Fidelity, Dispersal, and Fallback of Snake River Fall ... · to 2001. Returning yearling Snake River Fall Chinook salmon radio tagged by Garcia et al. (2004) were identified by the

Fidelity, Dispersal, and Fallback of Snake River Fall Chinook Salmon Yearling and Subyearling Adult Returns

Peter Cleary, Nez Perce Tribe Debbie Milks, Washington Department of Fish and Wildlife

Afton Oakerman, Washington Department of Fish and Wildlife Billy Connor, United States Fish and Wildlife Service

Kenneth Tiffan, United States Geological Service

May 8, 2017

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Background

The need to determine fidelity and fallback rates was proposed as a result of consultation with co-managers for the Snake River Fall Chinook Hatchery and Genetic Management Plan (HGMP) Addendum in association with the subsequent issuance of a Section 10(a)(l)(A) ESA take permit. The National Oceanic Atmosphere Administration (NOAA) Fisheries indicated that this research would contribute to satisfying the requirements for the Snake River Fall Chinook portion of the Federal Columbia River Power System (FCRPS) Biological Opinion Reasonable Prudent Action (RPA); specifically RPA 64 and 65.

The HGMP hatchery programs were developed to mitigate for the effects of the FCRPS and Idaho Power Company dams. These programs were developed by the US v. Oregon Parties who agreed to implement them according to the 2008-2017 US vs. Oregon Management Agreement. The hatchery programs are intended to supplement the natural spawning component of Snake River fall Chinook and provide for continued fisheries within and outside of the Snake River basin. Uncertainty exists regarding the success or impacts of supplementation on the natural population. Recent scientific evidence suggests (Araki et al 2007; Chilcote 2011) that a high percentage of hatchery origin spawners (pHOS) in salmon and steelhead populations may result in reduced natural productivity. NOAA staff recommended reducing the proportion of hatchery origin fall Chinook spawning naturally to reduce the potential risk to productivity. During consultation with NOAA Fisheries for ESA coverage for the programs, several critical data gaps were identified; including the feasibly of altering pHOS via modified hatchery release locations. An agreement was reached to design and implement studies to answer these questions as a special condition of Section 10 Permits 16607 and 16615. One of these studies sought to determine fidelity and fallback rates of hatchery fall Chinook for the HGMP proposed during the consultation. Prior to consultation, Garcia et al. (2004) tracked a total of 515 radio tagged fall Chinook from 1997 to 2001 to spawning areas in the Snake River Basin. They calculated dispersal and fidelity rates and assigned the radio tagged fish to one of three groups of adult radio tagged Snake River fall Chinook salmon; the Lower Snake River, Upper Snake River, and Lower Clearwater River.

The Interior Columbia Technical Recovery Team (ICTRT) stated in a draft 2003 identification of independent populations of the Evolutionarily Significant Units (ESUs) that the distribution and abundance of Snake River fall Chinook salmon suggested it was a single population. However, they noted there is finer-scale differentiation between spawning areas (ICTRT 2003). Core spawning areas identified by ICTRT were “a 32 km section of the mainstem Snake River starting approximately 10 km above the Asotin Creek confluence; lower portions of the Salmon, Clearwater, and Grande Ronde rivers and Snake River rkm 343 to rkm 353” (ICTRT 2003). In addition to core spawning areas, NPT has documented fall Chinook redds in the lower Imnaha River (Arnsberg et al. 2014) and as a result acclimated and released fall Chinook salmon in the South Fork Clearwater and Selway rivers.

Spawning aggregates within the Snake River Basin are not isolated and although the fish released from the Fall Chinook Acclimation Project (FCAP) facilities have relatively strong fidelity to their release location there is a measurable amount of interchange of fish. Garcia et al. (2004) determined that 32% of the supplementation fish overall spawned in areas other than their

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release reaches. For example, they estimated that 11% of the males and 4% of the females returning from Captain Johns Rapids acclimation pond (Lower Snake River Reach) yearling releases spawned in the Upper Snake River Reach. Since the early 2000’s, increased releases of subyearling smolts have occurred throughout the basin from FCAP acclimation facilities and as direct releases from hatcheries in Washington, Oregon and Idaho. Fidelity of adults to release site areas was unknown for these subyearling release groups. The study proposed during consultation attempts to understand spawner distribution associated with subyearling releases by replicating much of the Garcia et al. (2004) study using returning adults that were Passive Integrated Transponder (PIT) tagged as juveniles under the U.S. Army Corp of Engineers’ (COE) Evaluating the Responses of Snake and Columbia River Basin Fall Chinook Salmon to Dam Passage Strategies and Experiences study (Consensus Study) returning from 2013 to 2017.

Additionally, the study attempts to understand the behavior of adults released as subyearlings and yearlings below Lower Granite Dam (LGD) at Lyons Ferry Hatchery (LFH), that immigrate upstream of LFH to the natural production areas upstream of LGD. Subyearling and yearling releases at LFH are referred to as “On-station” releases and have been documented passing LGD through systematic sampling at the adult trap facility at the dam and from detections of PIT tags passing the ladder. Alternatively, subyearlings and yearlings reared at LFH, but released at sites upstream of Lower Granite Dam are referred to as “Off-station” releases. During the planning of the study NOAA was concerned that On-station adults contribute a significant number of hatchery fish to the spawning population upstream of LGR Dam. If these LFH On-station released fish do intermix with wild fish in significant numbers, they could be depressing development of within population diversity that may arise from spawning in diverse habitats. Mendel and Milks (1997) documented upstream migration, passage at dams and the ultimate spawning location of fall Chinook released from Lyons Ferry Hatchery returning as adults in 1992 and 1993. They found that a significant number of those fish fell back over or through the dam and thus did not remain in upstream spawning reaches. Radio tagging of subyearlings and yearlings from 2013 to 2016 was done to determine if subyearlings behave similarly to yearling releases. The intent of the study from 2013 to 2016 was to determine if: 1) homing fidelity from subyearling releases was sufficient to manage individual spawning aggregates, 2) homing fidelity was sufficient to develop localized brood stocks programs that will promote population substructure, 3) there were differences in fall back rates between LFH on-station and LFH off-station releases, and 4) fallback rates were consistent across years.

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Methods

Returning fall Chinook were trapped at Lower Granite Dam and radio tagged with Lotek VFH radio tags. Adult yearling fall Chinook salmon tagged by Garcia et al. returned from 1997 to 2001. Returning yearling Snake River Fall Chinook salmon radio tagged by Garcia et al. (2004) were identified by the presence of visual implant elastomer (VIE) tags posterior to the eye, and a small number (2-6%) of PIT tags. Colors of VIE tags were specific to release juvenile sites upstream of Lower Granite Dam.

Subyearling and yearling fall Chinook salmon from brood years 2007 to 2013 PIT tagged as juveniles were identified as they returned over dams downstream of Lower Granite Dam from 2013 to 2016. PIT tag codes were compiled weekly and submitted to PTAGIS and NOAA Fisheries for identification at the Lower Granite Dam adult trap. When these PIT tag codes were detected they were diverted into the Lower Granite Dam adult trap and radio tagged. Subyearling and yearling fall Chinook salmon were tracked using both stationary radio telemetry receivers and mobile receivers operating from automobiles and boats. The locations of radio telemetry receivers used to track adults during from 2013 to 16 were stationed at the locations described by Garcia et al. (2004) except a receiver was not placed at rkm 240.7 along the Lower Snake River, and a receivers were placed at Little Goose Dam and Lyons Ferry Hatchery. Stationary and mobile telemetry receivers used to track returning adult subyearling and yearling fall Chinook salmon from 2013 to 2016 operated in the same areas as shown in Figure 1.

The following groups were targeted for radio tagging from 2013 to 2017: 1) Lyons Ferry subyearlings(n = 125) 2) Lyons Ferry yearlings (n = 192) 3) Couse Creek subyearlings direct releases subyearlings (n = 110) 4) Captain John Rapids Acclimation subyearlings (n = 110) 5) Grande Ronde direct release subyearlings (n = 110) 6) Pittsburg Landing Acclimation subyearlings (n = 110) 7) Hells Canyon direct release subyearlings (n = 110) 8) Big Canyon Creek Acclimation, North Lapwai Valley Acclimation, and Nez Perce Tribal

Hatchery Acclimation subyearlings (n = 110) 9) Luke Gulch and Cedar Flats Acclimation subyearlings (n = 110)

Adult returns from LFH represented On-station releases below Lower Granite Dam. Snake

River releases near Couse Creek, Captain John Rapids, and Grande Ronde direct releases represented adult returns from the Lower Hells Canyon area. Pittsburg Landing Acclimation and Hells Canyon releases, represented adult returns from the Upper Hells Canyon area. Big Canyon Creek Acclimation, North Lapwai Valley Acclimation, and Nez Perce Tribal Hatchery Acclimation releases represented returns to the Lower Clearwater area. Luke Gulch and Cedar Flats Acclimation releases represented adult returns from the South Fork Clearwater and Selway rivers, or Upper Clearwater area.

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Radio tags were tracked into the last reach entered. Detection history was reviewed if the last reach entered differed from the furthest upstream reach entered or when multiple detections occurred at a stationary receiver located between reaches. Radio tags detected were considered to have either become non-functional, regurgitated, or harvested if only detected in Lower Granite Reservoir and therefore eliminated from further analysis. Radio tags last detected downstream of Lower Granite Dam were referred to as fallbacks. Radio tags last detected in Lower Granite Reservoir after entering an upstream spawning reach were thought to have spawned in next section above the reservoir and drifted downstream into the reservoir or could have been prespawning mortalities. Radio tags last detected in a reach upstream of Lower Granite Reservoir were referred to as spawners. Fidelity was defined as the number of radio-tagged fish that returned to their release area, or reach, divided by the number of fish tagged from that release that retained functional tags and were not harvested. Dispersal was defined as the number of radio-tagged fish that did not return to their release reach divided by the number of fish tagged from that release that retained functional tags and were not harvested. Appendix Tables A-1 and A-2 show the number of fish radio tagged and tracked for the two studies conducted from 1997 to 2001, and from 2013 to 2016.

Figure 1. Spawning areas and reach boundaries for the radio telemetry studies tracking fall Chinook salmon in the Snake River from 1997 to 2001 (Garcia et al. 2004) and from 2013 to 2016. Juvenile release locations are shown by the fish symbol. Stationary receivers are shown with a solid black circle.

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Results Inter-annual mean fidelity rates for the off-station releases of yearlings that returned as adults during 1997–2001 were highest for fish from Big Canyon Creek acclimation facility, followed by fish from Pittsburg Landing acclimation facility, and then by fish from the Captain John Rapids acclimation facility (Table 1; Figure 2). The inter-annual mean dispersal rates into the Upper Hells Canyon spawning area (i.e., the proposed natural production emphasis area) were much lower for the releases of yearlings releases from Big Canyon Creek acclimation facility compared to yearling releases from Captain John Rapids acclimation facility (Table 1; Figure 3).

Inter-annual mean fidelity rates for off-station releases of subyearlings that returned as adults during 2013–2016 from Captain John Rapids, Pittsburg Landing, and Big Canyon Creek acclimation facilities were higher compared to corresponding rates observed for the off-station releases of yearlings during 1997–2001 (Table 1; Figures 2 and 4). Inter-annual mean dispersal rates into the Upper Hells Canyon spawning area were similar between releases of Captain John Rapids yearling and subyearlings when viewed in terms of the SEs and point estimates of the two rates (Table 1; Figures 3 and 5). Along the same lines, the inter-annual mean dispersal rates of the Big Canyon Creek acclimation facility releases of yearlings and subyearlings were also similar (Table 1; Figures 3 and 5).

Lyons Ferry Hatchery subyearlings had the highest inter-annual mean dispersal rate into

the Upper Hells Canyon natural production emphasis area (Table 1; Figure 5). However, inter-annual mean dispersal for the Lyons Ferry subyearling adult returns includes 2013; represented by only 3 Lyons Ferry adults. If the 2013 Lyons Ferry subyearling dispersal rate is discarded the inter-annual mean dispersal rate becomes 8.6% ± SE of 4.4%. Dispersal of other release groups into the Upper Hells Canyon spawning area was lower by comparison to the Lyons Ferry Hatchery on-station releases of yearlings (Table 1; Figure 5).

Inter-annual mean fallback rates of Lyons Ferry Hatchery on-station releases of yearlings

and subyearlings were much higher compared to the fallback rates of off-station releases of yearlings and subyearlings (Table 1; Figure 6).

Take Home Message

This presentation was intended to demonstrate the progress we have made to understand fidelity, dispersal, and fallback of hatchery subyearlings and yearlings released both on-station at LFH and off-station upstream of Lower Granite Dam. The final year of data collection will be 2017. Future analysis of fidelity and dispersion will determine if sex and brood year influenced fidelity and dispersion rates. If sex and brood year does not influence fidelity or dispersion within release groups annual results will be grouped together in the final analysis. Once the final analyses are completed, they will be useful for evaluating the potential for dispersal of hatchery adults into the proposed natural emphasis area, as well for distributing hatchery adults among spawning areas for the purpose of life cycle modeling.

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Table 1. Inter-annual mean fidelity, dispersal, and fallback rates for yearlings from 1997 to 2001 and yearlings subyearlings from 2013 to 2016. Fidelity and fallback rates are highlighted in yellow and grey, respectively.

Release Group

Below Lower Granite

Dam

Lower Granite

Reservoir

Lower Hells

Canyon

Upper Hells

Canyon Salmon River

Clearwater River

Yearlings (1997-2001)

Captain John Rapids 2.5% 7.5% 49.9% 10.4% 0.4% 29.3%

Pittsburg Landing 6.4% 5.8% 22.7% 64.4% 0.0% 0.7%

Big Canyon Creek 4.0% 6.7% 13.0% 2.3% 0.0% 74.1%

Subyearlings and

Yearlings (2013-2016)

Lyons Ferry Subyearlings 44.0% 9.9% 10.5% 17.9% 0.0% 17.7%

Lyons Ferry Yearlings 50.3% 11.5% 9.3% 2.8% 0.0% 26.1%

Couse Creek 15.0% 0.0% 52.5% 2.5% 0.0% 30.0%

Captain Johns 3.1% 2.8% 63.2% 15.2% 5.0% 10.8% Grande Ronde 0.0% 1.3% 85.3% 3.8% 0.0% 9.7%

Pittsburg Landing 1.1% 1.6% 9.6% 86.3% 0.5% 1.1% Hells Canyon 3.8% 0.0% 11.6% 79.4% 0.6% 4.6%

Clearwater 1.2% 5.9% 1.2% 5.3% 0.0% 86.4%

Upper Clearwater 1.9% 7.7% 0.5% 2.8% 0.0% 88.7%

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Figure 2. Fidelity rates of yearling adult returns from 1997 to 2001 calculated by reanalyzing data collected by Garcia et al. (2004) to standardize the boundaries of release reaches and account pre-spawning mortalities.

Figure 3. Dispersion rates of yearling adult returns from 1997 to 2001 into the Upper Hells Canyon spawning area calculated by reanalyzing data collected by Garcia et al. (2004) to standardize the boundaries of release reaches and account pre-spawning mortalities.

       Big Canyon Creek  Captain John Rapids   Pittsburg Landing

Release group

30

40

50

60

70

80

90

Inter‐an

nual m

ean

 (+ SE) fidelity rate (%)

0

5

10

15

20

Inter‐an

nual m

ean

 (+ SE) dispersal rate (%

)

      Big Canyon Creek Captain John Rapids

Release group

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Figure 4. Fidelity rates of subyearling adult returns from 2013 to 2016.

Figure 5. Dispersion rates of subyearling and yearling adult returns into the Upper Hells Canyon spawning area from 2013 to 2016.

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Figure 6. Fallback rates of On-station subyearlings and yearlings are shown with fallback rates of Lyons Ferry Off-station subyearling releases at Couse Cr., Captain John Rapids, Pittsburg Landing, and Clearwater release groups. Also shown are fallback rates for subyearlings produced at the Nez Perce Tribal Hatchery and released at Luke Gulch and Cedar Flats acclimation sites on the South Fork Clearwater and Selway rivers, and subyearlings produced at Irrigon Fish Hatchery.

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Citations Arnsberg, B., P. Groves, F. Mullins, D. Milks, M. Allen. 2014. 2013 Snake River Fall Chinook

Salmon Spawning Summary. Online (May 8, 2017): http://www.fpc.org/documents/fachin_planningteam/2013CooperativeFallChReddSummary.pdf

Araki. H, B. Cooper, and M.S. Blouin. 2007. Genetic effects of captive breeding cause a rapid,

cumulative fitness decline in the wild. Science. 318:100-103. Chilcote M.W., K.W. Goodson, M.R. Falcy. 2011. Reduced recruitment performance in natural

populations of anadromous salmonids associated with hatchery-reared fish. Canadian Journal of Fisheries and Aquatic Sciences. 68: 511-522.

Garcia, A.P, W.P Connor, D. J. Milks, S. J. Rocklage and R.K. Steinhorst. 2004. Movement

and Spawner Distribution of Hatchery Fall Chinook Salmon Adults Acclimated and Released as Yearlings at Three Locations in the Snake River Basin. NAJFM 24:1134-1144.

ICTRT (Interior Columbia Basin Technical Recovery Team). 2003. Independent Populations of

Chinook, Steelhead, and Sockeye for Listed Evolutionarily Significant Units Within the Interior Columbia River Domain. Online (May 8, 2017): https://www.nwfsc.noaa.gov/research/divisions/cb/genetics/trt/col_docs/independentpopchinsteelsock.pdf

Mendel, G. and D. Milks. 1997. Chapter 1 in: Upstream Passage, Spawning, and Stock

Identification of Fall Chinook Salmon in the Snake River, 1992 and 1993. Editors H.L. Blankenship and G. W. Mendel. Final report to the Bonneville Power Administration. Project Number 92-046. DOE/BP-60415-2.

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Appendix A-1. Adult returns of yearling Snake River fall Chinook salmon radio tagged and tracked from 1997 to 2001 (data from Garcia et al. 2004).

Release Group Return Year Tagged Unknown

Tag loss Fallback

Pre-spawning Mortality Spawner

Big Canyon Cr. 1998 12 1 2 1 8 1999 28 4 2 2 20 2000 48 3 4 2 3 36 2001 84 2 5 2 75 Captain John Rapids 1999 7 7 2000 34 1 2 2 7 22 2001 118 7 18 1 92 Pittsburg Landing 1997 9 1 2 1 5 1998 30 8 2 2 18 1999 19 2 1 16 2000 43 6 3 34

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Appendix A-2. Adult returns of subyearling and yearling Snake River fall Chinook salmon radio tagged and tracked from 2013 to 2016.

Release Group Return Year Tagged Unknown

Tag loss Fallback

Pre-spawning Mortality Spawner

Lyons Ferry Subyearlings

2013 3 0 0 2 0 1 2014 25 11 0 6 1 7 2015 32 5 1 10 7 9 2016 34 15 1 5 1 12

Lyons Ferry Yearlings

2013 12 3 2 3 0 4 2014 85 46 2 17 6 14 2015 46 7 4 16 6 13 2016 32 8 0 16 3 5

Couse Creek 2013 12 1 1 0 0 10 2014 12 2 0 1 0 9 2015 4 0 0 0 0 4 2016 2 0 0 1 0 1

Captain John Rapids

2013 14 3 3 0 0 8 2014 73 18 2 4 6 43 2015 22 0 1 1 0 20 2016 5 0 0 0 0 5

Grande Ronde 2013 11 1 0 0 0 10 2014 47 6 2 0 2 37 2015 17 1 0 0 0 16 2016 3 0 0 0 0 3

Pittsburg Landing

2013 7 2 1 0 0 4 2014 60 10 2 2 3 43 2015 18 0 0 0 0 18 2016 1 0 0 0 0 1

Hells Canyon 2013 13 2 1 1 0 9 2014 52 11 1 2 0 38 2015 21 5 0 0 0 16 2016 3 2 0 0 0 1

Clearwater 2013 20 1 1 0 2 16 2014 48 6 1 2 1 38 2015 13 3 0 0 1 9 2016 10 1 0 0 0 9

Upper Clearwater

2013 10 2 0 0 0 8 2014 56 3 1 4 3 45 2015 21 0 0 0 0 21

2016 4 0 0 0 1 3

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Appendix B-1. They number of yearling fall Chinook salmon detected per reach as a fallback, pre-spawning mortality, or spawner from 1997 to 2001.

Release Group Year

Below Lower Granite

Dam

Lower Granite

Reservoir

Lower Snake River

Upper Snake River

Salmon River

Clearwater River

Captain John Rapids

1997 1998 1999 4 3 2000 2 7 18 2 2 2001 1 32 23 1 36

Pittsburg Landing

1997 1 3 2 1998 2 2 3 15 1999 1 16 2000 3 10 23 1 2001

Big Canyon Creek

1997 1998 1 1 7 1999 2 2 5 1 14 2000 2 3 5 2 29

2001 2 6 69

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Appendix B-2. They number of subyearling and yearling fall Chinook salmon detected per reach as a fallback, pre-spawning mortality, or spawner from 2013 to 2016.

Release Group Year

Below Lower Granite Dam

Lower Granite

Reservoir

Lower Snake River

Upper Snake River

Salmon River

Clearwater River

Lyons Ferry Subyearlings

2013 2 1 2014 6 1 3 3 1 2015 10 7 1 3 5 2016 5 1 3 1 8

Lyons Ferry Yearlings

2013 3 4 2014 17 6 7 7

2015 16 6 5 1 7 2016 16 3 1 2 2 Couse Creek 2013 5 5 2014 1 6 1 2 2015 2 1 1 2016 1 1 Captain John Rapids

2013 6 2 2014 4 6 27 9 7

2015 1 14 5 1 2016 3 1 1 Grande Ronde

2013 6 1 3 2014 2 34 2 1

2015 15 1 2016 3 Pittsburg Landing

2013 4 2014 2 3 5 35 1 2

2015 5 13 2016 1 Hells Canyon 2013 1 1 7 1 2014 2 7 29 1 1 2015 3 12 1 2016 1 Clearwater 2013 2 16 2014 2 1 2 36 2015 1 1 8 2016 1 8 Upper Clearwater

2013 8 2014 4 3 1 44 2015 1 20

2016 1 3