• Bryce Oldemeyer

Yellowstone Cutthroat Trout Management on the South Fork Snake River (Update 2021)

Updated: Jul 14

In February 2019, I wrote a blog highlighting native Yellowstone Cutthroat Trout management on the South Fork Snake River that provided background on Yellowstone Cutthroat Trout and Rainbow/Hybrid Trout dynamics in the system, management strategies aimed to protect Yellowstone Cutthroat Trout, and how reducing non-native Rainbow/Hybrid Trout abundances can help protect and promote native Yellowstone Cutthroat Trout in the system. This is a continuation of that blog.

Highlights

  • In 2020, the combined abundance of all trout in the South Fork Snake River at the Conant reach was the highest on record, and the abundance of Rainbow Trout and Rainbow x Yellowstone Cutthroat Trout hybrids was the second highest on record.

  • Hybridization and interspecies competition from non-native Rainbow Trout and Hybrid Trout pose a serious threat to native Yellowstone Cutthroat Trout in the South Fork Snake River.

  • Public opinion supports protecting and conserving native Yellowstone Cutthroat Trout in the South Fork Snake River.

  • Prior management practices have slowed the increasing trend of Rainbow and Hybrid Trout in the system but efforts have not been enough to reverse or stop the trend.

  • In an effort to conserve and protect Yellowstone Cutthroat Trout in the South Fork Snake River by decreasing Rainbow/Hybrid Trout abundances, the Idaho Department of Fish and Game has set a goal to remove approximately 12,000 Rainbow and Hybrid Trout from the South Fork Snake River in mid-April through the end of May.

Introduction

Yellowstone Cutthroat Trout, Rainbow Trout, and Rainbow x Yellowstone Cutthroat hybrids (hereafter referred to as, “Hybrid” Trout) all contribute to the world class South Fork Snake River fishery. Ideally, Yellowstone Cutthroat Trout and Rainbow/Hybrid Trout could cohabitate with minimal interspecies competition and hybridization. Unfortunately, Yellowstone Cutthroat Trout and Rainbow/Hybrid Trout share similar life history strategies, utilize the same habitat, and compete for the same resources, with Rainbow/Hybrid Trout exhibiting a competitive advantage in the system. Rainbow/Hybrid Trout would likely hybridize and outcompete native Yellowstone Cutthroat Trout if left unmanaged in the South Fork Snake River. Since 2004, at the direction of the public and the Idaho Department of Fish and Game Commission, the Idaho Department of Fish and Game (IDFG) has been managing the South Fork Snake River to protect and promote native Yellowstone Cutthroat Trout. Specifically, their overarching goals are to protect the genetic integrity and population viability of Yellowstone Cutthroat Trout and decrease the threats Rainbow/Hybrid Trout pose by reducing their abundance to less then 10% in the upper South Fork reach. These have been IDFG's goals since 2004 and IDFG has been working towards these goals through a three-prong approach of excluding Rainbow/Hybrid Trout from critical Yellowstone Cutthroat Trout spawning habitat, reducing Rainbow/Hybrid Trout spawning success through a springtime freshet flow, and reducing abundance of adult Rainbow/Hybrid Trout through angler harvest. The weir program has been effective at minimizing hybridization during Yellowstone Cutthroat Trout spawning at major tributaries but angler harvest and the spring freshet have been marginally effective at reducing Rainbow/Hybrid Trout abundances. Rainbow/Hybrid Trout abundances have continued to increase in proportion to Yellowstone Cutthroat Trout abundances and pose a serious threat to the Yellowstone Cutthroat Trout population (Figure 1). To prevent future declines in the Yellowstone Cutthroat Trout population, IDFG intends to boat electrofish Rainbow/Hybrid Trout when they congregate at redds during the spawning season in 2021, remove them from the South Fork Snake River, and translocate them to other public waterbodies in the Upper Snake River region. The Henry’s Fork Foundation - South Fork Initiative (HFF-SFI) recognizes this is not an ideal situation but we fully support the management decision in order to protect the Yellowstone Cutthroat Trout population.

Figure 1. Rainbow and Hybrid Trout (RBT) and Yellowstone Cutthroat Trout (YCT) abundances at the Conant survey reach of the South Fork Snake River, ID, 1982-2020 (credit: IDFG).

Question and Answer

How do Rainbow Trout impact native Yellowstone Cutthroat Trout?

Rainbow Trout impact native Yellowstone Cutthroat Trout in the South Fork Snake River in one of two ways; 1) introgression (hybridization) and 2) competition for limited resources. The IDFG released a blog discussing hybridization and introgression of Rainbow Trout and Yellowstone Cutthroat Trout in the South Fork so I will refrain from digging into that topic. Instead, I will focus on interspecies dynamics and competition between the two species.


Over thousands of years, native Yellowstone Cutthroat Trout have evolved and adapted to the South Fork system. They developed a diverse life history that maximized their reproductive success and survival within a natural South Fork system. In general, Yellowstone Cutthroat Trout in the South Fork exhibit a life history that is centered around migrating into tributaries and spawning after peak flows, typically in late-May through July. This allowed Yellowstone Cutthroat Trout to spawn in clean, cold, and clear headwater habitat but it also increased the chance that eggs didn’t get dislodged from the substrate during peak flows. This was a favorable strategy for a trout in a natural, unaltered South Fork system.

Figure 2. General migration and spawning period for Yellowstone Cutthroat Trout in the South Fork Snake River and accompanying hydrograph of median natural (unregulated) flow for the South Fork Snake River at Irwin, Idaho. Note the majority of Yellowstone Cutthroat Trout spawning occurs on the tail end of peak flows.

Rainbow Trout were stocked in the South Fork up until 1981 and have similar life history characteristics to Yellowstone Cutthroat Trout with one seemingly small, but significant difference to Yellowstone Cutthroat Trout. Rainbow Trout spawn 1-2 months earlier than Yellowstone Cutthroat Trout and tend to spawn in the main river. In a natural South Fork system prior to human alterations (i.e. dams and flow management), spawning earlier and in the main river would have been a poor choice for a trout. Not only are you spawning before peak flows (higher chance your eggs get dislodged from the substrate) you are spawning in the main river (again, higher chance your eggs get dislodged from the substrate).

Figure 3. General migration and spawning period for Rainbow and Hybrid Trout (RHT) in the South Fork Snake River and accompanying hydrograph of median natural (unregulated) flow for the South Fork Snake River at Irwin, Idaho. Note that the majority of Rainbow/Hybrid Trout spawning occurs prior to peak flows.

However, in a regulated system (i.e. system with dams and flow management) it can be advantageous to spawn earlier and in the main river if peak flows are not high. Spawning earlier allows juvenile trout a longer period to grow prior to the upcoming winter when there is a bottleneck for juvenile trout and mortality is high. As a trout, being larger in size increases your chances of survival through the winter because of increased fat reserves and the fact that competitive bouts for ideal holding positions in the river are based on size, so larger fish have better access to cover and food while minimizing effort necessary to maintain the spot. This is why Rainbow Trout have an advantage over Yellowstone Cutthroat Trout in the present regulated system.

Figure 4. Mean migration and spawning period for Yellowstone Cutthroat Trout and Rainbow/Hybrid Trout (RHT) in the South Fork Snake River and accompanying hydrograph of median natural flow (flow if there weren’t dams) and median regulated flow (current flow with dams in place) for the South Fork Snake River at Irwin, Idaho. Note the timing for the regulated hydrograph is consistent with the natural hydrograph but the magnitude of peak flow is ~6,000 cfs lower. The regulated hydrograph enables Rainbow/Hybrid Trout to be successful in spawning earlier in the spring which allows juvenile Rainbow/Hybrid Trout a longer growing season prior to winter.


Can’t you do restoration projects to increase Yellowstone Cutthroat Trout production?

Then there will be more juvenile Yellowstone Cutthroat Trout being produced in the system and you don’t need to remove Rainbows/Hybrids! Unfortunately, no. Restoration projects alone will not address the overarching issue that Rainbow/Hybrid Trout displace and outcompete Yellowstone Cutthroat Trout. I explained above how Rainbow/Hybrid Trout spawn earlier in the spring and this allows juvenile Rainbow/Hybrid Trout to have a longer growing period relative to Yellowstone Cutthroat Trout prior to the first winter. This allows Rainbow/Hybrid Trout to be larger going into the winter when juvenile trout have the highest mortality rates.


Completing restoration projects that increase juvenile Yellowstone Cutthroat Trout production will not provide much benefit if juvenile Yellowstone Cutthroat Trout migrate out of tributaries into the main river and come in direct competition with larger juvenile Rainbow Trout. Below are a series of figures that try to explain this bottleneck concept.

If trout populations in the South Fork Snake River were left unmanaged, Rainbow/Hybrid Trout would outcompete Yellowstone Cutthroat Trout based on the biology and data that during the winter when resources are limited, larger juvenile trout will have the greatest chance of acquiring resources and surviving.

If there are fewer juvenile trout competing for available resources, overall juvenile trout survival will increase over the winter. This is the concept behind removing Rainbow/Hybrid Trout in order to increase juvenile Yellowstone Cutthroat Trout survival (i.e. decrease interspecies competition). If there are more resources available for juvenile Yellowstone Cutthroat Trout, their survival would increase.

Trying to produce more juvenile Yellowstone Cutthroat Trout in a system that is saturated by Rainbow/Hybrid Trout may produce a few more Yellowstone Cutthroat Trout but it is more likely there would just be higher mortality rates of Yellowstone Cutthroat Trout during the winter. The larger juvenile Rainbow Trout will continue to outcompete smaller juvenile Yellowstone Cutthroat Trout for available resources and Yellowstone Cutthroat Trout survival would remain low.


It is anticipated that completing restoration projects, in conjunction with Rainbow/Hybrid suppression efforts, will increase juvenile Yellowstone Cutthroat Trout production out of the tributaries and propagate to increases in the Yellowstone Cutthroat Trout population. This is exactly why HFF-SFI, IDFG, local NGOs, and other federal partners have been collaborating and working with local landowners within the Rainey Creek drainage (major tributary of the South Fork that supports a fraction of the Yellowstone Cutthroat Trout spawning and rearing that it historically used to support) in order to restore most, if not all, of lower Rainey Creek.


How did IDFG come up with the goal of removing ~12,000 fish?

“A thesis completed in 2014 by Evalinda DeVita identified that RBT numbers should be decreased annually by approximately 20% to effectively manage threats to YCT. Due to inherent variability in all biological systems, and the record high abundances, we believe a suppression goal of 30% would be appropriate in order to decrease RBT abundance and halt the increasing trend of RBT in to subsequent years. In the fall of 2020, IDFG estimated 2,230 RBT/mi. (± 259) in the Conant monitoring reach (Figure 1). The Conant monitoring reach is a fraction of the upper river where RBT are most abundant, so to estimate the total number of RBT to remove through suppression, we multiplied 2,230 by the distance between Palisades Dam to Dry Canyon (19 mi.), to conservatively estimate 42,370 RBT in the SFSR. Thirty percent of the total number of RBT is 12,711. Therefore, our goal is to remove a minimum of 12,000 RBT from the SFSR in 2021.” – IDFG Rainbow trout suppression on the South Fork Snake River blog


Why doesn’t IDFG remove fish during the winter or some other time?

Electrofishing in the spring allows IDFG to target spawning areas where adult fish are congregated in high abundances. This increases electrofishing efficiency and essentially reduces the amount of time required to electrofish to get the same number of fish.


What can we expect during suppression efforts this spring?

To achieve our (IDFG) goals in 2021, IDFG plans to suppress RBT in the SFSR using boat electrofishing four days per week (Mon – Thur), from Monday, April 19 – Thursday May 27 (Table 1). Work should begin around 8:00 a.m. and will cease around 3:00 p.m. Additionally, RBT may be removed during fall surveys or at other times opportunistically." - IDFG Rainbow trout suppression on the South Fork Snake River blog

Table 1. Plans for Rainbow Trout suppression in the South Fork Snake River in 2021, including the river section planned for suppression by day of the week. (credit: IDFG)


What does this mean for total trout abundances once fish are removed (fish/mile)?

Total trout (fish/mile) in the Conant reach is estimated to be ~4,750 fish/mile if IDFG is able to hit their target of removing ~12,000 fish. This is ~130 fish/mile (2.7%) less than the 10-year average of 4,880 fish/mile. Take into account the typical sampling error in the population estimate is ~10% and the difference between this year (assuming IDFG can hit their target) and the 10-year average is not statistically significant.


What happens to the fish that are removed?

All RBT removed from the SFSR will be translocated to other waters. Some Rainbow Trout removed from the river will be stocked into public fishing ponds, including Louis (Swan Valley), Trail Creek, and Jim Moore ponds early during suppression efforts. However, as pond temperatures warm, the majority of the RBT removed from the SFSR are going to be stocked in the lower Henry’s Fork where RBT numbers are low. A proportion of the RBT released into the Henry’s Fork will be marked with orange T-bar anchor tags for IDFG’s “Tag, You’re It” program (Figure 2). These tags will help us determine how translocated fish benefit the receiving fisheries, and determine how far these fish move after being introduced into new waters. If you encounter one of these tags, please report it following the instructions on the tag, or at https://idfg.idaho.gov/fish/tag/add?no_cache=1617646869.” - IDFG Rainbow trout suppression on the South Fork Snake River blog


Will IDFG be electrofishing every spring?

It depends. First, this spring is likely going to be the largest boat electrofishing Rainbow/Hybrid Trout removal effort that IDFG conducts. Depending on the success of the electrofishing efforts this spring, it is likely that removal efforts in subsequent years could be much lower. If suppression efforts are successful this year, it may only require 3-4 weeks next year to remove 30% of the Rainbow/Hybrid Trout population. The year after that, it may only require 1-2 weeks to remove 30% of the Rainbow/Hybrid Trout population. Then maybe the year after that, angler harvest would be enough to achieve management objectives.


Ideally, angler harvest of Rainbow/Hybrid Trout from the South Fork would be enough to keep Rainbow/Hybrid Trout abundances low. Unfortunately, Rainbow/Hybrid Trout abundances have increased to record high levels and angler harvest alone is not enough to keep Rainbow/Hybrid Trout abundances from continuing to increase. This is why IDFG is having to use boat electrofishing to help reduce Rainbow/Hybrid Trout abundances.


How do you know that reducing Rainbow/Hybrid Trout abundances will actually help Yellowstone Cutthroat Trout abundances?

Combined trout abundance (Rainbow/Hybrid + Yellowstone Cutthroat) in the Conant reach has not changed much in the last 40 years. Yes, there is annual variability between years that is a product of changes in environmental condition but in general, the combined trout abundance has remained fairly consistent (Figure 5). What has changed is the composition of Rainbow/Hybrid and Yellowstone Cutthroat Trout. Rainbow/Hybrid Trout abundances continue to increase while Yellowstone Cutthroat Trout decline. Recently, we have seen an uptick in both species abundances which is in large part due to several consecutive years with above average water conditions. The concern is that when water conditions return to average, or below average like 2021 is shaping up to be, juvenile Yellowstone Cutthroat Trout will be disproportionately impacted if there are high abundances of juvenile Rainbow/Hybrid Trout outcompeting Yellowstone Cutthroat Trout for resources. There are strong biological and ecological mechanisms and data supporting the concept that if there is less competition for resources (i.e. less Rainbow/Hybrid Trout in the system), Yellowstone Cutthroat Trout will utilize the available resources and their population will increase.

Figure 5. Rainbow and Hybrid Trout (RBT) and Yellowstone Cutthroat Trout (YCT) abundances at the Conant survey reach of the South Fork Snake River, ID, 1982-2020.


I’ve heard all the Yellowstone Cutthroat Trout in the South Fork Snake River are already introgressed with Rainbows. Is this true?

No. There is strong evidence showing the contrary. See the IDFG Genetic Integrity of the South Fork Snake River Yellowstone Cutthroat Trout, Part I: Introgression/Hybridization blog that discusses this topic.


I’ve heard Yellowstone Cutthroat Trout in the South Fork Snake River aren’t even the native trout that were in the system historically. Is this true?

No, Yellowstone Cutthroat Trout are endemic to the South Fork Snake River and the entire Upper Snake River region. This includes Yellowstone Cutthroat Trout that exhibit both large spotted and fine spotted morphological forms.



Below are Q&A’s from the 2019 blog that are still relevant to this discussion. Information bookended with “*” are additional comments I have added to the old answers.



If you recognize that RHT and YCT both contribute to the world class South Fork Snake River fishery, why do you favor YCT?

RESPONSE: If the YCT population crashes there is potential they will get listed as a federally protected species through the Endangered Species Act, at which point management of the entire system would be hyper focused on YCT protection and recovery. This would likely mean aggressive RHT removal, prolonged recovery of a severely depleted YCT population (it is easier to protect a population of 1,800 fish/mile than recover a population of 200 fish/mile), and in the most extreme case, a shutdown of the entire fishery to prevent incidental by-catch and incidental mortality of YCT. While the most extreme case sounds unbelievable, a recent *2019* closure of steelhead fishing on the Main Salmon River and South Fork Clearwater River echo a similar situation. Even though hatchery steelhead are in the rivers and under normal circumstances could be caught and legally harvested, all steelhead fishing has been closed to prevent incidental by-catch and mortality of wild, ESA listed “threatened”, steelhead.

In summary, preventing a collapse of the South Fork Snake River YCT population is a better alternative than recovering a collapsed South Fork Snake River YCT population.


*An even greater justification to conserve and protect Yellowstone Cutthroat Trout is that they are an an iconic native species of Idaho. Not only do the citizens of Idaho overwhelmingly support conserving and protecting native trout but there only a few places where you can catch big, wild Yellowstone Cutthroat Trout in their native range; the South Fork Snake River being one of those places."


Okay, but what are the chances YCT get listed under the Endangered Species Act?

RESPONSE: From the 1880s through the 1980s, the introduction of non-native species (primarily Rainbow Trout, Brown Trout, Brook Trout, and Lake Trout), posed serious threats to pure, unaltered, YCT populations residing in their native range. In 1998, it was estimated that YCT occupied 43% of the historic range and only 17% of the populations exhibited no form of RHT introgression (May et al. 2003). Declining trends in YCT populations in their historic range motivated the petition to list YCT under the Endangered Species Act (ESA) in 1998. While the petition was officially deemed unwarranted in 2001, it emphasized the need to protect and prevent the decline of YCT populations to avoid future listing as a federally protected species.


From 1980-2001 (the period leading up to the ESA listing petition), YCT abundances averaged 2,541 fish/mile in the Conant index reach of the South Fork Snake River. Since 2002, YCT abundances have averaged 1,578 fish/mile. The recent increase in RHT abundances pose serious threat to YCT. If left unmanaged, the increased inter-species competition from RHT could severely impact juvenile YCT survival and overall YCT abundances in the near future.

*While I do not know of any organizations looking to petition YCT at this moment in time, it is not unimaginable to think if YCT populations continue to decline there could be another petition proposed to list them in the future.*