Our undergraduate research assistant, Ben Kline, continues to make impressive progress on analyzing fish behavior videos from the laboratory study we did in Leetown, West Virginia last year. This week, I’m turning the blog back over to him to share a brief introduction on why this study was done. If you missed his first post, be sure to check it out here. Looking forward to getting some results soon!
It is no secret that all living organisms require a few basic resources to survive. Often when we think of these necessities we list things like food, water, oxygen, shelter, etc. While it is obvious to us that we need to meet these basic requirements to survive, we often neglect that our aquatic counterparts have needs that vary slightly from our own. My most recent project in the lab is investigating just how important one of these lesser-known resources is.
There are many factors that impact the availability of essential resources in any given habitat. At a basic level, aspects of the environment, such as climate and geography, limit resources to a fairly narrow range of possible conditions. Just consider the resources available in a mountain stream and those in a coastal estuary. These systems may be fairly close to one another, but the resources are very different because of the physical location of the waterway.
Then there are human practices, such as land and water use, that can further restrict resource availability and/or make habitats more hospitable to particular species. For example, dams have been known to cause considerable changes to species composition, all because of how they alter resource availability, especially flow and water temperature.
Taken together, the distribution and abundance of resources have a major impact on the type and number of organisms that can inhabit a certain space. As promised in my previous post, this week’s post will detail a resource that is less understood by us, but critical to the survival of numerous trout species and other coldwater fish: thermal refuge.
Thermal refuge, in its simplest form, describes the availability of a cold water in a body of water that warms. I don’t know about you, but I have taken an unintentional dip or two while fishing in late spring and early summer and I would be hesitant to say that there is any shortage of cold water available for the fish. So what’s the deal?
To understand the significance of temperature in trout habitat, we should take a closer look at how water temperature shifts with the seasons. In larger bodies of water, such as lakes and large reservoirs, the issue of cold water access during summer is less pressing because of the depth of the water. In these large bodies of water, thermal stratification creates zones with varying water temperatures. At the surface, water is exposed to high summer air temperatures and heats up. And, while wind can cause it to mix and circulate, warm water stays at the surface because cold water is more dense and sinks to the bottom. Thus, the surface water warms while the deeper layers, which are largely not exposed to air, remain cool, even in the hottest parts of summer. This deep layer provides of a site of refuge for coldwater species to retreat to when the rest of the lake becomes too warm.
While this is great news for our lake dwellers, fish that are native to creeks and streams often find it significantly harder to find cold water during the hot summer months. As I mentioned in my last post, the shallow nature of most creeks and streams means that there is no easy way for these waters to remain cold in the summer. Being close to a cold water source, such as a spring or upwelling, can help to keep the water cool. So can the presence of a dense tree canopy or sufficient riparian vegetation. Ultimately; however, the main body of water can warm to the point that the habitat may be unfit to support trout populations for an extended period of time.
Contrary to popular belief, the most serious danger in inhabiting warmer waters is not entirely due to the fact that the fish cannot tolerate warmer temperatures. All organisms have an internal set point known as a thermal maxima, which is the highest temperature an individual can tolerate before it perishes. While brook trout prefer cold water, they have actually been observed to have a thermal maxima of around 25C, which is quite warm in terms of water temperature in temperate regions of the US. In fact, it is not uncommon for trout to favor warming waters that are abundant in food supplies over cool, less productive water for a short period of time.
The real danger with warm water is a little more subtle and lies in the change to the dissolved oxygen content in the water as it heats up . Trout are very sensitive to drops in oxygen, and, compared to other species of fish, do not fare well when the oxygen concentration is too low. As water heats up, the solubility of oxygen (i.e., the maximum amount of oxygen that can dissolve in water) starts declining. As you can see in the graph below, at around 20°C the solubility of oxygen is less than 55% of what it is at 5°C. In short, this means that warmer water has less oxygen. And, with less oxygen in warmer water, trout start becoming metabolically and physiologically stressed and mortality increases.
But, the plot thickens even more. As mentioned above, in thermally diverse systems, there can be a trade-off between cold, oxygen-rich water and warmer waters where there is more food. Too much of either can be a bad thing, and trout have to constantly make on-going decisions about which habitat type they want to occupy at any given moment.
Often times, though, the decision may not be entirely theirs to make as cold water refuge is a very limiting resource. One of the most common sources of cold water refuge are spring-fed tributaries. These tributaries are much smaller than the main channels and provide less habitat and fewer resources to support larger populations. These zones are therefore a major source of competition among fish. There is significant evidence that shows trout populations actively uses these refuge zones during hot times of the year, but there has really been limited observation of just how individual fish use and compete for these limiting resources. Enter the study I am assisting with, where we seek to understand the subtleties behind how individuals seek out and defend cold water resources.
At a basic level, our project involves observing brook trout behavior under a variety of thermal conditions. A population of brook trout, each tagged with a uniquely colored external tag, is placed into mock stream that we have created in the lab. The stream has three pools that we can manipulate to be different temperatures. Our goal is to compare individual interactions as stream temperature changes. So, I sit and watch, for endless hours, videos of fish being fish. I document how every individual interacts with every other individual in the stream and how much time fish spend in cold water vs. near food that is often in warm water. Why? Because we want to know how stable behavior is across temperatures. For example, we want to know how fish rank the importance of food vs. thermal refuge at various temperatures. We also want to see how fish interact among one another at different temperatures. We generally expect larger fish to rule the streams and dominate all other fish at cooler temperatures. But, when stream temperature heats up, larger fish become more stressed than smaller fish and may no longer be able to successfully compete for limiting resources. In short, big may not be better in warmer temperatures if you're a trout.
While it may be a bit soon to comment on the data we have gathered so far, this project definitely holds promise to shed some new light on how individual behavior may shape the complex populations of brook trout that we know and love. We also hope to demonstrate just how important these limiting resources are for sustaining trout populations in thermally complex environments.
It’s been awhile since I’ve posted a true research update. That’s because there’s not a lot going on. I mean, yes, I am working. And, I’m making good progress. But, not every day, or even week or month, leads to interesting results. But, I’m inching forward and I’ll reach the finish line eventually. Until then, I’m sparing you the details of how much pipetting and data entry I do on the average day. Trust me, it’s for your benefit.
This week I was able to get out of the lab and into the field to do my monthly tissue collections. While it’s great to get into the field, this work is always a little anti-climactic. The objective of this study is to determine how fish respond to temperature stress at a cellular level. So, we go out and collect tissue samples, hoping to capture increases and decreases in gene expression, the measure of stress, as stream temperature rises and falls. Seems like I would have a carefully designed, clear sampling plan, right?
Ha. My sampling dates are always a moving target. I try to predict stream temperature by looking at the five-day forecast. But, I’ve found that even obsessively checking all forecasting websites rarely gives a great prediction of air temperature or perception. Even if it did, air temperature doesn’t always predict stream temperature. But, it’s all I got. I then look at my calendar, try to scrounge up technicians and, voilà, I land on a date where it may or may not be the temperature I hoped for, but at least I have some help.
Once I’m in the stream, I have no idea what the temperature actually is. I have loggers recording stream temperature every 30 minutes. But, I don’t download the data until the end of the day so that I know what temperature was while sampling. Doesn’t really matter, though. After a two-hour drive I would sample regardless of the stream temperature.
So, we collect 20 or so fish. Sometimes it’s an easy 4-5 hours, other times it’s a 10-hour fight battling high flows and small fish sizes. When I return back to campus, the samples go in a deep freeze and sit. Sometimes for a few days, sometimes for a few months. Once they are delivered to our collaborator in West Virginia who actually measures gene expression, the samples sit again. Most samples from 2016 have been process at this point, so I have some idea of what the data show. But, it’s still a guess, and I just cross my fingers we’re doing it right.
So, I can’t tell you much about the data we are collecting. But, I can tell you, at least anecdotally, a little about how the populations are looking. Last summer was rough for trout. It was hot, it was dry, and our telemetry data showed that trout were getting picked out of the streams by birds and other animals left and right. There were then high rains in fall that washed away eggs, followed by a pretty mild winter. All in all, there was lot of concern in Pennsylvania about how the populations, particularly the young-of-years, were going to look this spring/summer.
Turns out, they are doing just fine. At least in the handful of streams we are sampling right now. Unfortunately, the one-year-old fish are still a little too small for us to sample just yet, but they are huge. And, come November, these fish will be recruited into our study. More impressive, the young-of-year and little floating footballs. I’m not sure I’ve ever sampled a trout stream with fish that were consistently so large. (You also notice I’m not telling you where we’re sampling. It’s a public stream, but I’d like to keep all the fish to myself, thank you).
Does that mean all the fish in Pennsylvania are doing well after the rough conditions over the last year? Absolutely not. The streams we sample are forested, have minimal fishing pressure, and at least one seems to have an exceptional forage base. In the weeks to come, a more extensive survey of Loyalsock streams will be undertaken by Susquehanna University. Until then, we won’t have a great picture on how Loyalsock populations faired over the last year.
Ten years after my very first field season as an undergraduate, the field season that solidified my love for trout ecology, I have all the data I need for my Ph.D. dissertation. While I’m still working on a side project that occasionally allows me to get my feet wet, the time has finally come to hang up my waders and turn hard-earned data into results.
This is the first summer in that time span that I’ve been home more than away. And, I don’t know how I feel about that. Sure, it’s great buying perishable groceries, taking hot showers, and having a roof over my head. And, I definitely don’t miss the unexplained bruises and deep soreness felt after carrying equipment that was a little too heavy for a little too long. But, I do miss the comradery of being in the field.
For the last ten summers, I’ve put my friends and family aside and welcomed a whole new family into my life. My field family. People who often started as complete strangers, but who quickly learned my favorite foods, my quirky sleep habits, and every one of my pet peeves (including how to push them, when they wanted). Some joined the field family for only a few weeks as temporary technicians. Others were with me for several years and have since become more like members of my real family. From all I learned something, even if just bad habits and the drinking preferences of a retired army vet.
There’s something special about a field family. Field partners see a completely different side of you that many of your closest friends and relatives may never know. I have a hard time describing why there is such a shift in demeanor, but the moment I begin packing the truck things change. It’s a mix of relaxation as you let go of any hopes of cell phone service and internet, but also a black cloud of anxiety as you’re trying to collect as much good data as possible despite constant equipment malfunctions and roadblocks. It doesn’t take long for pleasantries to fall to the wayside, particularly after you haven’t showered in days or seen another person outside of the crew. Everyone is always at some baseline level of exhaustion and frustration, but no one dare complain. Instead, you find laughter. You rib on each other, tell stories, and design elaborate practical jokes. At the end of the day, you squeeze out the last bit of sunshine doing various camp chores, preparing for the next day, and maybe even enjoying a few pages of a book. But, come nightfall, it’s just the crew and a campfire. And, let me tell you, campfire chat gets deep.
You spend a lot of time, celebrate a lot of holidays, and share a lot of experiences with your field crew. As a result, you’ll form a lot of memories with those people that only they will understand. A Corey Smith song playing while you’re driving around the backwoods of Virginia on a foggy evening. A YouTube video of movie outtakes from This Is 40. “Feesh, feesh.” Basement felonies. Fajitas. I can tell you the story behind every one of those, but it’s just not the same.
Nostalgia aside, field partners are also people who you blindly trust to keep you safe. Entering into a field family is an unspoken pact that you will have the other person’s back at all times. And, you take it seriously. Great data can’t be collected when fearing for your safety. Unfortunately, one of the toughest lessons every biologist must learn is where the fine line is between “probably safe” and “that was really, really stupid.” While young scientists dance back and forth around the line often, I don’t think you ever truly learn to not cross it. So, the best you can do is trust that someone won’t put you into the stupid category too often, and will be able to safely get you out when they do. If you can find that level of trust, you’re guaranteed a great friendship. And, nothing will bring you closer than having to test it. Close calls are harrowing experiences, but make for great stories for many years to come.
Even when you’re not pushing the limits, accidents happen and the only way to recover is to come together. I tore my ACL walking next to a stream, and then refused surgery for over a year until my field seasons were complete. I could do that because I am insanely stubborn, but also because I knew my field partner would pick up my slack. He became the defacto person to hike the furthest, carry the most weight, and even support me when my knee starting popping out under the force from high velocity stream flows. Why? Because he’s a great person, but also because we shared a common goal. We needed the data. There’s something special about being part of a large crew that is willing to do whatever it takes to accomplish the goals and see each other succeed.
So, yea, I’m excited that I can see a small light flickering at the end of the tunnel. But, you’ll have to excuse me if I’m feeling just a little sad to be entering into this next stage of my degree. The work may be mentally and physically exhausting, but many of my fondest memories and greatest achievements where made while in the stream with my field family.
Our team is growing! At the end of the semester, Ben Kline, an undergraduate at Penn State, contacted the lab looking for volunteer opportunities. We're always happy to introduce prospective fish biologists to our field, but with limited field time I wouldn't blame any volunteer for losing interest in the work we're doing right now. Not only has Ben not lost interest, but he's taken it upon himself to collect some really great data looking at how individual fish compete for access to thermal refuge. Ben has volunteered to provide some guest posts over the summer, which will chronicle his experience in the lab and a little about what interests him in fisheries science. So, welcome Ben with his looks at Penns Creek, and learn more about him here.
Down along a stream called Penns Creek, there’s a place for me
For as long as I can remember, Penns Creek has always been a part of my life. To be fair, I might be somewhat biased considering that my family farm has sat nestled on the bank of the Penns for over a hundred years. I often think back to my childhood sitting alongside the streambed, gazing into the murky water and just enjoying the quiet. If you have had the pleasure of spending some time on Penns Creek, then there is no denying that this location is certainly a lesser known gem of central Pennsylvania.
Penns Creek is a tributary of the Susquehanna River, which ultimately empties into the Chesapeake Bay and has a long running history in the state of Pennsylvania. The original name “John Penn’s Creek” was named for William Penn’s younger brother, but was eventually adapted to simply “Penns Creek”.
Penns Creek is considered to be Pennsylvania’s most impressive limestone stream in terms of size and length at a formidable 67.1-mile run. A limestone stream is characterized as being sourced primarily from groundwater, meaning that underground aquifers or springs are the source of water for the stream. This means the origin of the water feeding the stream could be countless miles from where the stream actually begins. Limestone streams are known to be shallow and slow moving, and typically are more resistant to changes in temperature once a certain set point is reached. The stream bottom consists primarily of gravel, mud, and sand substrate. Portions of the stream are littered with large boulders that add significant structure and habitat to the waterway and provide host to a variety of aquatic species.
The recreational use of Penns Creek is something that is well known to locals. Spending a day floating down the creek with your best buds or a nice day trip in the canoe or kayak sounds like the perfect way to spend a sunny Saturday in June. Aside from a nice paddle down the creek, Penns Creek also hosts countless opportunities for wildlife watchers with a large population of birds of prey, particularly Kingfishers and Bald Eagles. If birds aren’t for you, this is still a great place to catch a glimpse of painted turtles, muskrats, or even a mink along the streambank.
While Penns Creek offers a great number of opportunities in recreation, perhaps the most noteworthy way to spend ones time on Penns Creek is fishing. Penns Creek is one of the most productive trout fisheries in all of Pennsylvania. However, the Penns is also host to a number of other desirable species such as smallmouth bass, various panfish, and even the occasional walleye. These legendary trout waters are known to host extremely high densities of trout in certain sections of the creek, of which some portions are even considered Class A Wild Trout streams. Anglers have even reported catches exceeding 20 inches in length in some of these locations.
There are a few contributing factors to this highly productive environment. The secluded nature of much of Penns Creek aids in the preservation of these natural populations, with some portions of the creek only accessible by foot, or in some cases, bicycle. These portions of the creek contain large rocks that make excellent trout habitat and help to form deep pools and riffles. The stands of old growth forest that hug the banks of Penns Creek provide an excellent source of refuge for hatching insects from heavy spring rains and predators, which allows for abundant food supply in these locations. The nature of a natural limestone stream is that which enables the water to support abundant natural life, which in this case, is a dense insect population. Droves of caddisfly, stonefly, and mayfly nymphs provide for these productive trout waters. Penns Creek is well known for its hatches, and perhaps the most famous of all is the green drake hatch, which is sought by anglers across the entire country.
Habitat structure and food availability are two factors that make trout abundance high in Penns Creek; however, there is one resource that is becoming increasingly difficult to come by: cold water. Trout require thermal refuge, especially in the summer months when stream temperatures are known to rise significantly. In Penns Creek, the natural springs and seeping of cold groundwater provides cold habitat in the uppermost reaches of Penns Creek all the way into late August, which provides the trout with this limiting resource on a year-round basis.
Despite the presence of consistent cold water in the upper reaches of the Penns Creek that make for excellent trout habitat, the middle and lower sections face significant thermal issues. As the water moves father from its source, the shallow and slow-moving nature of Penns Creek causes the water temperature to rise. As stated before, the nature of the stream makes Penns Creek highly resistant to temperature changes once a significant increase is reached. Since trout require cold water to thrive, many trout populations begin to seek cold water tributaries as refuge in these lower reaches of the Penns.
This fragmented habitat may be the answer to sustaining these trout populations in times of thermal distress from rising stream temperatures. The lower third of the Penns becomes so warm in the summer that it is practically devoid of trout before it empties into the Susquehanna, and is now home to limited panfish and smallmouth bass populations only.
With climate change on the rise and cold water to support natural trout populations on the decline, we are currently seeking answers that may help us to better understand these growing concerns. I am currently working on a study that seeks to understand how individuals respond to a number of thermal conditions. This experiment hopes to identify what characteristics a fish might display that would make that individual more able to seek out and utilize these cold water refuges than others in a population. To do this, we are looking at a variety of data including movement, individual behavior, and genetics. The bulk of the work I am completing right now focuses on analyzing individual behavior and the interaction that individuals have with other members of the population.
There is much more to share about this upcoming project, but I will save that for another post. A very exciting summer awaits, so stay tuned to find out about the gritty details of our new project in the weeks to come.
My family is not the least bit outdoorsy. My mom came out to the field with me once before she died, but refused to step foot out of the car once I parked at the edge of the trail. At times my father has shown interest in my research. However, once I tell him I’m not trying to find new ways to grow larger, more tasty fish, he quickly loses interests. “What good is your research if the fish don’t get large enough to eat?” is a question that I hear all too often.
Little does he know, wrapped up in his disappointment is some interesting science that has lately been receiving a lot of attention. In addition to my dad (who doesn’t really fish, by the way), a common complaint among anglers is that fish aren’t getting as big as they used to. To add gas to the fire, technology makes it easy to find historic images of people proudly displaying their catch of 2+ foot long brook trout, surely caught with little more than a stick and line.
It’s 2017. Managers should be able to get the fish are large as we want them, right? Unfortunately, it’s not that easy. Yes, things like climate change, habitat loss, and invasive species have caused declines in the maximum growth of many fish species. But, we can restore and protect habitats to help minimize some of those impacts. What we can’t do is reverse time, and the reason we can’t get large fish today has a lot to do with harvest regulations (or the lack thereof) hundreds of years ago.
For most fish species, state and federal biologist have done a lot of math in order to determine the minimum harvestable size. This number is ultimately a compromise. You want the minimum size to be small enough that anglers have a good chance of being able to keep a fish, but you also want it large enough that the population remains robust and juveniles are not harvested before they can reproduce.
So, you go fishing. You check minimum harvestable size, and when you catch a big fish you put in your cooler. When you catch a small fish, you return it to the water so it can grow larger, reproduce, and be ready for you next year. The logic seems sound, right?
Not entirely. When you only harvest the biggest fish, you’re not only removing the oldest fish. You’re also removing the fish that are genetically programmed to grow faster and larger. Put another way, by keeping the big fish, you’re harvesting both the grandparents and the “tall kids” from the population. After many generations of anglers keeping only the big fish, the genes responsible for rapid growth are simply gone from the population. At that point, no amount of habitat restoration or food supplementation is going to end in larger fish. The population has lost the genetic capability of producing big fish.
This idea isn’t new to fisheries science, but has more prominence in marine ecosystems where biologists first recognized the need to protect both the smallest and the largest fish from harvest. Many marine fish species are regulated with slot limits, where only fish of a certain mid-range size are allowed to be harvested. Slot limits help protect both young juveniles, large pre-spawn females, but also the young fish with the “tall kid” genes.
Slot limits can help preserve some of the genetic integrity of a population. However, scientists have lately realized that traditional harvesting regulations are probably doing more than just removing genes. For example, it’s been shown that angling selectively targets largemouth bass with bold personalities, that populations exposed to heavy angling have altered rates of gene expression (recall: gene expression can be important for many things, including allowing fish to survive stressful situations like high stream temperatures), and that reproduction declines with increases angling pressure. Consequently, biologists are now predicting that angling is indirectly reducing overall population health and future evolutionary potential.
So, should you stop fishing? Absolutely not. But, it does highlight the need to rethink management goals and harvest regulations. We can’t just think about fish size, but need to start considering the more subtle effects that angling has on genetics, reproduction, and behavior.
This past weekend I went on a camping trip to New York with a few others to celebrate the joint birthdays of myself and another friend. It was a great weekend of many camp fires, little technology, and general acceptance of camp funk from the camp fires and lack of technology. Brings me back to field seasons.
Camping just outside Buffalo, we felt a little obligated to make the quick trip north to Niagara Falls. Walking around, I was asked several times whether fish could make the journey down the nearly 170-foot fall and survive. The answer is yes, absolutely! (Turtles can too, but this isn’t a turtle blog.) Generally speaking, as long as fish are falling in water (as opposed to falling through the air and hitting water at the bottom), they probability of surviving the fall is high.
But, what about getting back up? It goes without saying that a trip down a fall as large as Niagara is a one-way journey. But, smaller falls can potentially be traversed by fish moving in both directions. This is especially true in salmonids (including trout), which are natural-born high jumpers and are able to leap several feet into the air if they can get a good “running” start.
What makes a waterfall navigable by upstream migrants isn’t so cut and dry. A fall that is a straight drop is not going to be passable by even the most agile fish. But, smaller falls and falls made-up of a series of small step-downs can often be traversed. And, somewhat ironically, the ability of fish to navigate a waterfall increases with higher stream flows. Flooding increases water velocity in the center of the channel, which can give fish the extra boost of swimming speed needed to jump higher and further. High flows also cause streams to spill over onto the banks where it is normally dry, and fish seeking refuge in these temporary habitats often find new, easier routes, up waterfalls.
So, how do we determine if a fall is navigable? Genetics! Specifically, we can look at the results from a program called STRUCTURE.
STRUCTURE output can easily become difficult to understand. But, in short, you feed the genetic data from individual fish into the program, and it produces a diagram that shows you the most likely population assignment for each fish. You can then use the output to answer questions about where a fish was likely born, how connected populations are, and/or the extent an identified barrier (such as a waterfall) blocks fish movement.
I find it best to think about STRUCTURE output with an example. STRUCTURE analyses can be performed on any organism, and the below example is from a paper on the plant, creeping fig. The authors’ sampled 17 populations, and STRUCTURE determined that there were only two genetically unique populations (as represented by the red and green colors). The number of sampled populations is much higher than the number of genetically distinct populations because there is a high degree of population connectivity and movement of individuals among populations prevents genetic isolation.
If you look at the STRUCTURE diagram, you can see that there is a line for each individual, and each line is a stacked bar chart that is color-coded by the probability the individual assigns to each population. So, an individual with high assignment to the red population is represented by a solid red bar, and an individual with high assignment to the green population will be represented by a solid green bar. Bars that are of various degrees of both red and green represent individuals that have ancestors from both populations. For example, if an individual has a parent from each population, then they show up as 50% red and 50% green.
Big picture, the more isolated a population, the higher the probability that individuals will be from a single genetic population. As a result, isolated populations show up as solid blocks of color in STRUCTURE. Populations that are more open have individuals that have lower assignment probabilities to many genetic populations, and they appear as blocks of mixed color in STRUCTURE.
Now, let’s put this information to work using two examples from brook trout in Loyalsock Creek. The first is a fairly sizeable waterfall on Weed Creek. Normally when sampling for population genetics I don’t go above a known movement barrier. I know it is likely to separate a population, even if just a little, and so I would technically be sampling two populations instead of one. But, at this site, for reason that don’t matter, I decided to collect 40 fish downstream of the falls and ten from above. The STRUCTURE diagram looks like this.
Can you guess what’s going on? (Hint: there’s three genetic populations in this diagram, and the fish caught upstream of the waterfall are on the right).
If you guessed that fish weren’t moving upstream of this fall, then you’d be correct. The solid block of green on the right represents fish upstream of the fall, and they are all assigning with high probability to the “green” population.
Downstream of the fall, things are a little more interesting and a lot more confusing. We see several fish with high assignment to the “green” population, which probably represents fish that recently dropped down the falls. As you can see, there’s quite a few fish that make the journey down the falls and survive. There’s also several fish that are represented as mostly red or mostly blue. One of those colors probably represents the genetics of the resident fish of Weed Creek who living downstream of the falls. The other is probably fish that are moving in from another tributary. Which color is which is uncertain with the data at hand.
Lastly, we see fish that are combination of any two colors, or, in some cases, all three colors. This represents individuals that were spawned from some combination of fish dropping downstream, moving from outside of Weed Creek, and/or fish living downstream of the falls in Weed Creek. This is what it looks like to have a genetically diverse population!
Now, let’s look at another example for comparison. This time, I’ve chosen two different streams, separated by no known barriers, and quite literally a stone’s throw away from one another. Before scrolling down, take a second to think about what you might expect the STRUCTURE diagram to look like.
Not what you were expecting, huh? One stream is almost entirely genetically distinct and shows up as a nearly solid blue box. The other stream has a little more diversity, with two genetic populations nearly equally represented by green and red. But, more strikingly, we see almost no fish from the other site, the “blue” site, finding their way into this stream.
What’s going on here? I’m not sure. But, what this genetics data highlights is that movement barriers aren’t always so obvious. Sure, waterfalls, bridge crossings, and dry channels decrease movement. But, sometimes we can’t always see the barrier, and it may not be a physical barrier but could be driven by some sort of behavior. In the examples here, there was more movement downstream of a fairly large waterfall than there was in an open channel. But, now that we’ve uncovered this hidden barrier, we can start looking a little more closely and potentially find a way to reconnect these two populations.
Exactly one year ago, fueled by coffee and angst, I tagged my first telemetry brook trout and started what would be an 11-month study on movement and gene expression of four brook trout populations. I had no idea what I was getting myself into (for starters, it was supposed to only last six months). And, as I continue to analyze the data, I’m not entirely sure what I got myself into. But, what I do know is that one year later, a combination of good fortune and effort led to some pretty cool data.
So, what did I learn in the last year?
Having spent much of the last year working outside, I have to admit that it feels a little weird to not be frantically packing and preparing for field work right now. But, as much as I would rather be out in the streams, it’s time to hang up my waders and get to analysis. After all, I need to graduate eventually!
Ever have one of those weeks where you’re distracted by a million other things and get nothing done. Yea? Well, that was mostly me this week. Thankfully, I’m landing into the weekend with loose ends mostly tied back up and ready to actually work through this cold, rainy, graduation weekend (seriously…it could snow Sunday?).
With little appreciable progress on my end this week, I’m turning to some outside sources to showcase cool science. Lately, it’ been tough to turn a blind eye to the fact that funding for many government programs that support scientific research, and potentially my future career, is getting overhauled, sometimes completely nixed. Recent international marches for science and climate have brought light to the fact that many are opposed to these changes. But, have you stopped to hear out the science critics? I can’t say I agree, or even know, all of their views, but some of their arguments hold a lot of weight. For example, one of the biggest oppositions I’ve seen to government-funded science is that the average person feels “left out” of what is being said.
I hear you. I feel left out of science, and I’m a scientist. But, as I’ve campaigned before, it doesn’t have to be that way. And, there are some great resources out there to showcase some of the efforts of federal scientists. Case in point- if you’re interested in brook trout, stream temperature rise, climate change, or geography, go ahead and click on the website for the Spatial Hydro-Ecological Decisions System, or SHEDS http://ice.ecosheds.org/sheds/.
This website was produced by a team of scientists, many employed through the United States Geological Survey, a bureau of the Department of the Interior, to produce a visual tool to display hard to access data and the results of really complex models. If you click of the website, you’re brought to an interface that shows a map from Maine to Virginia. Though native brook trout extend as far south as Georgia, data on populations south of Virginia are more sparse and not easily incorporated into this larger dataset.
On the left is a series of drop-down menus where you can customize which data are displayed. It starts by selecting a spatial extent based on HUC watershed. For those unfamiliar with HUCs (short for Hydrologic Unit Code), just know that the larger the HUC, the smaller the watershed. So, for example, a HUC4 watershed is much larger than a HUC8, and HUC8 larger than HUC12. After you select a HUC size, the watershed outlines will appear on the map and the next drop-down menu is automatically populated to show the states that your selection covers. You can also select the state(s) you’re interested in directly from this second menu.
Now, after you find the watershed of most interest to you, the fun really starts. The “map variable” section has TONS of information to characterize the current and future habitat in and watershed and occupancy probability for brook trout. With a click of the mouse, you can have information such as average elevation, percent of forested land in the watershed, and average summer temperature. These are all variables that biologists have determined are the best predictors for brook trout occupancy, which you can also plot on the map. Simply select which variable you’re interested in, and hover over your watershed to see the value appear.
But, what about the future? If you look at the last three variables in that drop down list, you see occupancy probabilities with 2, 4, and 6°C increases in July temperature. Clicking on these values will show results of models that predict brook trout occupancy based on these three projected levels of stream temperature rise. For example, brook trout occupancy probability in Loyalsock Creek is currently 91%. But, it decreases to 84% and 58% with 2°C and 6°C increase in stream temperature, respectively.
Change in brook trout occupancy probability from present (left), 2C increase (middle), and 6C increase (right) in temperature. Click on each picture to view the full model output.
The fun doesn’t stop there. So far, we’ve been characterizing the habitat and occupancy for specific watersheds. What if you flipped that line of thought, and looked for watersheds that met specific habitat and occupancy values? For examples, what if you wanted to see all watersheds that currently have a >90% probability of brook trout occupancy? Easy! Simply go to the drop down menu on the right and select ‘probability of brook trout occupancy.’ A histogram of all the data will appear. Take the little plus sign cursor, and click on the blue line going through average value, and drag it to 100%. You’ll notice a box appear to highlight watersheds within the desired occupancy probability. By moving the upper and lower limit of that box, you can highlight watersheds with desired occupancy probabilities.
By using the drop down tools in the "Catchment Filters and Histograms" menu, you can start narrowing down watersheds that meet certain criteria.
Play around with the other variables. One of my favorite comparisons is to see how stream temperature rise might affect brook trout occupancy probability. It’s particularly interesting to zoom out at larger scales, and see larger trends in projected declines. Look how many watersheds are expected to lose quality brook trout habitat.
Watersheds with >80% probability of brook trout occupancy today (left), with 2C (middle), and 6C (right) increase in stream temperature. See how the number of watersheds declines with temperature? Click on the pictures for a closer look at model results.
Finally, what if wanted to play around with two variables? For example, we know that brook trout like forested watersheds, and you can visualize that relationship by clicking on both “% forest cover’ and ‘probability of brook trout occupancy.’ Again, play around with the sliding rules and see how forest cover affects occupancy.
You can click on multiple attributes in the "Catchment Filters and Historgrams" menu (as seen on the right). From there, you can slide the histograms around to see, for example, the watersheds that have a >60% probability of brook trout occupancy when there is <50% (middle) and >50% (right) forest cover in a watershed. As you can see, the number of watersheds with higher occupancy probabilities increases considerably with more forest cover.
For states fortunate enough to have cold water flowing through their hydrologic veins, native trout conservation tops the list of management goals for many state and federal fisheries biologists. Often times, we take a “if we build it, they will come (and stay)” approach to conservation. In other words, more habitat equals more fish. Every year, state and federal agencies, non-profit organizations, and local citizen groups spend millions of dollars on stream restoration and habitat additions. This includes everything from riparian plantings to decrease water temperature and sediment transport, instream structures to create pools and slow down stream flow, and even reconstruction of the stream channel.
Does it work? When done properly, yes. Stream restoration activities are great at increasing (sometimes for decades) local trout abundance and survival. But, habitat restoration does not discriminate between species. Good faith efforts to increase one trout species (like native brook trout on the east coast), will also increase populations of nonnative trout- in this case brown and rainbow trout.
If fish shared habitat peacefully, this wouldn’t be a problem. But, nothing in nature is ever that easy. Trout species share habitat like two toddlers in a toy box. Competitions for the best spawning and feeding spots are common, and champion fighters get a major advantage- their first pick of home territories; places that have the most food, the best hiding spots from predators, and not too much flow (otherwise the fish has to use too much energy to swim around). These spots are generally won by nonnative species, who’s faster growth rates and tolerance to warmer temperatures make them gold medal fighters. Worse yet, native species don’t just lose the fight, they are usually kicked entirely out of the playground.
Competition between brook and brown trout is not a new topic. We already know brown trout typically outcompete brook trout because brook trout grow slower and shift their habitat use when brown trout are present. However, figuring out exactly how the two species interact and divvy up space is more of a challenge. Streams are very complex environments with limited controllability. It’s hard to figure out how fish compete for small-scale habitat features (like the features we would typically add to a stream during restoration) when habitat quality changes so fast. We can develop very complex maps that accurately predict the best place in the stream for a fish, and then observe fish interact for those spots. But, one storm can completely change habitat availability and desirability. Likewise, one fish moving in to, or out of, a pool can shake up the competitive dynamics and turn winners into losers, and vice versa. It’s very difficult to make very small scale observations in natural systems.
Enter the experimental stream lab at the USGS Leetown Science Center in West Virginia. Than Hitt recently lead a study that looks at how brook and brown trout compete for different habitat requirements with rising stream temperature. The setup was fairly straightforward- four streams, each with three pools and two riffles. Stream temperature was gradually increased form 57°F to 73°F, all while the last pool was held at a constant 57°F to mimic cold water upwelling areas common in mountain streams. There was also a feeder that continually released food, but it was located at the top of the stream, far from the cold water upwelling. Two streams were stocked with 10 brook trout, and two streams were stocked with 5 brook and 5 brown trout.
The idea behind this design was to supply two areas of required habitat – food and cold water- and see how fish compete for each as temperature increased. When temperatures were cooler, food should be the most desirable resource, and competitions near the feeder should be fierce. But, as temperatures increased, competitions should shift away from food and towards spots in cold water. Brown trout added a layer of complexity, and the expectation was that brook trout should be the best fighters at cold temperatures and win access to food, but at warmer temperatures they would start losing competitions to brown trout.
The result? As expected, the desirability of the food patch declined with temperature. In the brook trout-only stream, fish slowly shifted from spending their time near the food, to spending the majority of their time in the cold water. Not a surprise. Fish can survive several days without food, but they can only survive a few hours in stressful temperatures.
But, when brown trout were present, brook trout couldn’t get near the food. Not at cold temperatures, and not at warm temperatures. Brown trout excluded brook trout from habitat patches were food was most abundant and, overall, brown trout influenced brook trout habitat selection more than temperature.
What this study shows us is that just because habitat is available, doesn’t mean that your target species is able to use it. Instead, removing competing species may do more to increase habitat availability than physically increasing the amount of habitat in a stream. In fact, because nonnative species can exclude native species from desirable habitats, increasing habitat availability could increase nonnative species abundance without doing much to increase population size of native species.
In this study, brook trout were excluded from foraging locations and restricted to habitat that was still thermally suitable. What if they had been kicked out of cold water and into warm water? In this case, brown trout would be pushing brook trout into lethal habitats. This is likely to be the reality moving forward with stream temperature rise. There are a growing number of streams that get seasonally too warm for trout, yet they still maintain populations because trout move into areas of cold water refuge during temperature spikes. For fish that are thermally stressed, these refugia are their last lifeline, and fish are willing to spend their last bit of energy vying for even a few minutes in cold water. Inevitably, competition for such a limiting resource reduces populations sizes as not all fish can occupy the refuge and many are forced into lethal habitats. But, when two species start competing, it will likely result in extirpation of the less successful competitor. And, if history repeats itself, we already know that brook trout are likely to lose.
*Note: Content in this post is my own and may not reflect the opinion of the manuscript's authors or the agencies they represent. I encourage you to read the manuscript so you can contribute to the discussion.
Pennsylvania plans to stock over 4.5 million adult trout this year, of which about half will be rainbow trout. Yet, despite such high stocking densities, we don’t see many stocked rainbow trout establishing breeding populations. How could this be?
For starters, stocked fish mortality can be upwards of 99%. And, dead fish don’t reproduce (science at its finest!).
But, I won’t focus on that today. For a more interesting roadblock, we have to think a little harder about stream ecology and the conditions rainbow trout evolved under. Opposite to brook trout, rainbow trout spawn in early spring from about January-May. In rainbow trout’s native range along the Pacific coast, snowmelt and heavy rains cause consistently high flows during early spring. Predictably high spring stream flows are critical for rainbow trout, as high flows scour the streambed, removing silt, gravel, and debris. Effectively, high flows are the street cleaners that come in after Mardi Gras and prepare the streambed for rainbow trout to spawn. After spawning, predictable summer low flows protect rainbow trout eggs from washing down stream until they can hatch a few months later.
In short, rainbow trout like predictability. Predictably high flows in winter, and predictably low flows in spring and summer.
Now, let’s think about Pennsylvania. Yes, early spring flows are generally higher than summer flows. But, they are far from predictable. One year there might be deep snowpack, the next year there might be no snow at all. Plus, summer flows can be equal to, if not exceed, winter flows. The combination all but assures near 100% mortality for rainbow trout eggs laid in the northeastern United States. Of course, there are exceptions to this statement, and the northeast does have naturally reproducing rainbow trout populations. However, it usually takes some assistance, with most occurring downstream of impoundments (which make flows more predictable) or selectively bred to reproduce in fall.
But, the story doesn’t end there. In the southeastern United States, at the southern edge of the brook trout’s native range, climate change is resulting in more frequent winter rain events and summer drought-like conditions. In short, the more predictable stream flows that rainbow trout need for reproduction. Down south, rainbow trout are not only reproducing, but are starting to outnumber brook, and even brown trout. This is, in part, due to rainbow trout’s higher thermal tolerance, but also because high winter flows decrease brook and brown trout egg survival. It’s not uncommon for entire year classes of brown and brook trout to fail because of high winter flows killing eggs.
Thinking ahead, with changing climates, could rainbow trout eventually becomes more successful at establishing in the northeast United States? Possibly. And, when if/when they do, we’ll see further declines to not only brook, but also brown, trout populations.