together all of the information we have about all of those complexes.
Tom: Can you tell me the name of that book that the American Fisheries Society published or the author?
Helen: I can. The primary editors are Trotter...
Tom: Okay. Yeah, I know that one. I have a copy of it. It's interesting because I have a copy of that book. And a podcast listener recently asked me if he could tell the difference between, you know, one cutthroat and another by looking at him. I said, "Well, it's really tough. They interbreed and, you know, you really have to do a DNA analysis, but there is a great book on cutthroat trout." And I looked it up and it must be out of print because it was like $200 or $300 per copy.
Helen: So, here it is. The actual title, which I should have remembered offhand, but is the Evolutionary Biology and Taxonomy of Cutthroat Trout, and the editors are Trotter, Bisson, Roper, and Shultz. It was published in 2018. Sorry. Hold on, one second. I'm looking at something. All right, let me back up there. Trotter, Bisson, Shultz, and Roper. The actual publication is Cutthroat Trout: Evolutionary Biology and Taxonomy. I think I was looking at an earlier report. It's published by the American Fisheries Society.
Tom: Well, maybe that's not the one I saw then.
Helen: So, if you get on their website, you should be able to order it from the American Fisheries Society.
Tom: Okay. I think the one that I saw was also by Trotter, who I think is not a scientist who is, you know, a fishing writer, outdoor writer. And I think that one was maybe kind of the public version instead of the scientific version. So, maybe the other one is still available.
Helen: Okay. Sorry. Cutthroat Trout: Evolutionary Biology and Taxonomy. I think I can do a quick search, but if you look it up on the American Fisheries Society website, it should be available.
Tom: That would be a cool book to have.
Helen: Seventy-nine dollars it looks like.
Tom: Okay. So, that must be still in print.
Helen: It's a little better.
Tom: Yeah, quite a bit better. I'll have to get a copy of that. That's probably worth having. So, you know, regarding the question of someone catches a cutthroat trout somewhere and they wanna know which kind of cutthroat it is, well, from a visual perspective, is there any way of knowing really what strain of cutthroat that is, or what subspecies?
Helen: Yeah. I mean, in some cases, yes. And you have to sort of put it in context. The true uncompromised lineages of these fish, to put it that way, have certain spotting patterns, for instance. There are morphological differences among them. They're not always the easiest for a person to tell in the field, but typically, somebody who really is deep in the natural history, they could tell them apart. The issue is that, you know, of course, these fish have been moved around for over a century now.
So, the other context I would say is knowing where you're fishing. And so, there are some areas that you might be fishing a small headwater stream that's now isolated or has always been isolated and is unlikely or known not to be stocked with stocked fish or hatchery fish, or have had fish moved into it. Then, you know, you can pair the two, the visual view of it and maybe a better understanding of where it is and come to some conclusion about what it likely is at least.
But there are inner breeding obviously among cutthroat trout species, and with rainbow trout, which is introduced into a lot of waters where it didn't exist historically and they can interbreed and hybridize with cutthroat trout. And so, that's very difficult to tell, you know, in a real true sense just from seeing the fish. So, genetic analysis is really necessary there.
Tom: When you have a cutthroat rainbow hybrid, you really don't know if it's a hybrid or not, do you? unless you do DNA because some of them look like rainbows and they might have barely a little cutthroat slash and maybe none, but they still might be a hybrid. Is that true?
Helen: Yes. It's really hard to tell. I mean, sometimes you see them and you're like, "Oh, yeah, that's a hybrid." But other times, you know, it can be very hard to tell. There've been studies where people have done field verifications and then evaluated the lab results, and they don't always match. So, if you really need to know for some reason, then it's important to do a genetic assessment.
Tom: And how old a DNA sample can you extract DNA from, or how old a tissue sample?
Helen: That's a great question. I mean, you read all the time now where people do it, you know, not necessarily in trout or salmon, but in ancient, you know, thousands of years if not millions of years old in some cases. But there is a limited amount of information you could get from that. But with sequencing, again, with modern methods to do these things, you know, they're exploring DNA from ancient discoveries now. From our sort of modern perspective, you know, we extract DNA and use that information from museum samples, for instance.
The issue is that the DNA degrades over time. So, when it gets exposed to light, for instance, or when it just starts degrading from the biological process, it gets fragmented and broken up into tiny little bits. And also it depends on what you store the DNA in. So, traditionally, in genetics, you would store it in formalin and then alcohol, and that can all degrade the DNA. So, it just gets to be harder and harder to get information out of it. That's why I do the drying, is because it works pretty well out here, at least, and can last several years. Again, it depends, that's why I was saying the sequencing where you're literally just reading the nucleotides, it's easier to do those methods on degraded DNA.
But the thing I talked about earlier, those microsatellite markers where you're looking at these pieces of DNA, and what you're looking at is the size of that fragment. Obviously, if it gets broken up, you can't really tell any information from that.
Tom: Okay. And how about hatchery fish? Let's say you catch a fish electrofishing or angling or whatever and you wanna know, let's say it's a brown trout, and you wanna know if this fish... Now, obviously, at one time it came from a hatchery, but can you tell if it had inner bred with a hatchery brown trout in four or five generations ago? Is that possible to tell?
Helen: I would say, genetically, yes it could be if you have the samples from the hatcheries of interest. You could look at the naturalized population of brown trout and kind of know something about the characteristics of that population and its genetics. And then you can compare that to, you know, the hatchery populations. I've actually done a few studies on this, looking at, for instance, brook trout out here in the West, brook trout are introduced. It's funny because in the East, we're working so hard to try and conserve them, and out West, they really are an issue for the conservation of our native trout, like bull trout and bull charr and cutthroat trout.
But out here, I did a study years ago looking at the mixtures of the fish that we see on the ground here when you go out and sample populations of brook trout here, and I took samples from all of the likely hatcheries that were used in Idaho and tried to just ask this question about, how does the hatchery variability relate to what we see on the ground today? Because it's an interesting question. The whole point to that paper was that one of the basic tenets of conservation biology, or conservation genetics is that genetic variability is the basic toolbox that individuals have to respond to their environment.
So, you think, the more genetic variability you're able to maintain in a population, the better. I mean, from a very basic perspective, if you think about something like disease resistance, if you lose the genetic variability and the complexes of genes that respond to diseases, you're less able to respond to new diseases when they come along. So, just from a very basic perspective, we know that genetic variability is important. But to me, it was a really interesting question, well, then how do we have all these populations of, in this case, trout that were introduced?
And so, they should have come from, you know, small sort of founding population from a hatchery or whatever was transferred from the East and they should have lost a lot of genetic variability in that process. So, I looked at the original hatcheries that were used out here, and, you know, from the first pass perspective showed that a lot of the hatcheries were mixed. So, we had a bunch of different hatchery stocks of brook trout that were used in Idaho. They were mixed in hatchery elsewhere, like in Colorado. There were all these sort of enthusiasts who had their own populations and strains and ponds, and all of that ended up getting introduced out here.
And so, the populations that we see on the ground today here are actually not that genetically depopper, they haven't lost that much genetic variability. And in some cases, they've probably benefited from that mixing before they were introduced.
Tom: We always talk about the detrimental effect of introducing hatchery fish into a wild fish population. You know, it's something we don't wanna do, but I wonder if in some cases where let's say, you have a brown trout population, and it's not affecting any native trout population, it's just a wild brown trout population, I wonder if introducing hatchery brown trout would increase the genetic variability?
Helen: Yeah, that's an interesting question. I mean, from what you just conveyed is right, is the way people typically think about this is that, you know, we know that these different native populations have evolved in their environment, you know, over thousands and thousands, sometimes millions of years, so they're very fine-tuned to where they live, and they've sort of generated the best biological strategies, life history strategies, we often call them, for dealing with where they have been able to persist. And so, when you introduce outside fish, you know, from bucket dumps or hatcheries, or whatever the case may be, you can compromise the ability of those native fish, you know, and their sort of fitness to respond in their own environment.
So, for the most part, we think about that as, you know, negative impact on those native fish which it is. But it is an interesting question. I mean, there's a lot of work being done right now now that we are in this world of genomics and starting to understand more about the function of these different genes, you know. So, the earlier studies that I've done and had talked about a minute ago, we're largely just focused on understanding the amount of variability we had, but that information wasn't related to the function of those genes, it was just the genetic variability was a sort of indicator of how much variability an individual holds overall, assuming it's related to some functions that we didn't really know about at the time.
But with genomics now, you know, we have the ability to build actual maps and map and annotate the function of different genes to different places on the genome. And so, we can now see a lot and understand a lot more now about what functions different genes relate to. There are now known regions of the genome that relate to the timing of migration, for instance, in anadromous salmon or things like that. So, it is kind of, you know, heat temperature stress, and the ability to handle heat, for instance, things like that. So, it is a whole new world there with what we can tell about individuals, and then, therefore, have the ability to think about and potentially, you know, in a hatchery environment, could you start to apply that information and that understanding to propagate fish that have higher thermal tolerance, for instance. And there are people that are working on these very questions.
Tom: Fascinating. Wow. If you can identify those genes, then could you genetically manipulate the fish? Or would you do it by breeding, or would you actually do it by...?
Helen: Yes. Well, you could do it by both, but you don't necessarily have to have a genetically modified fish, but you could just do it by simple, you know, old-fashioned breeding. And in hatcheries, you know, you have the ability to control pedigrees. So, you simply can choose the individuals that have the genotypes for the markers that you're interested in, you know, that have those warm tolerant genotypes, for instance, and use those individuals in your breeding program. But the thing that I think we don't still understand very fully is that it's not always just about the individual gene, the genetic material is typically related in these complexes. So, over evolutionary time, the genetic makeup of an individual across different genes are often related to each other.
So, if a change is induced in one, it sort of cascades through to these suites of changes that all come together. So, sometimes, you know, I think what we don't fully understand is how manipulating one area might break up these very adaptive genetic complexes for different traits.
Tom: Yeah. So, just disease resistance or warm water tolerance might be bred for, but then you might introduce something that is negative.
Helen: Yeah. Or it may come along with other things that aren't as adaptive, other parts of the gene complex that aren't quite as adaptive. Or by pushing toward one trait, you might lose important genetic variability in other traits. And the important thing to emphasize there is that we often don't know what a lot of this does, or we don't know the environment these fish will be in in the future. So, predicting, you know, "what we want now," so, saying that we want this thermal tolerance ability now may come with this inability to adapt to some other change that we're not thinking about in the breeding program or in the fish we're choosing to introduce into a new population, for instance. It gets pretty complicated and it's a fascinating part of genetics.
And just remember, I am talking about all of this not being deep in this world anymore, because I don't actually do these kind of studies in my current position, but I try to keep up with it generally as best as I can.
Tom: Well, I think you have a better understanding than I do or anybody that's listening does, so we're gonna use you as our expert. Can you tell for sure that a fish is a hatchery fish using genetics? So, let's say you have a population of fish and... Well, for instance, it is interesting, the Battenkill in New York state where it's had a robust wild brown trout population for, you know, probably 100 years. And New York state has started to or has been also introducing hatchery brown trout in the same stream. And I think the hatchery fish are fin clips.
So, when they do electro-shocking at the end of the season, they find that something like three-quarters of the fish are wild and the hatchery fish have disappeared. But if those fish weren't fin clipped and you went into a population, would you be able to tell which ones were hatchery fish and which ones were stream bred?
Helen: Typically I would say so, So, you know, again, for your audience, brown trout come from Europe, so they're introduced here in some cases, hundreds of years ago, over 100 years ago, sorry, not hundreds. And so, the populations that have naturalized in some of these systems, you know, may have been there for quite some time, up to 100 years in some cases. And so, over time, you would expect them to change, their genetic signature changes over time. It may not have changed dramatically, they're more related to other brown trout than anything else. But they'll have enough of a different genetic characteristic for that population that typically you could show that, you know, if you have samples of individuals from the hatcheries, they'd probably be distinct enough that you could tell the difference.
So, there's some really cool techniques that we can use these days where you can take an individual genotype and assign it back to a population. And for decades now, I used this technique in my dissertation. You can look at the genetic characteristics of different populations. So, in this case, it was like the actual native populations, even in one system, so in an interconnected river system. I took samples of different fish from different tributaries. This was the Lahontan cutthroat trout. And then I could capture individuals in the mainstream river that were like large migratory individuals that had moved down there, and take their individual genetic characteristics and assign it back to the most likely population of origin, with fairly high degree of confidence.
And it depends on how distinctive those populations are from each other in the system. But I could take an individual and say, "I'm highly confident that this individual came from this tributary and not these others." And again, that all depends on how different those source populations are from each other. But again, with the brown trout population in nature and the hatchery population, they should likely be distinctive enough from each other that you could assign that individual back to the hatchery or to the native population that it was found in.
Tom: Okay. So, you have to have kind of a baseline, there's no marker that says, "Oh, this is a hatchery fish." You have to know the breed.
Helen: Or there could be. Yeah, there can be. I mean, you know, what I was talking about earlier with the sequencing efforts where now what we're looking at is the genetic variability down to the actual nucleotides, you can go through the genome and find places that were only this, you know, marker that has this nucleotide in the hatchery populations and doesn't have it any of... So, you can find those as indicators of the hatchery fish. So, we do the same thing with, like I was saying, you know, sex markers, migratory timing markers.
Once we understand the function of these different things or the genetic characteristics, then you can evaluate different suites of the markers you're using or the low side, the places on the genome, and you can come up with little sets that give you high power to say, "This fish is a spring migrating fish, or this fish came from that population." So, you can use the genetic information in that way. It's pretty neat. And actually, now, I mean, the power that you have in a hatchery is that you know the individuals you're using for your breeding.
So, actually, they do use what's called parentage-based tagging a lot out here now, where even in these migratory populations that are returning, they have all the information from the parents and now the grandparents that begot the current generation. And so, they can take an individual that you find in a tributary, you know, coming back and assign it back to parents and grandparents to tell its origin.
Tom: So, you can tell if it was a wild-introduced fish or hatchery-introduced fish?
Helen: Mm-hmm. Highly powerful.
Tom: And how long ago it was stocked?
Helen: Yeah. I mean, you can't keep doing that forever, obviously. The power sort of erodes with each generation, but again, for some of those, if it's a marker that you're interested in and you find something that is only found in a certain population and that marker indicates that thing, then if you find that marker in a fish, you can, you know, have a lot of confidence that it came from that population, for instance.
Tom: Wow. What fascinating stuff. And we're gonna learn more. We're gonna just keep learning more and more about this.
Helen: Oh, yes. I mean, honestly, the whole field is entirely different than it was when I graduated in 2003 from my, you know, PhD. It's just advancing in leaps and bounds. It's really interesting.
Tom: Wow. Well, I want to thank you for sharing this with us. This has been fascinating. A little on the geeky side, but we like geeky podcasts.
Helen: Sorry.
Tom: No, it's cool stuff. It's really cool stuff and I know people are gonna love hearing about it because the podcast listeners really like to stay up on, you know, the latest research and what's going on and what we're learning.
Helen: Yeah. Well, I really appreciate the interest. I mean, I just think genetics are incredibly interesting and you can learn so much through them.
Tom: Yeah. And we have learned so much, and we'll hopefully get smarter about what we do with fish populations.
Helen: Well, that's the key right there. The knowledge doesn't always lead to great decisions. So, it's all putting it in context of what the goals are and what the downsides are, and considering all of it carefully.
Tom: Yeah. Well, thank you, Helen.
Helen: Thank you. I appreciate it.
Tom: Really appreciate your time.
Helen: I've enjoyed it. Thanks.
Tom: Again, we've been talking to Helen Neville, who is the chief scientist of Trout Unlimited, right?
Helen: Senior scientist.
Tom: Senior scientist.
Helen: I'm old apparently.
Tom: No, you don't sound old. You're the senior scientist of Trout Unlimited. So, thank you for all the great work you're doing. We really appreciate all the stuff you're doing and what Trout Unlimited is doing.
Helen: I appreciate the opportunity. Thanks.
Man: Thanks for listening to the "Orvis Fly Fishing Podcast" with Tom Rosenberg. You can be a part of the show. Have a question or a comment? Send it to us at