The Start of Something New

This fish, and roughly 2,100 of his cousins, proudly gave their fins for our study.

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. 

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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:

• Despite it being a hot topic in fisheries management, there aren’t that many studies on stream trout and introgression. If this topic had been well covered in the literature, we probably could have made an assumption about the degree of introgression and not sampled our hatchery strains.  But, we really didn’t have a strong hypothesis about how hatchery stocking was influencing wild genetic diversity.
• Previously, our ability to detect historical (i.e., 5+ generations ago) introgression was very limited. That means that if there was a stream that was previously stocked but had since been returned to natural reproduction, we wouldn’t be able to comment on how historic introgression influences present-day population genetics. Today, with some fancy mathematical voodoo, we can make better estimates about long-term introgression patterns. This could prove particularly useful in Loyalsock, where many sites in the study were last stocked 5-10 years ago but have since been unmanaged.
• If we see introgression, it suggests that we might want to evaluate stocking protocols to minimize reproduction between wild and hatchery strains. It’s possible that altering stocking densities, not stocking during certain times of the year, and even potentially stocking sterile hybrids could minimize the effect of stocking on wild trout genetics. It would also be of interest to see how introgressed populations compare to wild populations in growth rate, reproduction, and recovery from disturbance to see how introgression influences the functional properties of a population.
• If we don’t see introgression, it’s not a green light to stock more or ignore the potential for introgression. Our ability to detect introgression is high, but it’s not 100%. And, we are only working in a single watershed with data collected from a study not designed to detect introgression. But, if we don’t find evidence of introgression, it would give us a reason to investigate why we aren’t seeing it. Some streams we sampled get stocked with over 2,400 adult brook trout every spring. Do stocked fish not survive? Do they move? Do they not naturally reproduce?  Is there some happy accident with how we are stocking that limits their ability to naturally reproduce? If we can answer these questions it can help us make sure that we minimize future patterns of introgression.

 
So, any predictions?  Do you think Loyalsock brook trout have signs of introgression?