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Genetics: A Tool to Improve Bull Trout Sustainability

Three hydroelectric projects on the Clark Fork River in Montana and Idaho block upstream migration of bull trout, a threatened species. Avista Corporation, which owns two of these projects, uses genetic analysis of fin tissues from bull trout collected below the most downstream dam to determine each fish’s region of origin. The utility can then trap and truck the bull trout to the region where it is most likely to spawn successfully.

By Shana R. Bernall and Joseph M. DosSantos

Bull trout (Salvelinus confluentus) populations in the Pacific Northwest have been in decline for several decades as a result of habitat degradation and fragmentation and competition from non-native fish species. In fact, bull trout are a federally listed “threatened” species in the Pacific Northwest.

How the dams affect bull trout populations

Bull trout hatch in natal streams, where they spend one to three years as juveniles before migrating downstream to mature in larger bodies of water. Upon reaching maturity, bull trout migrate back upstream to their natal streams to spawn. However, bull trout habitat in the Pacific Northwest has been fragmented by man-made barriers (dams) that block fish migration.

On the Clark Fork River in Montana and Idaho, a series of three hydroelectric facilities prevent upstream movement of bull trout. (See Figure 1 on page 48.) Avista Corporation owns and operates two of these three facilities, 231-MW Cabinet Gorge and 466-MW Noxon Rapids. Cabinet Gorge is about 16 kilometers upstream of Lake Pend Oreille. Next is Noxon Rapids, 32 kilometers upstream of Cabinet Gorge. About 60 kilometers upstream of Noxon Rapids is 85-MW Thompson Falls, owned and operated by PPL Montana. None of these three hydro projects have permanent facilities for passing fish upstream.

During Avista’s work to obtain a new Federal Energy Regulatory Commission (FERC) operating license for the Cabinet Gorge and Noxon Rapids projects, the utility developed and finalized a fish restoration plan.1 This Native Salmonid Restoration Plan is a holistic approach to address issues affecting native salmonid populations in the lower Clark Fork River and identify actions needed to improve their long-term viability.

Researching ways to improve bull trout spawning

To address native salmonid restoration, Avista funded a number of projects designed to increase connectivity on the lower Clark Fork River and improve survival and spawning of native salmonids.

One of Avista’s goals under the restoration plan was to determine if bull trout captured below Cabinet Gorge Dam originated from tributaries downstream or upstream of the facility.

To complete this work, Avista captured 477 juvenile bull trout in tributaries below and 264 juvenile bull trout in tributaries above Cabinet Gorge Dam over a two-year period. In addition, a total of 68 adult bull trout were captured below the dam between 1997 and 1999. Personnel collected fin tissue samples from the pelvic fins of both juvenile and adult fish. Fin tissue samples were sent to the University of Montana Wild Trout and Salmon Genetics laboratory for analysis.

Genetic analysis revealed that adult bull trout captured just below Cabinet Gorge Dam were more closely related to juvenile bull trout populations in upstream tributaries than populations in downstream tributaries.2 These results reinforced the need to increase connectivity in the lower Clark Fork River.

To help bull trout return to their natal streams to spawn, Avista undertook a “trap and truck” program in 2001. The utility capturing bull trout below Cabinet Gorge Dam, using night electrofishing within a 1.3-kilometer reach of the river located directly downstream of the dam. The fish were placed in holding tanks. Personnel then implanted all fish in the tanks weighing a minimum of three pounds with radio transmitters. A transmitter could only be implanted if it weighed less than 2 percent of the body weight of the fish. Batteries in the transmitters had a minimum lifespan of 324 days in 2001 and 2002 and 560 days in 2003 and 2004. Personnel also collected fin tissue samples from all the fish to be used for a future genetic program.


Figure 1: Dams on the Clark Fork River block upstream movement of migrating bull trout, meaning Avista Corporation must trap and truck fish. To ensure fish are transported to the proper location, Avista uses genetic sampling to assign fish to one of four regions of origin.
Click here to enlarge image

Fish were then transported over the dam in trucks equipped with 150-gallon aerated tanks and released into Cabinet Gorge Reservoir. From 2001 through 2003, Avista tracked fish movement using the radio transmitters. During this project, migratory bull trout were documented moving into known spawning tributaries to Cabinet Gorge Reservoir.

Developing the genetic analysis program

Once the utility determined bull trout could be safely transported over Cabinet Gorge Dam, another problem had to be resolved. Because the series of three dams acted as barriers to upstream fish movement, personnel did not know in which body of water these fish belonged – Cabinet Gorge Reservoir, Noxon Rapids Reservoir, or Thompson Falls Reservoir. Again, Avista turned to genetic research to solve this problem.

The utility tapped fish geneticists at the Abernathy Fish Technology Center, U.S. Fish and Wildlife Service Conservation Genetics Laboratory in Longview, Wash., to develop a bull trout genetic baseline data set during the summer of 2003.3 Personnel collected additional bull trout fin clips from populations in each of the tributaries to the lower Clark Fork River and combined these samples with previous fin tissue samples analyzed by the University of Montana Wild Trout and Salmon Genetics Laboratory.

A total of 506 pelvic fin clips were taken from juvenile bull trout captured through stream electrofishing in tributaries below the dam; 511 fin tissue samples were taken from juvenile bull trout captured through stream electrofishing in tributaries above the dam. After capture, a small piece of pelvic fin tissue was clipped off the fish. The live fish was then released at its capture location. The fin tissue samples were then sent to the Abernathy lab for analysis. There, scientists extracted deoxyribonucleic acid (DNA) and analyzed this DNA based on 12 microsatellite loci, which are specific markers used to map genetic material.

The scientists then developed data sets for each of four regions shown in Figure 1: below Cabinet Gorge Dam (Region 1), between Cabinet Gorge Dam and Noxon Rapids Dam (Region 2), between Noxon Rapids Dam and Thompson Falls Dam (Region 3), and above Thompson Falls Dam (Region 4). These data sets could then be used to assign individual fish captured below Cabinet Gorge Dam to their most likely population and region of origin.

The probability of genetically assigning a fish to its region of origin was greater than 95 percent for Region 1, 3, and 4 fish, and 90 percent for Region 2 fish.4 This high confidence level made the possibility of transporting fish upstream to access their natal streams feasible.

Every year, 50 juvenile bull trout from five different populations are resampled and added to the existing baseline. This helps keep the baseline data set updated and allows detection of any genetic drift within or between populations.

Implementing the results of genetic analysis

Avista began its bull trout rapid response genetics protocol in the spring of 2004. Bull trout were captured from early April through September/October, using night electrofishing, trapping, or hook-and-line sampling below Cabinet Gorge Dam. Fin clips were taken and stored in micro-centrifuge tubes containing 95 percent ethyl alcohol. The morning after capture, each fin tissue sample was clipped in half, and half of the sample was shipped overnight to geneticists at the center. During the 48- to 72-hour waiting period from capture to results, bull trout were held in 1,500-gallon circular tanks containing about 1,000 gallons of spring-fed cold water.

The genetic samples arrived at the center around 10 a.m. Geneticists extracted DNA from each piece of fin tissue and compared it to the genetic baseline data set using the Whichrun computer program.5 This program assigned each fish to two populations, the most likely and second most likely population of origin.4 A report was e-mailed or faxed to Avista the same day the lab received the genetic sample. The report listed the population assignments for each fish, the associated statistical confidence for each assignment, and suggestions for transport of each fish.

The transport suggestions were used to determine the location of each bull trout release. If a fish was assigned to Region 1, Avista personnel released it below Cabinet Gorge Dam without implanting a radio transmitter. If a fish was assigned to the other three regions, Avista biologists implanted a radio transmitter in its abdomen to track its movements after release. Avista biologists continued monitoring each fish’s movements during the lifespan of the radio transmitter (minimum of 560 days).

Before the full program could be carried out, Avista needed to perform some smaller research projects. In 2004, 40 out of 42 of the fish assigned to Regions 2, 3, or 4 were released in Region 2. The goal was to identify a potential fish trapping site below Noxon Rapids Dam. Because of their upstream areas of origin, fish assigned to Regions 3 and 4 could be expected to migrate to the base of Noxon Rapids Dam, seeking further upstream passage. Remote radio telemetry stations positioned at various locations on the dam were used to pick up signals on these radio-tagged bull trout and were essential for pinpointing areas of the tailrace with higher rates of use. In the future, these high-use areas may be effective sites for the establishment of upstream fish passage facilities.

Beginning in 2005, fish assigned to Region 2 were no longer implanted with radio tags. At the same time, fish assigned to Regions 3 or 4 were radio-tagged and released in Region 3, this time to identify potential trap locations below Thompson Falls Dam.

Results and future work

From 2001 to 2004, 153 bull trout were captured for testing. Of these, 147 had viable genetic samples that could be used to asign them to a population and region. When transported over Cabinet Gorge Dam into Cabinet Gorge Reservoir, nearly half (49 percent) of these fish entered a tributary to the reservoir, while 27 percent approached the next upstream dam. The remaining fish moved within Cabinet Gorge Reservoir or were detected moving into other tributaries or passed downstream through Cabinet Gorge Dam.6,7,8,9 (Some fish that entered the East Fork Bull River also were detected below the dam, so these percentages can only be compared to the total, not to each other.)


Genetic analysis performed at the Abernathy Fish Technology Center, U.S. Fish and Wildlife Service Conservation Genetics Laboratory determines areas of origin of bull trout in the Clark Fork River, allowing them to be transported to the proper area for spawning.
Click here to enlarge image

Using the 2005 genetic data set, which included updated samples collected through 2004, genetic assignment results showed that 88 percent of fish that were captured and transported over the dam from 2001 through 2004 had genetic assignments to populations upstream of Cabinet Gorge Dam. Fifty-four percent of fish captured and transported over Cabinet Gorge Dam that approached Noxon Rapids Dam had population assignments upstream (Regions 3 or 4).4,8,9

Two other measures of the success of this program are evidence of increased bull trout egg deposition (estimated by the number of female fish that spawn and the average number of eggs per pound of fish) and juvenile abundance (estimated by direct electrofishing mark/ recapture population monitoring) in the East Fork Bull River, an important tributary to Cabinet Gorge Reservoir. Interestingly, from 2001 through 2005, 83 percent (20 of 24) of fish released in Cabinet Gorge Reservoir that had been assigned to East Fork Bull River using the genetic analysis were actually detected in this river during the fall spawning season. Fish must pass through a collection weir to reach this river.

In 2005, 29 bull trout were transported upstream. Eleven were genetically assigned to and released into Cabinet Gorge Reservoir (Region 2). The other 18 were assigned to Regions 3 or 4 and released in Region 3.10 Movements of a few of these fish, along with fish transported in 2006, are being monitored. These results, along with a few more years of study data, will provide valuable information on bull trout migration and spawning behavior in Region 3 and offer insight into the relationship between fish movements and genetic assignments.

Fish genetic research is an expanding field. The use of rapid response genetic analysis for this situation is unique, but becoming more common every day with many different fish species. The success of this project provides hope that this procedure could be used for additional programs both in and out of the Clark Fork River basin. The native salmonid restoration plan for Avista sets guidelines for future programs and steps to be taken to increase passage of other native salmonids, such as wetslope cutthroat trout and mountain whitefish. Avista is researching the need for passage of these additional species and the potential of using genetic tools.

The authors may be reached at Avista Corporation, P.O. Box 1469, Noxon, MT 59853; (1) 406-847-1293 (Bernall) or (1) 406-847-1284 (DosSantos); E-mail: shana.bernall@avistacorp.com or joe. dossantos@avistacorp.com.

Notes

  1. Kleinschmidt Associates and K.L. Pratt, “Clark Fork River Native Salmonid Restoration Plan,” Prepared for Avista Corporation, 1998.
  2. Neraas, L.P., and P. Spruell, “Fragmentation of Riverine Systems: The Genetic Effects of Dams on Bull Trout (Salvelinus confluentus) in the Clark Fork River System,” Molecular Ecology, Volume 10, 2001, pages 1,153-1,164.
  3. Ardren, W.R., P. DeHaan, and D.E. Campton, “Genetic Analyses of Bull Trout from the Clark Fork River, Phase I: Development of New Genetic Markers and Assessment of the Feasibility of Using Population Assignment Tests to Determine the Region of Origin of Bull Trout Captured in the Clark Fork River,” U.S. Fish and Wildlife Service, Abernathy Fish Technology Center, prepared for Avista Corporation, 2005.
  4. DeHaan, P., D.E. Campton, and W.R. Ardren, “Genetic Analyses of Bull Trout from the Clark Fork River, Phase II: Rapid Response Genetic Identification of Regions of Origin, Annual Report for Calendar Year 2004,” U.S. Fish and Wildlife Service, Abernathy Fish Technology Center, prepared for Avista Corporation, 2005.
  5. Banks, M.A., and W. Eichert, “Whichrun (version 3.2): A Computer Program for Population Assignment of Individuals Based on Multilocus Genotype Data,” Journal of Heredity, Volume 91, 2000, pages 87-89.
  6. Lockard, L., S. Wilkinson, and S. Skaggs, “Experimental Adult Fish Passage Studies Annual Progress Report – 2001, Fish Passage/Native Salmonid Program, Appendix C,” U.S. Fish and Wildlife Service, prepared for Avista Corporation, 2002.
  7. Lockard, L., S. Wilkinson, and S. Skaggs, “Experimental Adult Fish Passage Studies Annual Progress Report – 2002, Fish Passage/Native Salmonid Program, Appendix C,” U.S. Fish and Wildlife Service, prepared for Avista Corporation, 2003.
  8. Lockard, L., L. Hintz, S. Wilkinson, and S. Skaggs, “Experimental Adult Fish Passage Studies Annual Progress Report – 2003, Fish Passage/Native Salmonid Program, Appendix C,” U.S. Fish and Wildlife Service, prepared for Avista Corporation, 2004.
  9. Lockard, L., and L. Hintz, “Upstream Fish Passage Studies Annual Progress Report –2004, Fish Passage/Native Salmonid Restoration Program, Appendix C,” U.S. Fish and Wildlife Service, prepared for Avista Corporation, 2005.
  10. Hintz, L., and L. Lockard, “Upstream Fish Passage Studies Annual Progress Report –2005, Fish Passage/Native Salmonid Restoration Program, Appendix C,” U.S. Fish and Wildlife Service, prepared for Avista Corporation, 2006.

Shana Bernall is a research specialist for Avista Corporation, working on all aspects of the genetics work described in this article, from field collections and data management to close coordination with the laboratory. Joe DosSantos is the Clark Fork aquatic program leader for Avista.


µ Peer Reviewed

This article has been evaluated and edited in accordance with reviews conducted by two or more professionals who have relevant expertise. These peer reviewers judge manuscripts for technical accuracy, usefulness, and overall importance within the hydroelectric industry.


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