1 Nez Perce Tribe, Department of Fisheries Resources Management, P.O. Box 365, Lapwai, Idaho, 83540, USA

✉ Correspondence: Jay A. Hesse <>, Ryan N. Kinzer <>

Suggested Citation for Annual Results:
Hesse, J.A. and Kinzer, R.N., 2025. Snake River Anadromous Fish Status: Quasi-Extinction Threshold Analysis. Department of Fisheries Resources Management. Version: 01 October, 2025. Available: https://ryankinzer.github.io/SRAFS/

1 Quasi-Extinction Summary

Updates for the 2024 analysis:

  • Removed Little Salmon River due to limited data from only a small portion of the population.
  • Included multiple time-series of observations for each population if available (i.e, spawning ground survey data, weir observations, PIT-tag based estimates)
  • Performed model selection on multiple candidate models with varying numbers of state processes, process error, and observation error parameters

1.1 Spring/summer Chinook Salmon

Natural-origin (wild) and hatchery-origin returns of Snake River spring/summer Chinook Salmon past Lower Granite Dam.

Figure 1.1: Natural-origin (wild) and hatchery-origin returns of Snake River spring/summer Chinook Salmon past Lower Granite Dam.

Table 1.1: The table provides summary counts of spring/summer Chinook salmon populations currently below minimum abundance thresholds, 50 spawners, and meeting the quasi-extinction threshold (4 consecutive years below 50 spawners), and the number of populations predicted to fall below 50 by return year 2029.
Metric All Snake River Populations Extant ESA-listed Populations
Populations 34 27
Below Minimum Abundance Threshold 34 (100%) 27 (100%)
Current Return Below 50 12 (35%) 9 (33%)
Currently Below Quasi-Extinction Threshold 4 (12%) 3 (11%)
Predicted Below 50 by 2029 14 (41%) 11 (41%)
Current status of natural-origin Snake River spring/summer Chinook Salmon relative to the quasi-extinction threshold (QET) and Columbia Basin Partnership goals.

Figure 1.2: Current status of natural-origin Snake River spring/summer Chinook Salmon relative to the quasi-extinction threshold (QET) and Columbia Basin Partnership goals.

Estimated slope parameters for natural-origin Snake River spring/summer Chinook Salmon abundance trends indicate an average annual decline of 6% for the last 10-years.

Figure 1.3: Estimated slope parameters for natural-origin Snake River spring/summer Chinook Salmon abundance trends indicate an average annual decline of 6% for the last 10-years.

1.2 Summer Steelhead

Natural-origin (wild) and hatchery-origin returns of Snake River summer steelhead past Lower Granite Dam.

Figure 1.4: Natural-origin (wild) and hatchery-origin returns of Snake River summer steelhead past Lower Granite Dam.

Table 1.2: The table provides summary counts of steelhead populations currently below minimum abundance thresholds, 50 spawners, and meeting the quasi-extinction threshold (4 consecutive years below 50 spawners), and the number of populations predicted to fall below 50 by return year 2029.
Metric All Snake River Populations Extant ESA-listed Populations
Populations 22 22
Below Minimum Abundance Threshold 21 (95%) 21 (95%)
Current Return Below 50 3 (14%) 3 (14%)
Currently Below Quasi-Extinction Threshold 3 (14%) 3 (14%)
Predicted Below 50 by 2029 6 (27%) 6 (27%)
Current status of natural-origin Snake River summer steelhead relative to the quasi-extinction threshold (QET) and Columbia Basin Partnership goals.

Figure 1.5: Current status of natural-origin Snake River summer steelhead relative to the quasi-extinction threshold (QET) and Columbia Basin Partnership goals.

Modeled abundance trends of natural-origin Snake River summer steelhead indicate an annual 11% decline for the last 10-years.

Figure 1.6: Modeled abundance trends of natural-origin Snake River summer steelhead indicate an annual 11% decline for the last 10-years.

2 Methods

2.1 Datasets

  1. NOSAij: derived by co-managers and downloaded from Coordinated Assessments on 3/05/2025
    • Generally estimated from expanded redd counts or mark/recapture weir estimates
  2. Escapement: derived from PIT-tag observations and a branch occupancy model similar to Waterhouse et al. 2020
    • includes a time-varying component to better describe run-timings of different populations passing Lower Granite Dam

2.2 Data Analysis

2.2.1 Multivariate Auto-Regressive State Space Model (Holmes et al. 2012)

\[\begin{aligned} \textbf{State process:} \quad & \mathbf{x}_{t} = \mathbf{x}_{t-1} + \mathbf{u} + \mathbf{w}_t, \quad \mathbf{w}_t \sim \mathcal{N}(0, \mathbf{Q}) \\ \textbf{Observation process:} \quad & \mathbf{y}_{t} = \mathbf{Z} \mathbf{x}_{t} + \mathbf{a} + \mathbf{v}_t, \quad \mathbf{v}_t \sim \mathcal{N}(0, \mathbf{R}) \end{aligned}\]
  • \(\mathbf{x}_t\): vector of hidden state values at time \(t\)
  • \(\mathbf{u}\): state intercept (drift) vector
  • \(\mathbf{y}_t\): vector of observed values at time \(t\)
  • \(\mathbf{Z}\): observation matrix mapping states to observations
  • \(\mathbf{a}\): observation bias vector

2.2.2 Fitted Models

  • State process ( \(\mathbf{u}\) ):
    • A single basin-wide process (1)
    • A process for each major population group (7 - sp/sm Chinook Salmon and 5 - summer steelhead)
    • A process for each population (34 - sp/sm Chinook Salmon and 22 summer steelhead)
  • Process Error ( \(\mathbf{Q}\) )
    • Equal Variance-Covariance (2)
    • Diagaonl and Equal (1)
    • Diagonal and Unequal (equals number of state processes)
  • Observation Error ( \(\mathbf{R}\) )
    • Diagonal and Equal (1)
    • Diagonal and Unequal (equals number of observation time-series)

3 Results

3.1 Spring/summer Chinook Salmon

3.1.1 Observations

Table 3.1: Summary of abundance time-series used in modeling Snake River spring/summer Chinook Salmon populations (n = 48). Time-series length and data sources varied by population, with observations spanning from 1980 to 2024. Abundance estimates were primarily based on spawning ground surveys and weir counts, with PIT-tag detections included for select populations. The 10th, 50th (median), and 90th percentiles of observed abundance values are provided to summarize distributional characteristics across years.
MPG Population Method Years # Years 10% 50% 90%
Dry Clearwater Upper South Fork Clearwater PIT-tag 2012-2024 12 144 273 757
Grande Ronde / Imnaha Big Sheep Creek PIT-tag 2011-2024 13 20 49 120
Catherine Creek SGS and Weir 1980-2024 45 36 129 527
PIT-tag 2015-2024 9 90 132 361
Grande Ronde River Upper Mainstem SGS and Weir 1980-2024 45 14 56 187
PIT-tag 2018-2024 6 16 33 71
Imnaha River Mainstem SGS and Weir 1980-2024 45 189 417 1028
PIT-tag 2011-2024 13 222 483 1062
Lookingglass Creek PIT-tag 2010-2024 14 38 88 228
Minam River SGS and Weir 1980-2024 45 141 327 684
Wallowa/Lostine Rivers SGS and Weir 1980-2023 44 72 300 1018
Wenaha River SGS and Weir 1980-2024 45 61 279 652
PIT-tag 2019-2024 5 119 133 404
Lower Snake Asotin Creek SGS and Weir 1984-2016 33 0 4 18
PIT-tag 2010-2024 14 0 19 123
Tucannon River SGS and Weir 1980-2024 45 26 213 611
Middle Fork Salmon River Bear Valley Creek SGS and Weir 1980-2024 45 85 244 880
PIT-tag 2015-2024 9 10 232 648
Big Creek SGS and Weir 1980-2024 45 38 131 417
PIT-tag 2012-2024 12 198 585 1121
Camas Creek SGS and Weir 1980-2024 44 9 43 104
Chamberlain Creek SGS and Weir 1985-2024 36 30 187 526
Loon Creek SGS and Weir 1980-2024 44 10 53 107
Marsh Creek SGS and Weir 1980-2024 45 31 167 578
Middle Fork Salmon River Lower Mainstem SGS and Weir 1987-2024 37 0 3 23
Middle Fork Salmon River Upper Mainstem SGS and Weir 1995-2024 30 21 57 154
Sulphur Creek SGS and Weir 1980-2024 45 6 41 182
South Fork Salmon River East Fork South Fork Salmon River SGS and Weir 1987-2024 38 62 212 503
PIT-tag 2010-2024 14 243 629 1079
Secesh River SGS and Weir 1996-2024 29 161 434 1045
PIT-tag 2010-2024 14 270 666 1191
South Fork Salmon River SGS and Weir 1980-2024 45 162 551 1235
PIT-tag 2010-2024 14 213 675 2534
Upper Salmon River East Fork Salmon River SGS and Weir 1980-2024 45 18 219 630
Lemhi River SGS and Weir 1980-2024 45 60 142 363
PIT-tag 2010-2024 14 129 235 665
North Fork Salmon River SGS and Weir 1991-2024 34 6 52 184
PIT-tag 2016-2024 7 40 60 211
Pahsimeroi River SGS and Weir 1980-2024 37 24 122 354
Panther Creek PIT-tag 2018-2024 6 93 166 303
Salmon River Lower Mainstem SGS and Weir 1980-2024 45 19 98 230
Salmon River Upper Mainstem SGS and Weir 1980-2024 45 100 326 679
Valley Creek SGS and Weir 1980-2024 45 13 77 229
PIT-tag 2010-2024 14 87 242 484
Yankee Fork SGS and Weir 1980-2024 44 3 23 148
PIT-tag 2012-2024 12 35 62 279
Wet Clearwater Lochsa River PIT-tag 2017-2024 7 160 245 461
Lolo Creek PIT-tag 2012-2024 12 41 78 257

3.1.2 Model Fits

Table 3.2: Candidate models and number of parameters fit to spring/summer Chinook Salmon time-series observations to explain Snake River abundance trends.
Model Id Total Parameters U Q R logLik AICc \(\Delta\)AIC
4 106 7 2 48 -1409.39 3048.45 0.00
2 99 1 1 48 -1466.43 3146.20 97.75
10 133 34 2 48 -1434.48 3163.32 114.87
8 111 7 7 48 -1483.20 3207.85 159.39
6 105 7 1 48 -1497.10 3221.52 173.07
3 59 7 2 1 -1592.07 3307.45 259.00
1 52 1 1 1 -1644.39 3396.90 348.45
9 86 34 2 1 -1619.06 3421.60 373.15
7 64 7 7 1 -1658.74 3451.76 403.30
5 58 7 1 1 -1675.38 3471.89 423.44

3.1.3 State Process

Estimated abundance (natural-log) trends for the seven state processes (xtT) estimated from the best fitting Snake River spring/summer Chinook Salmon model (grey shading represents 95% CI's).

Figure 3.1: Estimated abundance (natural-log) trends for the seven state processes (xtT) estimated from the best fitting Snake River spring/summer Chinook Salmon model (grey shading represents 95% CI’s).

3.1.4 Modeled Observations

Empirical natural-origin abundance estimates for Snake River spring/summer Chinook Salmon (points) and estimated population trends (ytT) from the best fitting model (line).

Figure 3.2: Empirical natural-origin abundance estimates for Snake River spring/summer Chinook Salmon (points) and estimated population trends (ytT) from the best fitting model (line).

3.1.5 5-Year Predictions

Estimated and predicted population abundance trends for natural-origin Snake River Chinook Salmon. Red points and triangles indicated an estimated annual return of 50 or fewer spawners.

Figure 3.3: Estimated and predicted population abundance trends for natural-origin Snake River Chinook Salmon. Red points and triangles indicated an estimated annual return of 50 or fewer spawners.

3.2 Summer Steelhead

3.2.1 Observations

Table 3.3: Summary of abundance time-series used in modeling Snake River summer steelhead populations (n = 25). Time-series length and data sources varied by population, with observations spanning from 2010 to 2024. Abundance estimates were primarily based on PIT-tag detections, with spawning ground surveys and weir counts included for select populations. The 10th, 50th (median), and 90th percentiles of observed abundance values are provided to summarize distributional characteristics across years.
MPG Population Method Years # Years 10% 50% 90%
Clearwater River Clearwater River Lower Mainstem SGS and Weir 2010-2024 15 147 254 785
Lochsa River SGS and Weir 2017-2024 8 289 439 941
Lolo Creek SGS and Weir 2012-2024 13 104 187 589
Selway River SGS and Weir 2017-2024 8 232 408 802
South Fork Clearwater River SGS and Weir 2012-2024 13 131 353 1040
Grande Ronde River Grande Ronde River Lower Mainstem SGS and Weir 2019-2023 5 281 418 467
Grande Ronde River Upper Mainstem SGS and Weir 2013-2024 12 356 539 1301
PIT-tag 2010-2018 9 1300 2556 3589
Joseph Creek SGS and Weir 2011-2024 14 372 747 2045
PIT-tag 2010-2017 8 1487 1990 3735
Wallowa River SGS and Weir 2014-2024 11 359 508 956
Imnaha River Imnaha River SGS and Weir 2011-2024 14 683 1241 2881
Lower Snake Asotin Creek SGS and Weir 2010-2024 15 224 366 1312
Tucannon River SGS and Weir 2010-2024 15 232 452 841
PIT-tag 2010-2023 14 347 611 1196
Salmon River East Fork Salmon River SGS and Weir 2011-2019 8 0 14 40
Lemhi River SGS and Weir 2010-2024 15 49 161 416
Middle Fork Salmon River Lower Mainstem SGS and Weir 2011-2024 14 84 244 586
Middle Fork Salmon River Upper Mainstem SGS and Weir 2020-2024 5 19 29 53
North Fork Salmon River SGS and Weir 2017-2024 7 17 57 378
Pahsimeroi River SGS and Weir 2011-2024 14 9 33 140
Panther Creek SGS and Weir 2018-2024 7 101 137 196
Salmon River Upper Mainstem SGS and Weir 2010-2024 15 36 106 297
Secesh River SGS and Weir 2010-2024 15 27 57 252
South Fork Salmon River SGS and Weir 2010-2024 15 154 445 1511

3.2.2 Model Fits

Table 3.4: Candidate models and number of parameters fit to summer steelhead time-series observations to explain Snake River abundance trends.
Model Id Total Parameters u Q R logLik AICc \(\Delta\)AIC
2 53 1 1 25 -173.6063 477.5700 0.00000
4 58 5 2 25 -172.4959 490.7482 13.17829
10 75 22 2 25 -152.4930 508.5072 30.93727
6 57 5 1 25 -197.1921 537.0077 59.43771
8 61 5 5 25 -195.7174 546.7564 69.18648
1 29 1 1 1 -290.3841 645.4864 167.91640
12 74 22 1 25 -227.4331 654.7353 177.16530
3 34 5 2 1 -290.2449 657.8599 180.28994
9 51 22 2 1 -279.5091 683.3980 205.82803
7 37 5 5 1 -304.4895 694.1822 216.61226

3.2.3 State Process

Estimated abundance (natural-log) trend for a single state process (xtT) as estimated from the best fitting Snake River summer steelhed model (grey shading represents 95% CI's).

Figure 3.4: Estimated abundance (natural-log) trend for a single state process (xtT) as estimated from the best fitting Snake River summer steelhed model (grey shading represents 95% CI’s).

3.2.4 Modeled Observations

Empirical natural-origin abundance estimates for Snake River summer steelhead (points) and estimated population trends (ytT) from the best fitting model (line).

Figure 3.5: Empirical natural-origin abundance estimates for Snake River summer steelhead (points) and estimated population trends (ytT) from the best fitting model (line).

3.2.5 5-Year Predictions

Estimated and predicted population abundance trends for natural-origin Snake River summer steelhead. Red points and triangles indicated an estimated annual return of 50 or fewer spawners.

Figure 3.6: Estimated and predicted population abundance trends for natural-origin Snake River summer steelhead. Red points and triangles indicated an estimated annual return of 50 or fewer spawners.