I wrote last week of the two types of grad student vacations, conferences and field work. But, there’s another holiday that’s even rarer (at least for me) and merits even more celebration. I’m talking about your advisor’s vacation week, otherwise known as Grad Student Independence Week.
Truth be told, my advisor’s whereabouts don’t really influence my work ethic. For the time being, I’m working at my own self-defined pace (cross my fingers I can keep it that way). But, the closer we get to the beginning of the semester, the more sparse the office gets. With no one to pester during the day, why bother going in?
So, I didn’t. I slept in a little later (which for me is 6am), enjoyed coffee on my patio, and had one main goal: start working on the hatchery-wild hybridization manuscript. Data analysis is still on going, but at this point I know what the results are going to say. There’s no need to wait for the final numbers to crunch to start the long process of preparing the work for publication.
When I was an undergrad, I always thought that scientific publications were the works of brilliant scientists who wrote the equivalent of Shakespearian prose. I never thought I’d be smart enough to accomplish a similar feat. I actually still think that, except I’ve somehow been let into that elite crowd of published scientists seven times now. It still hard to believe I’ve reached the point in my career where I am the authority on a topic- someone out there is reading my manuscript and thinking I am the brilliant scientist. Crazy.
One thing I have learned along the way is that regardless of how smart you are, how great your research is, or how well you write, all manuscripts start in the same place. With a blank Word document that just stares at you. For me, it’s probably the single most intimidating and frustrating part of the publication process. Literally anything I put down “on paper” would represent an improvement over the blank page, but I just sit there for hours- staring, erasing, and getting more frustrated.
There’s all sorts of advice out there about how to be the best, most efficient writer- outline your ideas, write 30 minutes every day, discuss your paper beforehand, etc.- and I defy every single recommendation. That long, frustrating, fight with the blank page is just part of my process, and I need to work through before I can write something worth saving. And, the fight needs to be long and uninterrupted. Not a great task for tackling at the office where distractions are imminent, but a perfect job for celebrating my Grad Student Independence Week at home.
I actually only got one full day at home, but it was enough to win the battle and get a solid start on the manuscript. Time to save it, back it up, and not look at it for at least a few days. In the meantime, I go back to square one- read published manuscripts that I know are important for my study and that I will cite in my own publication to support why our study was needed and to add credibility to the results we found.
As I’ve said before, there aren’t a lot of studies on hatchery-wild interbreeding in brook trout. But, I did find one by Andrew Harbicht and colleagues (see below for a link to the manuscript) that looked at how the probability that hatchery trout will breed with wild trout changes depending on the environment. I’m still not releasing the result of our analysis, but studies like this are important regardless of what we find. Whether we find a high degree of interbreeding or not much at all, we need to know WHY we are getting that result. And, it makes sense that environmental conditions influence how much hatchery trout breed with their wild counterparts.
The study was conducted on several lakes in Algonquin Provincial Park in Ontario, Canada, of which some were never stocked with hatchery brook trout, and others had historic stocking that had been stopped 10+ years prior to their study. Immediately, you’ll notice there are some differences between their study and ours: we work on streams, and in areas that are currently being stocked with high densities of fish. Nevertheless, their results are important to keep in mind as we move forward. Most importantly, they found:
So, why is this study important for us? For starters, streams often support lower populations of brook trout than lakes, making us nervous that interbreeding may be more prevalent in streams than lakes- particularly, again, because stocking in our systems is frequent and on going. Our streams also have a wide range accessibility, pH, and other environmental variables (e.g., gradient and temperature) that influence population sizes and competition. Big picture, this study just shows us that introgression isn’t an all or nothing phenomena. Location matters a whole lot, and our results can’t be taken as the definitive response of trout to stocking.
But, all of this presumes that we are finding interbreeding. Which I’m not saying we are. I’m also not saying we aren’t. You’ll just have to stay tuned.
*Note: Content in this post is my own and may not reflect the opinion of the manuscripts' authors or the agencies they represent. I encourage you to read the manuscript, found here, so you can contribute to the discussion.
I’m on Vacation
In grad school there are two types of “vacations.” There are conferences, which you hope are in desirable cities that you can explore at night after you’ve turned your brain to mush hearing about cool research and talking to collaborators all day. And then there’s volunteer field work, where you are probably working harder than you would had you not gone on “vacation,” but are just happy to be seeing a different system and learning about a different project for a little bit.
Right now, I’m on the later form of vacation. I traveled six hours south to my alma mater in Ashland, Virginia to help put another year of Mechumps Creek post-restoration monitoring into the books. Some of you may recall Mechumps Creek from my post last year, where I described the need to rebuild this urban stream to restore and protect habitat from stormwater runoff. And, no, there are no trout in central Virginia. But, had it not been for a class on stream restoration featuring this tiny creek, I would have never pursued a career in fisheries. So, Mechumps Creek will always hold a special place in my heart and I’ll gladly “vacation” here anytime (but ask me again when vacation loses those quotation marks).
But, this year’s sampling was a bit different than past. Per the usual, we picked the hottest day of the year for fieldwork. With heat indices once again soaring to 110°F, I swear the Farmer’s Almanac could start using us for their long-term forecasts. And, there was no lack of poison ivy, dense thorns, and interesting animals. As it turns out, beavers don’t much appreciate 250 volts rolling through bodies.
The difference this year was that we got to do twice the work. Lucky us! Normally, our sampling is focused on one section of stream that was restored in 2010 and is now being monitored to determine the long-term response of fish populations (among other things) to restoration. Though there are still a few years left in monitoring, restoration of the first section went so well that a grant was recently received to restore the next reach located just downstream. Woohoo! But, before restoration can start, there needs to be baseline measurements of what the stream and fish community look like now so that later they can determine if restoration was successful. So, after sampling the post-restoration section, we headed downstream to complete the pre-restoration assessment of the fish community.
I was part of pre-restoration sampling of the original section seven years ago, but I’ve long forgotten what fish we caught way back then. So, it was interesting to see, back-to-back, the difference in habitat and fish diversity between pre- and post-restoration sites. Post-restoration, the stream is, on average, only a couple feet wide with maybe five pools in the entire 1,200-foot section, the deepest of which about three feet. Compare that to the pre-restoration reach, which was much wider, much siltier, and was pool after pool, with some too deep to wade through.
On the surface, the shift from many deep pools to mostly small riffles with restoration may seem a little undesirable, especially for all you trout enthusiasts out there. After all, big fish need big pools. But, not all streams are created equal, and management goals are not the same for all streams. While we may want to increase pool size and depth in a coldwater trout stream, Mechumps Creek is a tiny, warmwater system. We don’t necessarily care about the size structure of fish because no one is hoping to catch a citation sunfish out of Mechumps Creek. But, in order to preserve the integrity of large creeks and rivers downstream, we do care how well the ecosystem is functioning in Mechumps Creek. And, from a fish perspective, an indication of ecosystem function is how many different species are present (species richness) and how abundant each species is (species evenness). In short, we not only want to see many different species, we also want to see that individuals of each species are equally common throughout the stream as opposed to only one or two species dominating.
How do you increase both richness and evenness? By increasing habitat complexity and diversity- in this case reducing the number of deep pools and increasing the number of riffles and runs to provide habitat for many species that prefer many different types of habitat. This is one of the main goals of stream restoration that is best accomplished by reshaping the existing channel and reducing future streambank erosion (how this is accomplished is feat of skilled engineering, of which I won’t get into the details here).
So far, it seems past restoration efforts at Mechumps Creek have accomplished this goal. This year, while there were many species in the downstream, pre-restoration site (i.e., moderate richness), many of them were fairly rare (low evenness). Most of the fish we caught in the pre-restoration site this year were catfish, sunfish, and mudminnows, all species that we see most commonly in muddy backwaters with low oxygen(i.e,, the habitat that was most prevalent).
In the post-restoration site, we found many more species (higher richness) and improved evenness. There were fewer catfish and mudminnows, and far more darters, dace, and chubs, species that all prefer habitats with more moving water and less silt. So, we can tell from the difference between the fish communities that habitat restoration has long-term improvements to species richness and ecosystem function of Mechumps Creek. Hence the reason for moving on to phase two!
This year wasn’t just special because of the ability to do pre- and post-restoration comparisons. Because we’ve focused all of our attention on the post-restoration reach the last few years, I hadn’t visited the pre-restoration reach in about ten years, back when I was a college freshman hoping to pursue a career in surgery. So much has changed since then, but walking through the stream was like rewinding the clock. Trees we used for survey benchmarks still stood strong, sandbars we had group meetings on had only grown larger, and our little foot paths through the dense brush still seemed completely intact. I can remember many cold, rainy afternoons spent roaming around that stream with my comrades, Sonni and Arba, naïve to the future to come (nor knowing what I even wanted the future to hold), but having the time of my life trying to learn about stream ecology.
Now, here I am, ten years later. I’m turning the corner on my Ph.D., still naïve, but still having fun learning stream ecology. Surveying Mechumps Creek this year, I’m reminded of the leap of faith I took in deciding to pursue a career in Ecology. I won’t lie, I sometimes wonder what might have happened if I didn’t ____ (fill in the blank with any of about 100 serendipitous decisions that got me where I am today) and I had pursued medicine. But, I think back to the experiences I’ve had over the last ten years, the utterly ridiculous things I still find interesting about fish, and the curiosity I still have for research, and there’s no doubt I made the right call.
I’m excited for this next phase of restoration- the restoration project I pitched to Ashland Town Council ten years ago and worked on tirelessly my entire first year of college is finally being realized. But, it’s also bittersweet. The little ecosystem that taught me a love for field ecology was practically unchanged. But, in just a few months, it will all get ripped out with a few swings from the backhoe. It’s a little like renovating your childhood home. I now it needs restoration, but some good memories and a lifetime worth of professional gratitude are tied up in those ugly, eroding banks.
So, I bid farewell to pre-restoration Mechumps Creek. But, the story doesn’t stop here. I’ll go back next year to visit the new and improved stream, meet the new tenants, and start the next chapter of Mechumps Creek.
Summer Trout Bod
It seems like I was just out in Loyalsock, but the calendar doesn’t lie. Two weeks had come and gone and it was time to head back out and collect more blood samples. A full day in the woods, avoiding the ever-increasing traffic around town, handling native trout in the clear, cool stream? A pity, my life.
It’s been a fairly wet summer, especially compared to the severe drought of last year. Nonetheless, streams flows have really dropped in the last few weeks and are reaching summer lows. Yet, I continue to be surprised with some fairly large brook trout in some pretty crappy habitat. But, hey, no complaints here. Work smarter, not harder, right? Or, more accurately, thank you field Gods for blessing me with good fortunes.
But, it’s not just stream flows that have been changing. Over the last few weeks, the trout have put on their summer figures: long, lean, and almost unhealthy looking. How could this be? Just a few months ago I posted about how fat and “football-like” the trout were.
The answer is simple. They’re starving.
It’s a common misconception I often hear about stream trout. In the summer, we’re constantly getting bit by bugs, we see a bunch flying around, and we may even flip rocks and see various aquatic invertebrates crawling around. Insects are everywhere, and so it would make sense that summer would be buffet season for trout.
But, not all insects are created equal. Think about the type of bugs that you see in summer and those you might see during a spring hatch, the time of year when many invertebrate species are transitioning between aquatic larvae and terrestrial adults. Spring hatches may be brief, but the number of bugs swimming and flying around is unmatched. And, many of these bugs are floating on the surface of the stream or in the middle of the water column, making them easy targets for trout. In spring, almost all of a brook trout’s diet is comprised of these aquatic prey forms.
Now, think about the bugs you see in summer. Hatches are over, and most of the invertebrates that are left in streams are difficult for trout to eat because they are glued to the bottom, hiding between rocks, and, in cases like caddisflies, armored is shells. By summer, stream trout are feeding almost entirely on terrestrial insects. But, this food source doesn’t come easy. Most terrestrial insects aren’t buzzing around the water surface for too long, and it takes a lot of energy for trout to jump out of the water to capture their prey, especially when most attempts are unsuccessful. In all, these terrestrial insects are much harder to capture, and in many cases offer fewer calories than the spring hatches.
Making matters worse, as stream flows recede, habitat starts collapsing down giving fish fewer places to forage, but also fewer places to hide from increasing predation pressure. Given the choice between eating and hiding, trout will usually choose hiding until they are at the extremes of starvation.
The degree of summer food deprivation certainly varies by region, and even by stream. Lakes and large rivers go largely unaffected, but in smaller streams, there is often not enough food available for fish to maintain basic metabolic functions. When this happens, fish growth stops and condition factor (the ratio of length to weight) takes a sharp drop. That’s when fish get that long, lean appearance I’ve dubbed “summer trout bod.”
Long-term food deprivation can of course result in death, but can also have long-term effects for survivors. As brook trout are fall spawners, summer is the time they should be devoting calories to production of gametes (eggs and sperm). When fish are barely meeting basic metabolic demands needed for survival, they are can’t devote energy towards gamete production. As a result, they produce fewer and lower quality gametes, leading to fewer and lower quality eggs and juveniles. It’s a vicious cycle.
So, when you head out to your favorite trout stream this summer, the fish might bite like crazy. But, it’s not because they are having a alive and well. It’s probably because they are in desperate need of calories and willing to take more risks and eat a larger variety of prey than they normally would. There’s some controversy in angling if it’s ethical to take advantage of fish when they are in heightened states of vulnerability. Usually this centers around discussions of “bed fishing” (targeting bass on their spawning nests) and targeting coldwater zones that attract fish during high temperatures. But, you could certainly argue that summer trout fishing starts edging closer towards the category of giving humans the unfair advantage. I’m not here to play fishing police (I was fishing just the other day, in fact), but just something to think about next time you grab your fishing pole.
The Start of Something New
We turned a new page this week. After two years, our population genetics dataset is finally complete. This means I have the genotypes (essentially the genetic identity) for over 2,100 fish across the Loyalsock Creek watershed and some of the most common hatcheries that stock in the area. It’s a huge step forward. I had reached a standstill with just about every project I am working on because they all needed the genetic data for some reason or another. Now I can finally start producing some much-anticipated results.
So, which project do I start with? The obvious answer is with a study that is beyond the scope of any grant and not one of the original chapters of my dissertation. The original intent of collecting population genetics data was to describe the degree of connectivity among 20 tributaries in the watershed. And, I’ll still do that. In fact, I’ll be doing it for 29 tributaries because I got a little overzealous in the summer of 2015 and just kept sampling. Oops.
After running some preliminary analyses on those 29 tributaries back in December and talking to some locals about stocking events, it became clear to us that we couldn’t faithfully report any final genetic results without accounting for the potential influence of stocked fish on natural population genetics. Simple enough, but adding the hatcheries into the dataset resulted in a seven-month delay in data analysis.
Thankfully, the analysis goes a little faster than the lab work, and I’ve already gotten some preliminary results on the hatchery + wild dataset. It looks like the dataset was worth the wait and some interesting things are showing up. So interesting so that we’ve decided to add another study that quantifies the amount of introgression between wild and hatchery brook trout. I’ve briefly discussed introgression in a previous blog, but in short it’s a fancy term to describe the mating between wild and hatchery fish. Generally speaking, introgression is a negative consequence of stocking. Hatchery fish often lack genetic diversity, and may carry genes that are maladaptive to natural environments. This isn’t a big problem if the stocked fish aren’t spawning because all of the maladaptive genes are removed from the population before they can get carried into the next generation.
But, when hatchery fish do spawn, there can be problems. You can think of reproduction as essentially taking the average between two parents. If you take the average of a genetically rich wild fish and a genetically poor hatchery fish, the result is offspring that are genetically inferior with lower survival and reproduction when compared to offspring spawned from two wild parents. This effect, known as outbreeding depression, often happens when there is a high degree of introgression between wild and hatchery fish, and can quickly lead to population collapse.
Unfortunately, while I can tell you that hatchery fish and wild fish are genetically very different from one another, the analyses are still a little too young and the topic potentially a little too controversial, to comment on the degree of introgression we are finding. But, I can tell you why, regardless of whether we see introgression or not, these results are really interesting:
So, any predictions? Do you think Loyalsock brook trout have signs of introgression?
Lice Lice, Baby
There’s no way around it. Sometimes my job sucks. Like days when I’m sampling in sub-freezing temperatures in November, or grabbing my gear as I hear the weather man use words like “oppressive heat warning.” There’s also 18-hour days, days spent hiking up cliffs, days where you feel like you must be wallowing in a pit of stinging nettle, poison ivy, and mosquitos, and days were all three of those events combine.
And then there are days where I have the burden of electrofishing a stream loaded with 9+ inch native brook trout in the breeze of an unseasonably cool summer day.
Yeah, I didn’t say my job always sucks. And, this week, my job didn’t suck. In one of the easiest field days in recent memory, we recruited 22 new brook trout into my study (yes, I know I just jinxed myself, but I’m hoping it’s retribution for some of the other days I’ve had this year). That’s 22 more blood and gill samples packed away in very deep freeze to be studied for their expression of stress proteins.
In most of my field work descriptions, I’ve taken the easy way out and said I’m collecting a “blood sample.” That’s not entirely accurate. I’m collecting a blood sample, which I then use to get a plasma sample. Though it is the largest component of blood (making up about 55% of blood, by volume), plasma may seem a bit foreign to you unless you’ve donated or received it. Masked by the more obvious color of red blood cells, straw-colored plasma is practically invisible when suspended in whole blood. But, it’s made up of some of the most important elements in the body- water, salt, enzymes, and, you guessed it, proteins. This includes all the stress proteins we are interested in measuring as stream temperature rises.
With a little know-how, it’s actually quite easy to separate red blood from plasma. The folks at the American Red Cross do it with a big machine that takes your whole blood and spins it in a circle really fast (otherwise known as centrifuging). Red blood cells are heavier than plasma, so centrifuging pulls the heavier red blood cells to the bottom, and the lighter plasma components to the top. Once separated, it’s then possible to remove plasma and, in the case of the Red Cross, return red blood cell components back to the donor.
In the fish world, we do things a bit differently. First, there are no big machines. There are small centrifuges running off car batteries or borrowed electricity from the Snack Shop at World’s End State Park (the view is inarguably better here than in the plasmapheresis center). And, forget return to donor, we’re greedy and keep both the plasma and red blood for analysis. But, other than that, the process is about the same. Collect blood, centrifuge blood, remove plasma, repeat. (We may also be feeding ourselves the sugary post-donation snacks. But, we checked, the fish don’t mind.)
In total, it takes about three hours to remove plasma from 22 blood samples. And, what would you know, we meet a lot of people curious as to why there’s a few college kids with a centrifuge and sterile gloves next to the Snack Shop. Luckily, I like to chat fish to anyone willing to listen. And, I’ve pretty much memorized my spiel when asked “what the heck are you doing?” So, I start chatting about climate change, fish movement, and gene expression. And, you want to guess the number one question I get asked in return?
Have you found any gill lice?
Seriously? I’m over here teaching a course in fish phlebotomy and toting around the equipment that allows me to electrocute fish WHILE I walk in the water, and you want to know about a parasite? Move along!
In all seriousness, I do get asked some great questions about my research, and I appreciate that so many people are so attune to this rising threat. Fortunately for me, even after taking gill biopsies from over 400 fish in the last year, I have never personally encountered a trout infected with gill lice. And, I am thankful for that.
What’s the big deal with gill lice? Despite the name, gill lice are not related to the form of head lice common to elementary schools and daycares. Gill lice are small crustaceans (yes, just like shrimp, crabs, and crayfish) in the genus Ergasilus. Male gill lice free-float throughout the water column and females attach to the gills of fish. That may seem innocent enough, but once attached gill lice start feeding on blood pumping through gills, thereby interfering with a fish’s ability to “breath” (absorb oxygen and release carbon dioxide). After prolonged, intense infection, fish can have reduced growth and reproduction, compromised immune systems, altered behavior, and can eventually die.
Gill lice are a bit unique in that they are host-specific, meaning any given species of gill lice (of which there are several) is selective as to which species of fish it is willing to parasitize. So, there is a species of gill lice for brook trout, and a gill lice species for rainbow trout. So far, gill lice in Pennsylvania have only been shown to infect brook and rainbow trout, but other species of gill lice have been shown to infect salmon, bluegill, bass, walleye, and yellow perch, among many others.
While the press coverage is new, gill lice have been infecting streams throughout the United States for decades. It was only recently that gill lice started making front page headlines in Pennsylvania when a large outbreak was discovered in Centre County in 2016. The origin of the gill lice in Pennsylvania can be debated, as they could have gone undetected in wild streams for years prior to the 2016 discovery. However, there is also a smoking gun pointed towards a cooperative fish hatchery, which was known to have infected trout in the hatchery around the time of discovery. Regardless, what we know now is that gill lice have established residence in many Pennsylvania streams. And, once we started looking for gill lice we kept finding them. So, the number of streams infested with gill lice only continues to climb.
How many streams are infected with gill lice? We don’t know. How are gill lice affecting trout populations in Pennsylvania? We don’t know. And, how can we stop the spread? You guessed it, we don’t know. So far, the state is trying to minimize the spread by decontaminating hatcheries and sampling streams to determine the extent of infection. It’s going to be a tough battle, though, because gill lice are resistant to chemical treatments that can be used to reduce parasite loads. So, unfortunately, managers’ hands are largely tired in trying to eradicate the parasite from wild streams.
While we in Pennsylvania may be on the very start of an outbreak, we can look west to predict how trout populations may fare. Reports from Colorado and Wisconsin suggest two important things. First, trout populations decline after gill lice infestation. Second, warmer temperatures lead to higher infection rates. This could be because gill lice are more productive in warmer temperatures, trout become more susceptible at warmer temperatures, or a combination of both.
What can you do to prevent the spread? As a general rule of thumb, always disinfect your gear when you’re leaving a stream. This includes hopping across major watersheds, but even if you’re just moving between neighboring tributaries. Gill lice may be present without you knowing it, and even if they aren’t you can help prevent the spread of other aquatic and terrestrial invasives. Also, it goes without saying, don’t move fish between streams, as this could result in new infections.
When you’re fishing, keep an eye out for little rice-like nodules on the gills, opercula, or pectoral fins. Take a picture if you can, and report any suspicious findings to your local authorities. It’s always disheartening to put another stream on the infection list, but it will help managers contain the spread and devise a plan forward.
Also, keep in mind, stream temperatures are rising and for many it’s getting close to that time of year where you should consider switching your target species. Angling mortality greatly increases at 65F and above, so take a thermometer and fish responsibly.