IDAHO ADULT CHINOOK SALMON MONITORING

2016 ANNUAL REPORT

Photo: Matt Belnap

Prepared by:

Matthew J. Belnap, Fisheries Biologist

Bruce Barnett, Fisheries Data Coordinator Kimberly A. Apperson, Fisheries Biologist

Matt Amick, Fisheries Technician I Carlos Camacho, Fisheries Biologist

Robert Hand, Fisheries Biologist Mike Peterson, Fisheries Biologist

Evan Brown, Sr. Fisheries Data Coordinator

IDFG Report Number 17-07 June 2017

Idaho Adult Chinook Salmon Monitoring

2016 Annual Report

By

Matthew J. Belnap Bruce Barnett

Kimberly A. Apperson Matt Amick

Carlos Camacho Robert Hand

Mike Peterson Evan Brown

Idaho Department of Fish and Game 600 South Walnut Street

P.O. Box 25 Boise, ID 83707

IDFG Report Number 17-07 June 2017

THIS PAGE IS INTENTIONALLY BLANK

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ACKNOWLEDGEMENTS

Report Authors: Matthew J. Belnap Bruce Barnett Kimberly A. Apperson Matt Amick Carlos Camacho

Robert Hand Mike Peterson Evan Brown

Report Contributors: Data and Field Work IDFG Southwest Region (Nampa) • Jared Kunz • Kayla Kinkead • Wyatt Tropea IDFG Southwest Region (McCall) • Dale Allen • Laurie Janssen • Paul Janssen • Dave Rhinehart • Breanna Anderson IDFG Salmon Region • Mike Biggs • Heidi Messner • Jessica Buelow • Morgan Solomon • Mark Komoroski • Maggie Stenvers • Schuyler Mace • Matt Pumfery • Brent Beller • Greg Schoby • Patrick Uthe • Alissa Tiemann • Ben Casscles

• Sarah Foster • Tristen Kienenberger • Chris Gratton • Matt Lyon IDFG Clearwater Region • Cody Black • Brett Bowersox • Desiree DelaVega • Marika Dobos • Jason Fortier • Tyler Gross • Brent Haverkamp • Brian Knoth • Scott Putnam • Adam Scheirer • Michael Soukup • Grant Truskowski • Clayton Waller IDFG Nampa Research • Micah Davison • Kim Knuth • Dave Venditti • Bruce Barnett • Carlos Camacho • Megan Heller • Kyle Gatt

IDFG Headquarters • Evan Brown • Chris Harrington • Tim Copeland IDFG Eagle Fish Genetics Lab • Brian Ayers

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ACKNOWLEDGEMENTS (continued)

Report Contributors: Data and Field Work (alphabetical, continued) Nez Perce Tribe • Justin Bretz • Mike Kosinski • Jay Oatman • Sherman Sprague • Devayne Lewis • Tyler Williamson Shoshone-Bannock Tribes • Scott Cazier • Lytle Denny • Ronald Diaz • Melissa Evans • Kurt Tardy • Angelo Teton • Rob Trahant • Joshua Taryole • Wyatt Peterson • S. Ponzo • S. Murphy • R. Croy • N. Suppah • Y. Yglesias • N. Hall • A. Young • B. Kohr • R. Croy • K. Bacon • F. Mckean • J. Melchor • S. Broncho • S. Sequints • K. Morris

U. S. Forest Service • Scott Brandt • Ed Fochtman • John Guzevich • Christine Stewart • Russ Thurow

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ACKNOWLEDGEMENTS (continued)

Project Funding (alphabetical) • Bonneville Power Administration: project 1991-073-00 Idaho Natural Production Monitoring

and Evaluation; project 1999-020-00 Analyze Persistence and Dynamics in Chinook Redds; ISEMP project

• Intensively Monitored Watershed; National Oceanic and Atmoshperic Administration • Idaho Power Company, Hells Canyon Mitigation • National Marine Fisheries Service, Pacific Coast Salmon Recovery Funds ; National Marine Fisheries Service Pacific Salmon Treaty Implementation Grant • U. S. Fish and Wildlife Service, Dingell-Johnson Sport Fish Restoration Program • U. S. Fish and Wildlife Service, Lower Snake River Compensation Program Project Administration and Other Assistance (alphabetical) • Megan Heller (IDFG), Kyle Gatt (IDFG), and Leslie Reinhardt (IDFG / PSMFC) processed

and aged the fin rays. • Paul Bunn (IDFG / PSMFC) coordinated BioSamples database management and created

the maps for this report. • Russell Scranton (BPA), contracting officer’s technical representative, provided

administrative support for project 1991-073-00 Idaho Natural Production Monitoring and Evaluation.

• Tim Copeland (IDFG), Bill Schrader (IDFG), and Brett Bowersox (IDFG) reviewed this

report. • Idaho Department of Fish and Game (IDFG) Information Systems Bureau, especially Chris

Harrington, provided database management and technical oversight for the entire redd count dataset.

• Cheryl Leben (IDFG) helped format and edit this report. • Northwest Power and Conservation Council, especially Idaho representatives Bill Booth and

Jim Yost, provided policy support. • Pacific States Marine Fisheries Commission provided personnel support. • Russ Thurow (USFS), Rocky Mountain Research Station, oversaw Middle Fork Salmon

River aerial redd counts.

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Suggested citation: Belnap, M.J., B. Barnett, K. A. Apperson, M. Amick, C. Camacho, R. Hand, M. Peterson, and E.

Brown. 2017. Idaho adult Chinook Salmon monitoring. Annual report 2016. Idaho Department of Fish and Game Report 17-07.

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ABBREVIATIONS AND ACRONYMS

ASMS Anadromous Salmonid Monitoring Strategy

BPA Bonneville Power Administration

BY Brood Year

CV Coefficient of Variation

CWT Coded Wire Tag

DJ Dingell-Johnson Sport Fish Restoration Program

ESA Endangered Species Act

ESU Evolutionarily Significant Unit

FINS Fish Inventory System Hatchery Database

GSI Genetic Stock Identification

ICBTRT Interior Columbia Basin Technical Recovery Team

IFWIS Idaho Fish and Wildlife Information System

IDFG Idaho Department of Fish and Game

IPC Idaho Power Company

ISS Idaho Supplementation Studies

LSRCP Lower Snake River Compensation Program

MPG Major Population Group

MFSR Middle Fork Salmon River

NMFS U.S. Department of Commerce, National Marine Fisheries Service

NPCC Northwest Power and Conservation Council

PA Percent Agreement

PIT Passive Integrated Transponder

PCSRF Pacific Coast Salmon Recovery Funds

PSMFC Pacific States Marine Fisheries Commission

R/S Recruit per Spawner

SFSR South Fork Salmon River

SGS Spawning Ground Survey

SGSA Spawning Ground Survey Application

USFS U.S. Forest Service

USR Upper Salmon River

VSP Viable Salmonid Population

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TABLE OF CONTENTS Page

ACKNOWLEDGEMENTS ............................................................................................................ i ABBREVIATIONS AND ACRONYMS ......................................................................................... v ABSTRACT ................................................................................................................................. 1 INTRODUCTION ........................................................................................................................ 2 METHODS .................................................................................................................................. 4

Redd Surveys .......................................................................................................................... 4 Spawning Ground Survey Training ........................................................................................ 4 Index Surveys ....................................................................................................................... 4 Census Surveys .................................................................................................................... 4 Additional Surveys ................................................................................................................ 5

Carcass Surveys ...................................................................................................................... 5 Carcass Age Composition ........................................................................................................ 6

Laboratory Processing of Dorsal Fin Rays ............................................................................ 6 Dorsal Fin Ray Age Validation ............................................................................................... 7

Genetics Samples at Weirs and Traps ..................................................................................... 7 Data Management and Analysis .............................................................................................. 8

RESULTS ................................................................................................................................... 9 Redd Surveys .......................................................................................................................... 9

Index Surveys ....................................................................................................................... 9 Census Surveys .................................................................................................................... 9 Additional Surveys .............................................................................................................. 10 Redd Distribution Maps ....................................................................................................... 10 Evaluation of Peak Spawn Timing ....................................................................................... 10

Carcass Surveys .................................................................................................................... 10 Carcass Age Composition ...................................................................................................... 11 Genetics Samples at Weirs and Traps ................................................................................... 12

DISCUSSION............................................................................................................................ 13 RECOMMENDATIONS ............................................................................................................. 16 LITERATURE CITED ................................................................................................................ 17 TABLES .................................................................................................................................... 20 FIGURES .................................................................................................................................. 34

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LIST OF TABLES Page

Table 1. Single-pass redd count index surveys that were conducted for spring-

summer Chinook Salmon in Idaho during 2016. Surveys are organized by major population group (MPG). .......................................................................... 21

Table 2. Multiple-pass redd count census surveys that were conducted for spring-summer Chinook Salmon in Idaho during 2016. Surveys are organized by major population group (MPG). .......................................................................... 25

Table 3. Additional redd count surveys that were conducted for spring-summer Chinook Salmon in Idaho during 2016. Surveys are organized by major population group (MPG). .................................................................................... 26

Table 4. Carcasses observed on spring-summer Chinook Salmon spawning grounds in Idaho by origin and sex during 2016. Surveys are organized by major population group (MPG). F = female; M = male; U = unknown sex. Hatchery fraction is sum of segregated hatchery and integrated hatchery divided by the sum of segregated hatchery, integrated hatchery, and wild carcasses........................................................................................................... 27

Table 5. Brood year and age class frequencies of wild spring-summer Chinook Salmon carcasses sampled from Idaho spawning grounds during 2016. Samples are organized by major population group (MPG). Saltwater ages were derived from fin rays and freshwater ages (X) were assumed to be one year. ............................................................................................................ 29

Table 6. Marsh Creek spring-summer Chinook Salmon age-frequency distribution for 2016. An age-length key based on combined 1998-2016 Marsh Creek and Bear Valley Creek fin ray age subsamples (n = 2,730) was applied to all Marsh Creek carcass length information (n = 115) to derive age composition (Schrader et al. 2016). ................................................................... 31

Table 7. Bear Valley Creek spring-summer Chinook Salmon age-frequency distribution for 2016. An age-length key based on on combined 1998-2016 Marsh Creek and Bear Valley Creek fin ray age subsamples (n = 2,730) was applied to all Bear Valley Creek carcass length information (n = 68) to derive age composition (Schrader et al. 2016). .................................................. 32

Table 8. Mean fork length (cm) at age for spring-summer Chinook Salmon in Idaho during 2016. Ages were derived using dorsal fin rays. Samples are organized by major population group (MPG). Range of lengths is given in parentheses. ...................................................................................................... 33

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LIST OF FIGURES Page

Figure 1. Spring-summer Chinook Salmon populations and major population groups

(MPGs) in the Snake River evolutionary significant unit (ESU). Red dots represent impassable dams. .............................................................................. 35

Figure 2. Location of spring-summer Chinook Salmon monitoring infrastructure used in Idaho during 2016. Numbers correspond to IDFG infrastructure sites in the lower left inset. Major population groups are highlighted and independent populations are delineated. ............................................................ 36

Figure 3. Spring-summer Chinook Salmon index redd count trends in Idaho major population groups (MPGs), 2011-2016. Numbers shown are raw counts entered by biologists responsible for respective counts. Missing index counts from population (year) include: East Fork South Fork Salmon River (Upper Salmon River MPG; 2011-2012); Yankee Fork Salmon River (Upper Salmon River MPG; 2012-2013); Lolo Creek (Wet Clearwater River MPG; 2011-2012); and Moose Creek (Wet Clearwater River MPG; 2011-2012). ................................................................................................................ 37

Figure 4. Distribution of Spring-summer Chinook Salmon index redd counts completed by the Idaho Department of Fish and Game in the South Fork Salmon River in 2016. ........................................................................................ 38

Figure 5. Distribution of Spring-summer Chinook Salmon redds identified during index redd surveys completed by the Idaho Department of Fish and Game in Boulder Creek, a newly established transect in the Little Salmon River drainage in 2016. ............................................................................................... 39

Figure 6. Distribution of Spring-summer Chinook Salmon redds identified during index and census redd surveys completed by the Idaho Department of Fish and Game and the Rocky Mountain Research Station (RMRS; US Forest Service) in the Middle Fork Salmon River MPG in 2016. .................................... 40

Figure 7. Distribution of Spring-summer Chinook Salmon redds identified during index redd surveys completed by the Idaho Department of Fish and Game in Panther Creek, the North Fork Salmon River, and the mainstem Middle Salmon River below the Pahsimeroi River populations in 2016. Survey methods were a combination of ground and aerial (helicopter). ......................... 41

Figure 8. Distribution of Spring-summer Chinook Salmon redds identified during a combination of ground index redd surveys and census surveys completed by the Idaho Department of Fish and Game in the Lemhi River and Hayden Creek in 2016. Pink lines denote areas where census surveys were completed, and blue lines indicate areas where an index survey was completed. ......................................................................................................... 42

Figure 9. Distribution of Spring-summer Chinook Salmon redds identified during an aerial index count completed by the Idaho Department of Fish and Game in the Pahsimeroi River and Patterson/Big Springs Creek in 2016. .................... 43

Figure 10. Distribution of Spring-summer Chinook Salmon redds identified during aerial index counts completed by the Idaho Department of Fish and Game in the Upper Salmon River, the East Fork Salmon River, and Valley Creek in 2016. .............................................................................................................. 44

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Figure 11. Relative length frequency distributions of the entire wild spring-summer Chinook Salmon spawning cohort in Idaho during 2016. Fish collected at hatchery traps, hatchery weirs, and research weirs for integrated broodstock were not included in proportions calculated here. The summation of all proportions irrespective of age is equal to 1. Carcasses were collected on the spawning grounds and ages were determined from fin ray analysis (n = 908). ................................................................................... 45

Figure 12. Age bias plot illustrating pairwise comparisons of fin ray determined age with known age for spring-summer Chinook Salmon in Idaho, 2016 (BioSamples database, fin ray data; PTAGIS database, PIT-tag data; RMIS database, CWT data). Dashed line represents the 1:1 relationship. Error bars represent 95% confidence intervals around the mean fin ray assigned age for all fish of a given tag-assigned age. Mean coefficient of variation (CV) is over all individual CVs (n = 80). PA = percent agreement. Fin ray freshwater ages were assumed to be 1 year. ..................................................... 46

Figure 13. Number of genetics samples collected from wild and integrated hatchery adult Chinook Salmon released at IDFG hatchery weirs (dots), hatchery traps (squares), and research weirs (triangles), 2012-2016. Crooked River samples for 2014 (n = 44) have not been located. ............................................. 47

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ABSTRACT

The Idaho Department of Fish and Game wild salmon and steelhead program monitors the status of wild Snake River spring-summer Chinook Salmon Oncorhynchus tshawytscha populations in the Salmon River and Clearwater River, Idaho. In this report, we summarize adult Chinook Salmon monitoring information collected during 2016 including redd counts, carcass data, and weir samples. Surveyors observed 2,891 redds during trend surveys in single pass index transects. Of the 2,660 redds counted in the Salmon River transects, 824 redds were in the South Fork Salmon River major population group (MPG), 695 redds were in the Middle Fork Salmon River MPG, and 1,141 redds were in the Upper Salmon River MPG. Of the 231 redds counted in the Clearwater River transects, 92 redds were in the Dry Clearwater River MPG and 139 redds were in the Wet Clearwater River MPG. Index redd count trends in all MPGs have generally been flat over the last five years, though annual totals have varied widely. Redd counts in three of the five MPGs were higher in 2016 than 2015 while two were lower in 2016 than 2015. Surveyors also used multiple-pass census surveys (to obtain a total rather than a peak redd count) to count 226 redds in Marsh Creek, 167 redds in the Lemhi River, and 448 redds downstream of the Sawtooth Hatchery weir to Redfish Lake Creek. Redds were not evenly distributed throughout most populations with most redds confined to very specific reaches in streams. The fraction of hatchery carcasses ranged from <1% in the Middle Fork Salmon River MPG to 91% in the supplemented Dry Clearwater River MPG. Wild carcass sex ratios were 63% female in the Salmon River subbasin and 60% female in the Clearwater River subbasin. We aged 1,070 carcasses using dorsal fin rays. Age-4 (brood year 2012) adults were the dominant age class. The percentage age-4 was 65% in the South Fork Salmon River MPG (n = 292); 48% in the Middle Fork Salmon River MPG (n = 69); 53% in the Upper Salmon River MPG (n = 130); 63% in the Dry Clearwater River MPG (n = 12); 74% in the Wet Clearwater River MPG (n = 37); and 57% from wild fish used for various integrated hatchery programs combined (n = 124). Estimating ages of spawning Chinook Salmon using fin rays continues to be the preferred method for population-specific age composition. Percent agreement between reader-determined age and known age was 90.0%; mean coefficient of variation was 2.3% (n = 80). An accounting of genetics samples collected from wild Chinook Salmon released at adult weirs and traps operated by Idaho Department of Fish and Game is presented.

Authors: Matthew J. Belnap Fisheries Biologist Bruce Barnett Fisheries Data Coordinator Kimberly A. Apperson Fisheries Biologist Matt Amick Fisheries Technician I

Carlos Camacho Fisheries Biologist Robert Hand Fisheries Biologist Mike Peterson Fisheries Biologist Evan Brown Sr. Fisheries Data Coordinator

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INTRODUCTION

Populations of Chinook Salmon Oncorhynchus tshawytscha in the Snake River basin declined substantially following the construction of hydroelectric dams in the Snake and Columbia rivers. Raymond (1988) documented a decrease in survival of Chinook Salmon from the Snake River following the construction of dams on the lower Snake River during the late 1960s and early 1970s. Abundance rebounded slightly in the early 1980s, but then escapements over Lower Granite Dam into the Snake River basin declined again (Busby et al. 1996). In recent years, abundance in the Snake River basin has slightly increased; however, the returns of naturally produced (hereafter wild) Chinook Salmon remain critically low compared to historic levels. As a result, Snake River spring-summer Chinook Salmon were classified as threatened in 1992 under the Endangered Species Act (ESA). In 2004, the Interior Columbia Basin Technical Recovery Team (ICBTRT) was formed by the National Marine Fisheries Service (NMFS) to define independent populations within the evolutionary significant unit (ESU) and to develop viability criteria for each population. The ICBTRT defined a hierarchical structure for Snake River spring-summer Chinook Salmon. From spatially largest to smallest they include the ESU, the major population group (MPG), and the population. Within the Snake River spring-summer Chinook Salmon ESU there are seven MPGs in areas currently accessible to salmon, five of which are in Idaho (Figure 1; ICBTRT 2003, 2005; Ford et al. 2011; NMFS 2011, 2016). The Dry Clearwater River and Wet Clearwater River MPGs are considered to have been extirpated but have been mostly refounded with stocks from other Snake River MPGs. A total of 28 extant populations have been identified in the ESU.

A primary goal of Idaho Department of Fish and Game’s (IDFG) wild salmon and steelhead

monitoring program is to provide information on the status of Idaho’s wild Snake River spring-summer Chinook Salmon (hereafter Chinook Salmon) with respect to viable salmonid population (VSP) criteria. The key metrics used to evaluate viability of salmonid populations are abundance, productivity, spatial structure, and diversity (McElhany et al. 2000). This report focuses on the adult life-history stage of these viability metrics with respect to wild Chinook Salmon. We define “wild” fish as those fish whose parents spawned naturally in the wild. This is in contrast to “wild” versus “natural” designations traditionally used by IDFG to distinguish lineage or history of hatchery stocking (e.g., Hassemer 1993a).

In Idaho, it is difficult to census all wild adult Chinook Salmon returning to each population

to spawn due to the large geographic area encompassed, the difficulty accessing remote wilderness areas, and funding constraints. In the 1950s, IDFG developed a program to index annual spawning escapement by enumerating Chinook Salmon redds in select areas at time of peak spawning. The intent was to monitor population trends over time. Hence, the core transects that were and are surveyed annually are referred to as index transects. Although sporadic surveys were made as early as 1947, consistent index surveys date back to 1957.

Index transects cover a large portion of the wild Chinook Salmon spawning habitat in Idaho

(Pirtle 1956; Hassemer 1993b). The use of single-pass index surveys of spawner abundance continues to be the most efficient, albeit least precise, method to monitor the status and trends of Chinook Salmon populations across the landscape (ASMS 2010; Gallagher et al. 2010). Recent efforts have been undertaken to expand the index survey data to actual spawner abundance in the Salmon River populations for the 2015 ESA status assessment (NMFS 2016). These derived spawner abundance data can be obtained at the Idaho Fish and Wildlife Information System website (https://fishandgame.idaho.gov/ifwis/portal/), the IDFG Follow Idaho Salmon Home website (http://216.206.157.62/idaho/web/apps/index_main.php), the NMFS Salmonid

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Population Summary website (https://data.noaa.gov/dataset/sps-abundance-salmon-population-summary-database), and the StreamNet website (http://www.streamnet.org/data/).

In addition to reporting index redd survey information for 2016, we also report four

additional types of information that were collected by IDFG as part of monitoring wild adult Chinook Salmon in Idaho. First, multi-pass census redd surveys are conducted in intensively-monitored populations where complete spawner abundance data are not obtainable through infrastructure such as fish weirs or PIT-tag arrays. The census surveys provide in whole or in part the high precision fish-in information needed for VSP life-cycle monitoring (at least one population per MPG) and habitat effectiveness monitoring (ASMS 2010). The intensively-monitored populations identified in Idaho (in parentheses, the high precision methodology used and the responsible agency or tribe) include: 1) South Fork Salmon River Mainstem (census redd surveys and PIT-tag arrays by Nez Perce Tribe; McCall Hatchery weir by IDFG); 2) Secesh River (census redd surveys, Didson sonar weir, and PIT-tag array by Nez Perce Tribe); 3) East Fork South Fork Salmon River (census redd surveys, weir, and PIT-tag array by Nez Perce Tribe); 4) Big Creek (PIT-tag array by IDFG); 5) Bear Valley Creek (combination of census redd surveys and video weir by Shoshone-Bannock Tribes); 6) Marsh Creek (census redd surveys by IDFG); 7) Lemhi River (census redd surveys and PIT-tag arrays by IDFG); 8) Pahsimeroi River (Pahsimeroi Hatchery weir by IDFG); 9) Salmon River Upper Mainstem Above Redfish Lake (census redd surveys downstream of the Sawtooth Hatchery weir and the Sawtooth Hatchery weir by IDFG); and 9) Lolo Creek (census redd surveys, weir, and PIT-tag array by Nez Perce Tribe). Chamberlain Creek was dropped from the initial ASMS candidate list due to its remoteness. This report will summarize census redd surveys conducted by IDFG in Marsh Creek, Lemhi River, and downstream of the Sawtooth Hatchery weir to Redfish Lake Creek.

Second, additional redd surveys are conducted in various streams for a variety of reasons

such as assessing relative spawner abundance, assessing spatial distribution of spawners, or assessing spawn timing. For example, in the Appendix we report the third year of Chamberlain Basin additional redd surveys that were conducted in areas outside the standard index transects. These additional surveys will inform future Chamberlain Creek population spawner abundance estimates that rely on the traditional index surveys.

Third, carcass surveys are generally conducted in tandem with, or in addition to, redd

surveys to provide spawning biological assessment information such as origin (wild or hatchery), age composition, length at age, and sex ratio. We combine our data with Nez Perce Tribe (NPT) and Shoshone-Bannock Tribes (SBT) data, where acknowledged, to provide a truly comprehensive Idaho summary of this type of information. We do not report genetics results but note that carcass fin tissue samples are archived by IDFG for future reference.

Finally, fish weirs and traps are used by IDFG to capture, enumerate, and manage adult

Chinook Salmon returning to several Idaho streams (Figure 2). Many weirs are integral to the high precision life-cycle monitoring as described above, as are screw traps and other monitoring infrastructure such as PIT-tag arrays (ASMS 2010; Apperson et al. 2017). Most weirs and traps are operated by IDFG hatchery personnel who typically collect hatchery fish for broodstock and release wild or integrated hatchery fish at the weir to spawn naturally. Some additional weirs are operated by IDFG personnel for research or monitoring purposes, but none were specifically operated for Chinook Salmon in 2016. We refer the reader to IDFG hatchery reports and to the Fish Inventory System Hatchery Database (FINS; http://www.finsnet.org/) to obtain adult Chinook Salmon return and disposition information relative to IDFG hatchery weirs and traps. Wild fish returning to weirs and traps are not able to be aged accurately using scales (Copeland et al. 2007), and fin rays are not collected from live fish that are released. We do not report genetics

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results but we do summarize the fin tissue samples that were collected by IDFG hatchery personnel and archived for future genetic reference.

METHODS

Redd Surveys

Spawning Ground Survey Training

To maintain consistency among cooperators and crews, all personnel responsible for surveying redds and sampling Chinook Salmon carcasses attended an annual joint spawning ground survey training at the beginning of spawning season. Surveyors were trained in the identification of redds, use of global positioning systems, data recording, and techniques for proper collection of biological information and samples from carcasses. In 2016, NPT hosted the statewide spawning ground survey workshop in McCall, Idaho, to provide standardized training for all State, Federal, and Tribal agencies conducting redd counts and carcass surveys in Idaho.

Index Surveys

Methods used for Chinook Salmon index redd surveys during 2016 were the same as recent years. Standardized redd count protocols are described in Hassemer (1993b), and all surveys were conducted in August and September. Single-pass, peak-count surveys were made in each index transect. Each survey was originally timed to coincide with the period of maximum spawning activity on a particular stream, based on historic observations, and assigned a target survey-time window. The method chosen for each survey was dependent upon a) the best visual technique for each transect, and b) the ability to maximize the number of river miles surveyed. Methods included low-flying helicopter or single-pass ground surveys conducted on foot. Methods have varied within some transects over the years. A ground survey index transect was established for the Little Salmon River population in 2016, in the lower reaches of Boulder Creek. Currently no redd count index transects are identified for the following populations: Middle Fork Salmon River Above and Including Indian Creek, Potlatch River, Lapwai Creek, Lawyer Creek, or Meadow Creek.

Census Surveys

Streams in some intensively-monitored populations, or in portions of intensively-monitored populations like downstream of the Sawtooth Hatchery weir, are typically surveyed three or more times to provide a census of all redds. Objectives of intensively-monitored populations and their associated high precision life-cycle monitoring are described in the Anadromous Salmonid Monitoring Strategy (ASMS 2010). Standardized redd count protocols are described in Hassemer (1993b). In contrast to the index surveys, timing of these census surveys is population-specific and designed to begin and end with spawning activity. Census surveys are designed to enumerate all redds, and they use multiple-pass ground counts that generally include all probable spawning habitat. Heavily used spawning reaches also benefit from multi-pass census surveys to accurately count redds in areas that are subject to redd superimposition.

Multiple-pass ground counts allow observation either during redd construction or shortly

thereafter and aid in redd identification. Redds observed during multi-pass ground counts are flagged, assigned a unique number, and waypoints recorded using a global positioning system; flags are removed during the last count. Surveyors also record the presence of any live adult fish

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observed to help ascertain if spawning is complete. For streams that are counted multiple times on the ground, the final redd count is the sum of all new redds observed during each pass. Multiple-pass counts also increase the number of adult Chinook Salmon carcasses recovered over what would have been collected in a single-pass design.

Additional Surveys

Additional redd surveys were conducted in various streams to address specific questions regarding habitat effectiveness monitoring or to obtain specific spawner metrics in data limited areas. For example, in the Pahsimeroi River, habitat actions and flow agreements were implemented in a major tributary (i.e. Patterson/Big Springs Creek) which ultimately resulted in a substantial increase in suitable spawning habitat. Additional surveys in places like this were necessary to accurately represent the spawning population in the Pahsimeroi river population. Unless specifically noted, additional redd surveys follow standardized redd count protocols described in Hassemer (1993b).

Carcass Surveys

Chinook Salmon carcasses were sampled from spawning areas throughout the Idaho portion of the study area consistent with methods in Copeland et al. (2004). The 2016 carcass survey locations were chosen to include: 1) all redd count index transects that were surveyed from the ground; 2) index transects or portions of transects that were aerially surveyed and required revisiting from the ground to collect carcasses; 3) index transects or portions of transects that were surveyed from the ground but additional carcass data from revisits was desired; 4) areas outside index transects where additional carcass data was desired; or 5) upstream of hatchery weirs located in the Pahsimeroi River, the upper Salmon River (Sawtooth Hatchery), South Fork Salmon River (McCall Hatchery), and Johnson Creek where wild fish are collected and used for integrated broodstock programs.

For each carcass encountered during the surveys, we recorded its location, origin (wild or

hatchery), any marks or tags, length, sex, and whether the fish succumbed to prespawn mortality. All carcasses were measured for fork length (cm). Lengths were measured using a tape measure. If any carcasses, male or female, were found washed up on weirs or during early surveys before the construction of any redds, they were considered prespawn mortalities if their gonads were fully intact. After the construction of redds began, only females with fully intact skeins were considered prespawn mortalities as it could not be determined if males had spawned or not. Visceral cavities were inspected to determine sex and whether the fish succumbed to prespawn mortality, both of which are used to calculate females per redd and associated productivity metrics. During examination, female carcasses were given a percent spawned value that ranged from zero (skeins fully intact) to 100% (no or few eggs remaining) in 25% increments. Fish that were greater than 0% spawned were considered successful spawners.

We used marks and tags to identify origin for all carcasses encountered. Two types of

hatchery Chinook Salmon are present: segregated and integrated. Segregated hatchery fish are crosses of hatchery fish only, while integrated hatchery fish are crosses of either two wild parents or one wild parent and one hatchery parent. Smolts from both types of stocks are marked to distinguish them from each other and from natural-origin fish. In the Salmon basin, all segregated fish are marked with an adipose fin clip; a subset is additionally marked with an internal coded wire tag (CWT) or an internal passive integrated transponder (PIT) tag. In the Clearwater basin, there are segregated fish released without an adipose fin clip in the Selway River, the Lochsa River, Clear Creek, tributaries of the South Fork Clearwater River, and mainstem Clearwater

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River. Integrated fish are all marked with a CWT only with the adipose fin left intact and some have a PIT-tag inserted. Hence, hatchery-origin carcasses were determined by the visual presence of any external mark, such as an adipose fin clip, or by scanning for the presence of an internal CWT tag. We used PTAGIS to identify the origin of all PIT tagged Chinook carcasses.

Dorsal fin ray samples for age analysis and tissue samples for genetic analysis were

collected from a designated target number of carcasses per survey location. If a carcass was extremely decomposed or missing its dorsal fin, fin rays or tissue samples may not have been collected. Four to five fin rays from each fish were removed, placed in a coin envelope, and dried. A tissue sample was collected from the least decayed fin and stored on a piece of paper inside separate coin envelopes. Fin ray and tissue samples were delivered to the IDFG Nampa Research Anadromous Ageing Laboratory located in Nampa, Idaho. Otoliths were collected in Middle Fork Salmon River tributaries and archived by the Rocky Mountain Research Station laboratory in Boise, Idaho (BPA project 1999-020-00, Analyze Persistence and Dynamics in Chinook Redds).

Fin ray sample size goals for 2016 were set following procedures given in Stiefel et al

(2016). The target for each population was determined using power analysis combined with a preseason forecast to predict abundance of wild spawners. The power analysis consisted of using a simulation program in R (R Development Core Team 2010) to evaluate accuracy and precision of age proportion estimates across varying sample sizes and spawner abundances. This unpublished analysis showed that the marginal increase in accuracy and precision for age-3, age-4, and age-5 age proportions diminished when sample sizes exceeded 30% of total spawners. Accurate and precise estimates of age-6 proportions could not be achieved in any population with a reasonable amount of effort due to the extremely low incidence of this age class. There was little benefit to increasing fin ray sample sizes beyond n = 150 regardless of population size.

Fin ray processing is a time-intensive process and collecting only needed samples will

allow for more efficient use of resources. A length-at-age comparison was completed between Marsh Creek and Bear Valley Creek populations to determine if an age-length key could be used in lieu of collecting samples at both locations (Schrader et al. 2016). We found that a fixed stratified sample of 100 fin rays collected in Marsh Creek can be used interchangeably for Bear Valley Creek, and vice versa, to build a generalized age-length key. In 2016, there were some length classes that were not represented in the Marsh Creek samples that were represented in the Bear Valley samples. To account for these missing samples, historical data (i.e. that used to construct the age-length key in Schrader et al. 2016) were used to fill in gaps after it was determined that the age-length relationship in 2016 was not different than that of previous years.

Carcass Age Composition

Laboratory Processing of Dorsal Fin Rays

Chinook Salmon are assigned ages based on dorsal fin ray samples. Fin rays were processed and assigned a saltwater age. Freshwater age was assumed to be one year for all fin rays. Summing saltwater age with freshwater age, plus 1, yields total age (hereafter age). Fin rays were dried, set in epoxy resin, cut into cross sections with a bone saw, and mounted on microscope slides. All samples were aged independently by two technicians. Personnel were trained with reference fin rays and were required to demonstrate 90% accuracy in an ageing test before they were allowed to begin ageing new samples. If there was disagreement in age determination or the age did not match what was expected for fish length, then fins were aged again in a referee session. A referee session requires that three personnel observe the fin

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together and arrive at a consensus age. In some cases, a consensus could not be achieved and the sample was removed from analysis (Wright et al. 2015).

Dorsal Fin Ray Age Validation

For age validation purposes, we rely on fish of known age from two sources. Hatchery personnel collect dorsal fin rays from tagged hatchery adults returning to Rapid River, McCall, Pahsimeroi, and Sawtooth hatchery facilities. Hatchery fish PIT tags and CWTs are recorded during spawning operations and provide a known-age mark for total age validation (Campana 2001). PIT tags encountered on the spawning grounds from wild fish could also be used but they provide only saltwater age validation and not total age validation. For simplification, only known total age samples are presented in this report (i.e., those that are a result of a hatchery-released PIT-tag or CWT).

Metrics used to assess accuracy of our age assignments were percent agreement and

percent bias expressed as mean coefficient of variation; both assess accuracy because assigned age is compared to known age. Percent agreement (PA) is calculated as the percentage of assigned ages that agreed with the known age based on tag information. The following equation was used:

𝑃𝑃𝑃𝑃 = 100 × 𝑃𝑃𝑁𝑁

where A is the number of correctly assigned ages and N is the total number of fish aged. A PA that is ≥90% is desired to prevent bias (Buckmeier 2002). An age bias plot was constructed to illustrate pairwise comparisons between assigned fin ray age and known age based on tags. A bias is apparent if the paired estimations (95% confidence intervals) depart from the 1:1 line.

The coefficient of variation (CV; Chang 1982, Campana 2001) is the ratio of the standard deviation to the mean when two readers assign ages to each fish, or when an assigned age is compared to the validated age. These values are then averaged over the samples to obtain the mean coefficient of variation. The following equation was used:

𝐶𝐶𝐶𝐶𝑗𝑗 = 100 × �∑

(𝑋𝑋𝑖𝑖𝑗𝑗 − 𝑋𝑋𝑗𝑗)2𝑅𝑅 − 1

𝑅𝑅𝑖𝑖=1

𝑋𝑋𝑗𝑗

where CVj is the precision estimate for the jth fish, Xij is assigned age, Xj is the validated known age, and R is the number of times each fish was aged. Using the assigned age and known age in this CV formula gives an estimate of percent bias (Copeland et al. 2007). A CV that is ≤10% is desired.

Genetics Samples at Weirs and Traps

All adult Chinook Salmon captured at IDFG weirs or traps had the following data recorded: origin (wild or hatchery), any marks or tags, fork length, and sex. We refer the reader to IDFG hatchery reports and to the Fish Inventory System Hatchery Database (FINS; http://www.finsnet.org/) to obtain more specific information. Tissue samples for genetics analysis were collected from all wild and integrated hatchery fish released at the weir. Tissue samples

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were stored on Whatman sheets and delivered to the IDFG Eagle Fish Genetics Laboratory located in Eagle, Idaho.

Data Management and Analysis

Spawning ground survey (SGS) data, including redd count and carcass survey data, are recorded in the field on standardized paper data sheets and with global positioning systems devices. Waypoints are captured for new redds, carcasses, and survey boundaries using standardized naming conventions. Personnel from IDFG and the Shoshone-Bannock Tribes enter survey data into a local Spawning Ground Survey application (SGSA), and the global positioning systems data are imported into their respective surveys in the SGSA. The data are quality checked by the compilers against the paper survey forms. The waypoint data are visually inspected by the compilers to ensure accuracy in the SGSA. Upon verification of complete and correct surveys, the data are uploaded to the centralized, Microsoft Sequel Server SGS database. Other organizations such as the Nez Perce Tribe and USFS transfer their index redd survey data to IDFG biologists who then enter it into a local SGSA. The transferred index data are checked for completeness and correctness by data managers, and corrections are uploaded from their SGSA to the SGS database if necessary. Non-index data collected by other organizations are housed and maintained in their separate databases.

Index transects are assigned their transect code (WS-1, NS-1, etc.) based upon the

criteria described in Hassemer 1993b (location, timing, redds, live fish, and carcasses). Index count assignments are reviewed by the biologists who compiled the survey data. The data from all compilers are accessible in read only views from the Idaho Fish and Wildlife Information System (IFWIS) web reports which query the SGS database. (https://fishandgame.idaho.gov/ifwis/portal/).

Carcass sample data such as fin ray, genetics, and otolith data that are recorded on the

spawning grounds are entered into SGSA, uploaded to the SGS database, and then transferred from the SGS database to the BioSamples database, which is located on a Microsoft Sequel Server. The transfer is performed by the ageing laboratory coordinator who uses a data template in Microsoft Excel to reformat data from the SGS database for entry into the BioSamples database. A unique fish identification code from the SGS database is entered into BioSamples database to assist in joining the two databases. Carcass records in the SGS database with fin ray samples are joined to the ageing data in the BioSamples database using the unique fish identification code and the sample number. When the fin rays are analyzed, the estimated age from the BioSamples database populates the Estimated Total Age field in the SGS database.

For this report, all index and census redd survey data were entered into preformatted (no

hyphen) tables by biologists responsible for their collection. Fin ray ageing data were downloaded from the BioSamples database on 2/2/2017. Length-at-age data were downloaded from the BioSamples database on 2/2/2017. Adult weir and trap data are stored in and accessed from the Fish Inventory System Hatchery Database (FINS; http://www.finsnet.org/). These data include all adult Chinook Salmon that are trapped, spawned, or released to spawn naturally. Weir and trap genetics sample data were downloaded from the IDFG Eagle Fish Genetics Laboratory Progeny database on 2/9/2017 (Jesse McCane, IDFG, personal communication).

We show the spatial distribution of redds on the spawning grounds with maps constructed

in ArcMap 10.3. Single pass index redd counts and census redd counts (where noted) were used to derive the waypoints for the maps. Each map displays at least one and up to three populations total. We used data from both ground and aerial survey methods.

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Based on a recommendation from this report in 2015, we evaluated the spawn timing of

the Lemhi River population to assess our peak-spawning target survey date. According to Hassemer et al. (1993a), the ratio of redds to live fish should exceed one to one at the time of the target survey date (September 8 in the Lemhi).The Lemhi River has a separate aerial index count as well as multi-pass ground counts. This allows us to compare the timing of spawning in the multi-pass survey to the single pass aerial index count. Using redd count data and live fish data from spawning ground surveys from the previous five years (2012-2016), we evaluated the timing of the aerial index count relative to this desired ratio.

Summaries of some of the data collected in this report are available at the IDFG Follow

Idaho Salmon Home website (http://216.206.157.62/idaho/web/apps/index_main.php).

RESULTS

Redd Surveys

Index Surveys

Staff from IDFG and cooperating agencies surveyed 91 of the 100 current index transects and observed 2,891 Chinook Salmon index redds in 2016 (Table 1). The Colt Killed Creek (Lochsa River) transect (NC-13) was partially surveyed because a road washed out preventing access to the majority of the transect. Moose Creek (Selway River) transect WC-3a were not surveyed due to fire. The other Moose Creek transect (WC-3b) and one of the mainstem Selway River transects (WC-5) were partially surveyed. Six index transects in the Upper Selway River population are no longer surveyed due to discontinued helicopter use (White Cap Creek, WC-1; Running Creek, WC-4a and WC-4b; and mainstem Selway River, WC-6, WC-8, and WC-9) while two transects in the Upper Selway River are maintained as ground counts (WC-5 and WC-7).

A total of 2,660 redds were observed in Salmon River subbasin index transects (Table 1).

Of these, 824 redds were counted in the South Fork Salmon MPG with 468 redds in the South Fork Salmon River Mainstem population (the most in this MPG). The Middle Fork Salmon River MPG had 643 redds with 248 redds in the Bear Valley Creek population (the most in this MPG). There were 1,141 redds in the Upper Salmon River MPG with 373 redds in the Salmon River Upper Mainstem Above Redfish Lake population (the most in this MPG).

A total of 231 redds were observed in Clearwater River subbasin index transects (Table

1). Of these, 92 redds were counted in the Dry Clearwater River MPG and 139 redds in the Wet Clearwater River MPG. All of the Dry Clearwater River MPG redds counted were in the Upper South Fork Clearwater River population.

Census Surveys

For the 2016 census surveys, multiple-pass ground counts were conducted in Marsh Creek, the Lemhi River (including Hayden Creek), and in that portion of the Salmon River Upper Mainstem Above Redfish Lake population downstream of the Sawtooth Hatchery weir (Table 2). The Marsh Creek population spawned from the first week of August to the second week of September and constructed 226 redds; redd construction peaked in the third week of August. The Lemhi River population was surveyed from the Lemhi Store to the headwaters and produced 167 redds including redds counted in Hayden Creek. Hayden Creek spawn timing was from the

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second week of August to the first week of September whereas the rest of the Lemhi population spawned one to two weeks later. The Salmon River Upper Mainstem Above Redfish Lake population was surveyed from the Sawtooth Hatchery weir downstream to Redfish Lake Creek; 448 redds were counted between August 30 and September 23 with peak spawning in the first week of September.

Additional Surveys

In 2016, additional redd count surveys were done in the Upper South Fork Clearwater River population, the Upper Selway River, and Bargamin Creek. In the Upper South Fork Clearwater River population, staff counted 11 redds in American River and 89 redds in Red River to assess spawner abundance. In the Upper Selway River population, staff counted 17 redds to assess spawner abundance and spatial distribution. No redds were documented in Bargamin Creek (Table 3).

Redd Distribution Maps

Redds tended to be clustered in particular reaches rather than dispersed throughout the available habitat (Figures 4-9). The surveyed areas represent the current high quality spawning habitat in most populations. In certain populations (e.g. Lemhi River; Figure 7) the surveys extend into tributaries that historically supported spawning Chinook Salmon, though they do not currently.

Evaluation of Peak Spawn Timing

The target survey date for the index Lemhi survey is September 8 (Table 1). Based on the previous five years of data (2012-2016), the second survey (which is usually completed in the first week of September) was, at the longest, five days before the target date (2013), and at the shortest, on the target date (2014 and 2015). When redd count was plotted by survey, in three of five years, the largest number of redds were counted in the second survey. In the other two years, the largest number of redds were counted on the first survey. In 2013, the year in which the second survey was furthest from the target date, we counted the largest number of redds on the second survey. According to Hassemer et al. (1993a), peak spawning should be identified by when the redd to live fish ratio exceeds one on a given survey. In 2016, this proportion did not exceed one on any surveys. In the other four years of this evaluation, this proportion exceeded or equaled one on the first survey, and in three of the five years, the proportion remained above one on the second survey as well. The aerial index count was completed on September 5 in two of the five years (2013 and 2015) and September 6 in two of the five years (2012 and 2014). In 2016, the second pass ground count (September 6 and 7) was used in place of the aerial survey in 2016 because of poor visibility from the aircraft.

Carcass Surveys

During 2016, staff from IDFG and cooperating agencies and tribes sampled 2,497 Chinook Salmon carcasses in 25 populations (Table 4). Of these, 32 carcasses or 1% were of unknown origin. Of the remaining 2,465 carcasses where origin could be determined, 1,339 carcasses or 54% were wild. In the Salmon River subbasin 1,242 carcasses or 56% were wild, whereas in the Clearwater River subbasin 97 carcasses or 34% were wild. Carcass collection efforts were not equal across all populations.

In the Salmon River subbasin, 63% of 1,231 wild carcasses where gender could be

determined were female, whereas 59% of 936 hatchery carcasses were female (Table 4). In the

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Clearwater River subbasin, 60% of 95 wild carcasses where gender could be determined were female, whereas 50% of 184 hatchery carcasses were female.

In the South Fork Salmon River populations, the percentage of hatchery carcasses

observed, or hatchery fraction, ranged from 2% in the Secesh River (n = 188) to 83% in the Little Salmon River (n = 7; Table 4). The hatchery fraction upstream of the South Fork Salmon River McCall Hatchery weir was 78% (n = 186), but note that hatchery adults are deliberately released upstream of this weir to achieve IDFG integrated hatchery program goals. The hatchery fraction in the East Fork South Fork Salmon River was 30% (n = 347), but note that hatchery smolts and adults are deliberately released to achieve the Nez Perce Tribe Johnson Creek supplementation program goals.

In the Middle Fork Salmon River populations; one hatchery fish was recovered during

spawning ground surveys in Big Creek (Table 4). Hatchery fraction was 0% in Chamberlain Creek (n = 11); 5% in Big Creek (n = 22); 0% in Camas Creek (n = 13); 0% in Loon Creek (n = 11); 0% in Sulphur Creek (n = 13); 0% in Bear Valley Creek (n = 68); and 0% in Marsh Creek (n = 117). Overall hatchery fraction was <1%.

In the Upper Salmon River populations, hatchery fraction was 0% in three populations –

North Fork Salmon River (n = 4 carcasses), Lemhi River (n = 29 carcasses), and Valley Creek (n = 15 carcasses; Table 4). Hatchery fraction was 69% (the highest observed) in that part of the Salmon River Upper Mainstem Above Redfish Lake population upstream of the Sawtooth Hatchery weir (n = 223 carcasses). Integrated fish were deliberately released upstream of this weir. Many fish of hatchery and wild origin dropped out below the weir. Next highest was downstream of the weir at 46% (n = 655 carcasses). In the Pahsimeroi River population, hatchery fraction was 4% upstream of the Pahsimeroi Hatchery weir (n = 29 carcasses) and 0% downstream of the weir where sampling was sparse (n = 3 carcasses), but note that hatchery adults are deliberately released upstream of this weir to achieve IDFG integrated hatchery program goals. Hatchery fraction was 10% in the Salmon River Lower Mainstem Below Redfish Lake population (n = 52 carcasses). In the Yankee Fork Salmon River population, where the Shoshone-Bannock Tribes operate a hatchery supplementation program, hatchery fraction was 20% (n = 57 carcasses).

In the Dry Clearwater River populations, hatchery fraction was 91% in the Upper South

Fork Clearwater River (n = 180 carcasses; Table 4). In the Wet Clearwater River populations, hatchery fraction was 43% in the Lochsa River (n = 47 carcasses), 24% in Lolo Creek (n = 45 carcasses), and 0% in the Upper Selway River (n = 10 carcasses).

Carcass Age Composition

In general, sample size targets were not achieved. Dorsal fin ray samples were collected from 921 wild carcasses from the spawning grounds and 216 wild carcasses that were used for integrated hatchery broodstock programs for a total of 1,137 samples (Table 5). Ages were assigned to 1,124 of these samples or 99%.

Age-4 adults were the dominant age class (though there were more age-5 adults than in

previous years) in all MPGs except the Middle Fork Salmon River and all populations except Marsh Creek, Sulphur Creek, and Panther Creek (Table 5). In the Salmon River subbasin, 65% were age-4 in the South Fork Salmon River MPG (n = 292), 48% in the Middle Fork Salmon River MPG (n = 69), and 53% in the Upper Salmon River MPG (n = 130). In the Clearwater River subbasin, the percentage was 63% in the Dry Clearwater River MPG (n = 12) and 74% in the Wet

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Clearwater River MPG (n = 37). For various integrated hatchery programs including Pahsimeroi, Sawtooth, McCall, and Johnson Creek, the overall percentage was 57% (n = 124). Of the assigned ages in the Salmon River subbasin, 2% were brood year BY 2013, 58.56% were BY 2012, 39.20% were BY 2011, and 0.24% were BY 2010. Brood Year 2010 fish were left out of figures as they comprised a fraction of a percent of the adult population. In the Clearwater River subbasin, 3% were BY 2013, 71% were BY 2012, and 26% were BY 2011. Note that our South Fork Salmon River MPG ageing data will be used by the Nez Perce Tribe to develop age-length keys to derive their final age composition.

We did not age any of the Bear Valley Creek samples because a single age-length key

for Marsh Creek and Bear Valley Creek was used to derive their final age compositions (Table 6; Table 7). Auxiliary analysis showed that there was not a statistically significant difference between Marsh Creek and Bear Valley Creek age-length keys, in total or by year, over multiple years (Schrader et al. 2016). Marsh Creek and Bear Valley Creek fin ray age data from 1998-2016 were used to derive the 2016 age-length key as certain length frequencies in represented in Bear Valley were not represented in Marsh Creek. In Marsh Creek, 0.3% of carcasses were age-3, 45.8% were age-4, 52.5% were age-5, and 1.5% were age-6 (Table 6). In Bear Valley Creek, 0.5% of carcasses were age-3, 51.6% were age-4, 46.6% were age-5, and 1.3% were age-6 (Table 7).

Fish between 54 and 96 cm fork length dominated the relative length frequency

distributions and comprised 59% of the spawning cohort (n = 540; Figure 10). There was substantial overlap between age-4 and age-5 in the 80 to 90 cm length categories, as well as some overlap between age-3 and age-4 fish between 60 and 70 cm. Mean length-at-age for age-3 fish ranged from 62.8 cm in the Upper Salmon River MPG (n = 4) to 66.5 cm in the South Fork Salmon River MPG (n = 12), disregarding the Dry Clearwater River, Wet Clearwater, and Middle Fork Salmon River MPGs due to small sample sizes (n = 1 for all MPGs; Table 8). The means for age-4 fish were between 72-76 cm with the exception of the Dry Clearwater River MPG, which was 68.8 cm (n = 11). The means of age-5 fish ranged from 84.0 cm in the Dry Clearwater River MPG (n = 11) to 88.6 cm in the South Fork Salmon River MPG (n = 143).

Fin ray ages from 2016 are accurate (Figure 11). Of the 80 known-age fin rays, percent

agreement between assigned age and known age was 90.0%, which attained our desired goal of ≥90% (Buckmeier 2002). Our estimated mean coefficient of variation or percent bias was 2.3%, well within our desired goal of ≤10%. Assigned age assumed that freshwater age was one year. Overall, there were 13 known-age samples from BY 2013, 44 samples from BY 2012, and 23 samples from BY 2011. There were no BY 2010 fish in the known-age samples, and there were two BY 2010 in the in the general collection of samples (Table 5).

Genetics Samples at Weirs and Traps

A total of 1,696 tissue samples were collected from wild and integrated hatchery adult Chinook Salmon released at IDFG hatchery weirs, hatchery traps, and research weirs during 2016 (Figure 12). Most samples (n = 709) were collected at the McCall Hatchery weir in the South Fork Salmon River. The East Fork Salmon River weir was not operated for Chinook Salmon in 2016 and no samples were collected. Chinook Salmon are incidental catch at the Fish Creek research weir, which is operated for steelhead O. mykiss.

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DISCUSSION

For monitoring wild spring-summer Chinook Salmon spawner abundance in Idaho, redd surveys cover a large proportion of each population’s available spawning habitat. Idaho Department of Fish and Game maintains a long-term (1957-current for many populations) dataset of index redd surveys across much of the available spawning habitat. The importance and utility of maintaining the long-term index redd survey dataset is a high priority, and IDFG intends to continue monitoring index transects as well as multiple-pass census transects in specified areas (i.e., Lemhi River, Marsh Creek, and the Salmon River Upper Mainstem below Redfish Lake Creek). During the Idaho Supplementation Study (cite completion report) (1992-2014), many populations were intensively monitored using multiple-pass census redd surveys. Since the completion of ISS, IDFG staff have maintained only a subset of census surveys. Index surveys are now the primary survey method in most spawning areas. Idaho Department of Fish and Game has used the protocol authored by Hassemer et al. (1993b) to direct spawning ground sampling. This protocol is useful and has been the basis for sampling since its inception. Updating the protocol to incorporate changes in methodology and updated sampling strategies would be beneficial as a resource for future surveyors.

Spring-summer Chinook Salmon index redd counts in all Idaho MPGs have generally

trended flat over the last five years but with large annual fluctuations (Figure 3). Counts in three of the five MPGs were higher in 2016 than 2015 while two were lower in 2016 than 2015. Derived from these counts, the estimated abundance of wild adult spawners in Idaho is low compared to historical estimates and no population currently meets viability criteria; hence all populations continue to be listed under the ESA as threatened (Ford et al. 2011; NMFS 2016). Because spawner abundance is low compared to the vast area of spawning habitat that is available, the poor dispersion of spawning fish – a direct result of patchy and disjunct spatial structure over this habitat – is not unexpected. This observation is not surprising given current status of Chinook populations. It is likely that as Chinook recover and increase in abundance, they will distribute throughout the habitat. The Clearwater basin is an example of measures taken to address issues like the one above. Salmon and steelhead (lower case?) runs were extirpated by the construction of the Lewiston Dam in the 1920s. Since that time, IDFG and the NPT have implemented programs to reseed previously vacant habitat. Now the Wild Chinook Salmon runs in the Clearwater are re-established though fisheries in the Clearwater target hatchery fish alone. The Idaho Supplementation Studies project sought to determine if supplementation of wild populations could help increase the population over time. One main finding was that supplementation did have a short effect though the effect did not persist after the cessation of supplementation (Venditti et al. 2015). This result suggests that to sustain long term benefits, supplementation programs should be consistent and long term. This may be a strategy to seed unused habitat for Idaho Chinook populations.

We did not establish any new index transects in the Upper Selway River or in Patterson Big Springs Creek per recommendations from Stiefel et al. (2016). While these transects are surveyed each year, establishing index transects should be a high priority for future years. We did establish a new index transect in Boulder Creek (a tributary to the Little Salmon River) to enhance our understanding of the Little Salmon River population for the ESA status assessment.

Adult Chinook Salmon returns were dominated by age-4 (BY 2012) adults in 2016 though

compared to 2015, the age-5 proportion of the run was higher in 2016 (Stiefel et al 2016). Since 2011, age-4 was the most abundant age class in adult Chinook Salmon returns to Idaho for all populations. There were more age-5 (BY 2011) adults than age-3 (BY 2013) adults across all MPGs, and this is consistent with observed age structure in previous years. In 2016, there were

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two age-6 (BY 2010) adults encountered across all MPGs compared to zero in 2015 (Stiefel et al. 2016). This suggests that the age structure of returning adult Chinook Salmon is relatively consistent between years, at least in the short term. Based on the comparison of the age structure in Bear Valley Creek and Marsh Creek detailed by Schrader et al. (2016), it is likely that age structure between populations spatially proximal to one another may be consistent on a longer term basis as well. If the age structure of our populations shifts dramatically, it could indicate a year class failure in freshwater spawning/rearing habitat, poor ocean conditions for juveniles, or unfavorable corridor migration conditions for adults.

The process by which we identified Chinook Salmon fin ray sample size targets is specific

to Idaho populations and is better suited than targets identified in previous publications. These targets for 2016 were n = 150 for larger populations or 30% of forecasted spawner abundance for smaller populations. Our collection targets fall between the 40 samples recommended by Gerritsen and McGrath (2007) and 500+ recommended by Thompson (1987). While these publications provided a one target solution, they do not take into account how population abundance influences the accuracy and precision estimating multinomial proportions. Population abundance is an important consideration as small populations represent a finite scenario and proportions can be accurately measured with a smaller sample size. Conversely, large populations require a larger sample size to accurately measure proportions. Given the spectrum of population sizes in Idaho, from Camas Creek population (small; less than 100 spawners) to South Fork Salmon River Mainstem population (large; over 900 spawners), we suggest our population-specific targets are more appropriate for the populations we monitor as they provide a level of accuracy and precision that guide management decisions and are logistically achievable. Most population fin ray sample target goals were not met in 2016. This is primarily because of less intensive redd surveys (i.e. fewer multiple-pass census counts) completed throughout Idaho. In the future, managers may consider adding effort to specific surveys for collection of carcasses to supplement biological data for populations where information is limited or increased precision is desirable.

The frequency of hatchery carcasses encountered on the spawning grounds varied among

MPGs and populations. The Middle Fork Salmon River MPG has no history of supplementation or hatchery influence, and the disposition (i.e. hatchery or wild/natural) of carcasses reflected this history. As expected, MPGs with a history of supplementation or hatchery influence had greater proportions of hatchery carcasses on the spawning ground. For populations like the South Fork Salmon River Mainstem and Salmon River Upper Mainstem above Redfish Lake Creek which support large fishery mitigation hatchery programs experience both intentional supplementation with targeted release of integrated adults and a form of de facto supplementation from segregated hatchery adults which are not harvested in downstream fisheries or trapped at the release location. Surveys immediately downstream from a hatchery weir generally had a greater proportion of hatchery spawners than other surveys when suitable spawning habitat is directly downstream of the weir. This means that not all redds in these areas can be attributed to spawning by wild/natural adults. For the purposes of this report, we don’t distinguish redds reported by origin of adults. For higher level analyses like the ESA status assessment, IDFG partitions redds by the hatchery proportion as identified by carcasses collected during spawning ground surveys.

Chinook Salmon used to reseed the spawning habitat in the Clearwater basin were from an out-of-basin non-localized broodstock (i.e. Rapid River in the Salmon basin). As a result, wild Chinook in the Clearwater are descendants of a hatchery stock and they are indistinguishable from the hatchery broodstock. In the Salmon basin, the hatchery broodstocks were founded from local wild stocks, so the opposite scenario occurred. While artificial selection has likely occurred

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in the hatcheries, based on the current genetic techniques and methodology, no distinction can be drawn between wild and hatchery stocks in either basin.

Biological data from carcass surveys provides population metrics including age

composition, sex composition, length-at-age, and hatchery fraction. In previous status assessments, NOAA was provided raw data relating to productivity, spawner abundance, distribution, and diversity. Idaho Department of Fish and Game and other management agencies identified the need to analyze these data “in-house” and provide the results to NOAA which has resulted in the current flow of information. For IDFG, this change represents an important shift by incorporating the proper limitations and inferences made by local managers and researchers most familiar with the data and collection methods.

Redd distribution maps display a disproportionate number of redds in tributary populations

compared to mainstem populations. In the tributaries, there are many stream miles of unused but suitable habitat. These maps demonstrate that the current wild spawning Chinook Salmon populations exhibit patchy distribution across much of their range in Idaho. Additionally, we infer that the mainstem river populations in Idaho are limited in abundance compared to the tributary populations which sustain the majority of spawners throughout Idaho.

To demonstrate the amount of habitat available to Chinook, we recommend that future

reports include graphic presentation of long-term trends in spawning distribution across the landscape. This could be accomplished by using georeferenced redd information from multiple years to develop a color specific continuum (e.g. green displays limited use and red displays frequent use) showing the habitat that is commonly used by spawning Chinook Salmon year after year regardless of adult escapement.

The target date of the index count in the Lemhi based on criteria specified by Hassemer

et al. (1993b) appears to be valid. Peak spawning activity was documented before the target date in all years evaluated. The criteria used to identify timing of peak spawning may need more thorough evaluation. In four of the five years, the redd to live fish ratio was at or above one on the first survey of the multi-pass ground counts (typically the last week of August). Based on the current criteria, the index count should have been completed earlier in the spawning season in four of the five years in this evaluation. Importantly, if this adjustment were made, in four of the five years, between 65% and 92% of the redds would not have been counted during the index count in the Lemhi. Using the current index target date, between 13% and 35% of the redds were not counted during the index count in the Lemhi. This validates that the current target date in the Lemhi is past peak spawning activity, but this also identifies a less than ideal metric to evaluate peak spawning which should be refined. Future evaluations of spawn timing will determine if this is a consistent observation in other populations or if this is limited to the Lemhi.

Based on these summaries, Chinook populations in Idaho have low though stable short-

term mean abundances, stable age structures, patchy distributions, and variable hatchery influences across the landscape. The distribution maps presented here highlight the general lack of mainstem spawning adults compared to tributary populations, though there is not a lack of spawning habitat.

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RECOMMENDATIONS

1. Maintain the IDFG redd count index surveys. Potential spatial or temporal changes to these surveys should be thoroughly documented and vetted at the policy level (e.g., evaluate change and/or annual fluctuations in peak spawn timing).

2. Publish current protocols for redd surveys and carcass surveys to ensure standardized

methods are used. This publication would be an update of Hassemer (1993b). 3. Evaluate the peak spawn timing and accuracy of the target survey dates for the index

surveys in at least one population per year.

4. Establish index surveys in Patterson Creek in the Pahsimeroi and the Upper Selway River

to gain understanding of spawning in these areas.

5. Continue to refine spawning ground survey data management, from quality assurance in

the field to quality control of the Spawning Ground Survey database and its output to ensure timely and accurate summaries.

6. Enhance redd distribution maps to include historic georeferenced redd densities as a color

coded continuum that describes frequently used spawning habitat since the advent of GPS. Annual redd waypoints would then be overlaid on the historic spawning distribution to show habitat use in the current year compared to previous years.

17

LITERATURE CITED

Apperson, K.A., E. Stark, K.K. Wright, B. Barnett, D.A. Venditti, R. Hand, P. Uthe, M. Belnap, B. Knoth, R. Roberts, L. Janssen. 2016. Idaho anadromous emigrant monitoring. 2014 and 2015 annual report. Idaho Department of Fish and Game Report 16-07, Boise, Idaho.

ASMS (Anadromous Salmonid Monitoring Strategy). 2010. Anadromous salmonid monitoring

strategy viable salmonid population criteria and subset of tributary habitat and hatchery effectiveness. Columbia Basin Coordinated Anadromous Monitoring Workshop, draft version July 2010. Available at https://www.nwcouncil.org/fw/am/monitoring/monitoring-strategies/

Buckmeier, D. L. 2002. Assessment of reader accuracy and recommendations to reduce

subjectivity in age estimation. Fisheries 27:10-14. Busby, P. J., T. C. Wainwright, G. J. Bryant, L. J. Lierheimer, R. S. Waples, F. W. Wauneta, and

I. V. Lagomarsino. 1996. Status review of West Coast Steelhead from Washington, Idaho, Oregon, and California. NOAA Technical Memorandum NMFS-NWFSC-27.

Campana, S. E. 2001. Accuracy, precision, and quality control in age determination, including a

review of the use and abuse of age validation methods. Journal of Fish Biology 59:197-242.

Chang, W. Y. B. 1982. A statistical method for evaluating the reproducibility of age determination.

Canadian Journal of Fisheries and Aquatic Sciences 39:1208-1210. Copeland, T., J. Johnson, and P. R. Bunn. 2004. Idaho natural production monitoring and

evaluation. Idaho Department of Fish and Game Report 04-47. Prepared for U.S. Department of Energy, Bonneville Power Administration, Division of Fish and Wildlife. Project 1991-073-00. Portland, Oregon.

Copeland, T., M. W. Hyatt, and J. Johnson. 2007. Comparison of methods used to age spring-

summer Chinook Salmon in Idaho: validation and simulated effects on estimated age composition. North American Journal of Fisheries Management 27:1393-1401.

Ford, M. J., A. Albaugh, K. Barnas, T. Cooney, J. Cowen, J. Hard, R. Kope, M. M. McClure, P.

McElhany, J. Myers, N. Sands, D. Teel, and L. A. Weitkamp. 2011. Status review update for Pacific salmon and steelhead listed under the Endangered Species Act: Pacific Northwest. US Department of Commerce, NOAA Technical Memorandum NMFS-NWFSC-113.

Gallagher, S., P. Adams, D. Wright, and B. Collins. 2010. Performance of spawner survey

techniques at low abundance levels. North American Journal of Fisheries Management 30:1086-1097.

Gerritsen, H. D., and D. McGrath. 2007. Precision estimates and suggested sample sizes for

length-frequency data. Fisheries Bulletin 106:116-120. Hassemer P. 1993a. Salmon spawning ground surveys, 1989-1992. Idaho Department of Fish

and Game. Project F-73-R-15. Pacific Salmon Treaty Program Award No. NA17FP0168-02. 32 p. plus appendices.

18

Hassemer, P. 1993b. Draft manual of standardized procedures for counting Chinook Salmon

redds. Idaho Department of Fish and Game, Boise. ICBTRT (Interior Columbia Basin Technical Recovery Team). 2003. Independent populations of

Chinook, Steelhead, and sockeye for listed Columbia Basin ESUs. ICBTRT draft report July 2003http://www.nwfsc.noaa.gov/trt/.

ICBTRT (Interior Columbia Basin Technical Recovery Team). 2005. Updated population

delineation in the interior Columbia Basin. Memo to NMFS Northwest Regional Office May 11, 2005.

McElhany, P., M. H. Ruckelshaus, M. J. Ford, T. C. Wainwright, and E. P. Bjorkstedt. 2000. Viable

salmonids populations and the recovery of evolutionarily significant units. National Oceanic and Atmospheric Administration Technical Memorandum NMFS-NWFSC-42.

NMFS (National Marine Fisheries Service). 2011. Five-year review: summary and evaluation of

Snake River Sockeye, Snake River Spring-Summer Chinook, Snake River Fall-Run Chinook, Snake River Basin Steelhead. NMFS, Northwest Region.

NMFS (National Marine Fisheries Service). 2016. Five-year review: summary and evaluation of

Snake River Sockeye, Snake River Spring-Summer Chinook, Snake River Fall-Run Chinook, Snake River Basin Steelhead. NMFS, Northwest Region.

Pirtle, R. B. 1956. Field studies to estimate the size and timing of runs of anadromous species of

fish in the Columbia and Snake River and their tributaries above the confluence of the Snake River. Idaho Department of Fish and Game, Boise.

Raymond, H. L. 1988. Effects of hydroelectric development and fisheries enhancement on spring

and summer Chinook Salmon and steelhead in the Columba River basin. North American Journal of Fisheries Management 8:1-24.

R Development Core Team. 2010. R: A language and environment for statistical computing. R

Foundation for Statistical computing. Vienna, Austria. Available at http://www.cran.r-project.org/.

Schrader, B., B. Oldemeyer, K. Wright, and B. Barnett. 2016. Comparison of Chinook Salmon

age-length keys for Marsh Creek and Bear Valley Creek, Idaho. Fisheries Management Brief 2016-01. Idaho Department of Fish and Game, Boise.

Stiefel, C., B. Barnett, K.K. Wright, K.A. Apperson, M.J. Belnap, R. Hand, M. Peterson, E.

Ziolkowski, E. Brown, L. Hebdon, W.C. Schrader. 2016. Idaho adult Chinook Salmon monitoring. Annual Report 2015. Idaho Fish and Game Report 16-12.

Thompson, S. K. 1987. Sample size for estimating multinomial proportions. The American

Statistician 41:42-46. Venditti, D. A., R. Kinzer, K. A. Apperson, B. Barnett, M. Belnap, T. Copeland, M. P. Corsi, W. T.

Gross, L. Janssen, R. Santo, K. Tardy, A. Teton. 2015. Idaho supplementation studies project completion report 1991-2014. Idaho Fish and Game Report 15-18.

19

Wright, K.K., W. Schrader, L. Reinhardt, K. Hernandez, C. Hoffman, T. Copeland. 2015. Process and methods for assigning ages to anadromous salmonids from scale samples. Idaho Fish and Game Report 15-03.

20

TABLES

21

Table 1. Single-pass redd count index surveys that were conducted for spring-summer Chinook Salmon in Idaho during 2016. Surveys are organized by major population group (MPG).

Population Transect name

Target survey

date

Actual survey date(a) Method(a) Redds(a)

South Fork Salmon River MPG Little Salmon River(a) TBA 9/5-9/10 9/9 Ground 11 South Fork Salmon River Mainstem NS-26 9/5 9/1 Ground 100 NS-27(c) 9/5 9/6-9/8 Ground 227 NS-28(c) 9/5 9/6-9/7 Ground 106 NS-29 9/5 9/7-9/9 Ground 24 Subtotal 468457 Secesh River WS-16 8/25-9/1 8/25 Ground 40 WS-17 8/25-9/1 8/25 Ground 25 WS-18 8/25 8/24 Ground 24 WS-19 8/25 8/24 Ground 61 WS-20 8/25 8/24 Ground 0 Subtotal 150 East Fork South Fork Salmon River NS-30(d) 9/1-9/5 9/1 Ground 202 NS-31(d) 9/1-9/5 9/15 Ground 4 Subtotal 206

Total MPG 824

Middle Fork Salmon River MPG Chamberlain Creek WS-1 8/25 8/25 Ground 11 WS-1a 8/25 8/26 Ground 39 Subtotal 50

Middle Fork Salmon River Below Indian Creek WS-15(e) 9/8 9/11-9/19 Aerial 1

Subtotal 1 Big Creek WS-13 9/5 8/30 Ground 44 WS-14a 9/5 8/30 Ground 16 WS-14b(e) 9/5 9/11 Aerial 31 WS-14c(e) 9/5 9/11 Aerial 10 WS-14d(e) 9/5 9/11 Aerial 2 Subtotal 103 Camas Creek WS-8(e) 8/25-9/5 9/9-9/10 Aerial 23 Subtotal 23 Loon Creek WS-6(e) 8/25-9/5 9/8-9/9 Aerial 4 WS-7(e) 8/25-9/5 9/8-9/9 Aerial 36 Subtotal 40

Middle Fork Salmon River Above and Including Indian Creek n/t(b) n/t 9/11-9/19 Aerial 52

22

Table 1. Continued.

Population Transect name

Target survey

date

Actual survey date(a) Method(a) Redds(a)

Middle Fork Salmon River MPG, continued Sulphur Creek OS-4 8/21 8/22 Ground 4 WS-12 8/21 8/22 Ground 16 Subtotal 20 Bear Valley Creek WS-9a(e) 8/27 8/23 Ground 0 WS-9b(e) 8/27 8/23 Ground 5 WS-9c 8/27 8/23 Ground 37 WS-9d(e) 8/27 8/23 Ground 42 WS-10a 8/27 8/23 Ground 53 WS-10b 8/27 8/23 Ground 1 WS-11a 8/27 8/24 Ground 75 WS-11b 8/27 8/24 Ground 29 WS-11c 8/27 8/24 Ground 6 Subtotal 248 Marsh Creek WS-2a 8/15-8/20 8/18 Ground 6 WS-2b 8/15-8/20 8/18 Ground 98 WS-3 8/15-8/20 8/17 Ground 28 WS-4 8/15-8/20 8/19 Ground 1 WS-5 8/15-8/20 8/16 Ground 25 Subtotal 158

Total MPG 695

Upper Salmon River MPG Panther Creek NS-11a 9/8 9/15 Ground 11 NS-11b 9/8 9/15 Ground 52 NS-11c 9/8 9/16 Ground 8 Subtotal 71 North Fork Salmon River NS-25a 9/8 9/8 Ground 5 NS-25b 9/8 9/8 Ground 11 NS-25c 9/8 9/9 Ground 8 Subtotal 24 Lemhi River NS-9 9/8 9/5 Ground 80 NS-10 9/8 9/5 Ground 13 Subtotal 93

Salmon River Lower Mainstem Below Redfish Lake NS-17 9/8 9/4 Aerial 34

NS-18 9/8 9/4 Aerial 20 NS-19 9/8 9/4 Aerial 6 NS-20 9/8 9/4 Aerial 12 NS-21 9/8 9/4 Aerial 3 NS-22 9/8 9/4 Aerial 2 NS-23 9/8 9/4 Aerial 0 NS-24 9/8 9/4 Aerial 0 Subtotal 77

23

Table 1. Continued.

Population Transect name

Target survey

date

Actual survey date(a) Method(a) Redds(a)

Upper Salmon River MPG, continued Pahsimeroi River NS-33a 9/8 9/27 Aerial 75 Subtotal 75 East Fork Salmon River NS-1a 9/8 9/4 Aerial 43 NS-1b 9/8 9/4 Aerial 41 NS-2a 9/8 9/4 Aerial 32 NS-2b 9/8 9/4 Aerial 35 NS-2c(f) 9/8 n/c n/c n/c Subtotal 151 Yankee Fork Salmon River NS-5(f) 9/8 8/11-9/9 Ground 152 NS-6(f) 9/8 8/12-9/8 Ground 47 NS-7(f) 9/8 9/7 0 NS-8(f) 9/8 9/9 21 Subtotal 220 Valley Creek NS-3a 9/8 9/4 Aerial 2 NS-3b 9/8 9/4 Aerial 35 NS-4 9/8 9/4 Aerial 20 Subtotal 57

Salmon River Upper Mainstem Above Redfish Lake NS-12 8/31-9/5 9/4 Aerial 2

NS-13a 9/8 9/4 Aerial 0 NS-13b 9/8 9/4 Aerial 0 NS-15a 9/8 9/4 Aerial 103 NS-15b 9/8 9/4 Aerial 13 NS-15c 9/8 9/4 Aerial 7 NS-16 9/8 9/4 Aerial 248 OS-1 8/31-9/5 9/7 Ground 0 OS-2 8/31-9/5 9/7 Ground 0 OS-3 8/31-9/5 9/7 Ground 0 OS-5 9/8 9/4 Aerial 0 OS-6 9/8 9/8 Ground 0 Subtotal 373

Total MPG 1,141

Grand Total Salmon River 2,660

Dry Clearwater River MPG Potlatch River n/t(b) n/t n/t n/t n/t Lapwai Creek n/t(b) n/t n/t n/t n/t Lawyer Creek n/t(b) n/t n/t n/t n/t

24

Table 1. Continued.

Population Transect name

Target survey

date

Actual survey date(a) Method(a) Redds(a)

Dry Clearwater River MPG, continued Upper South Fork Clearwater River NC-1 9/3 9/6-9/8 Ground 45 NC-2a 9/3 9/7 Ground 7 NC-2b 9/3 9/8 Ground 4 NC-3 9/3 n/c n/c n/c NC-4 9/1-9/5 9/7 Ground 8 NC-6 9/3 9/21 Ground 10 NC-8(d,g) 9/3 9/8 Ground 18 Subtotal 92

Total MPG 92

Wet Clearwater River MPG

Lolo Creek NC-14(d) 9/3 9/6 Ground 62 Subtotal 62 Lochsa River NC-10 9/3 9/6 Ground 32 NC-11 9/3 9/6 Ground 14 NC-13(g) 9/3 9/7 Ground 0 Subtotal 46 Meadow Creek n/t(b) n/t n/t n/t n/t Moose Creek WC-3c(j) 9/8 9/14 Ground 1 WC-3d(h,j) 9/8 n/c n/c n/c Subtotal 1 Upper Selway River WC-1(i) 9/8 n/c n/c n/c WC-2 9/8 9/12 Ground 7 WC-4a(i) 9/8 n/c n/c n/c WC-4b(i) 9/8 n/c n/c n/c WC-5(g) 9/8 9/13 Ground 6 WC-6(i) 9/8 n/c n/c n/c WC-7 9/8 9/12 Ground 17 WC-8(i) 9/8 n/c n/c n/c WC-9(i) 9/8 n/c n/c n/c Subtotal 30

Total MPG 139

Grand Total Clearwater River 231

(a) Transect established in 2016 in Boulder Creek, proposed for trend monitoring. (b) Index transects for trend monitoring have not been established (n/t = no transect). (c) Surveyed by both Idaho Department of Fish and Game and Nez Perce Tribe; counts are combined. (d) Surveyed by Nez Perce Tribe. (e) Surveyed by U.S. Forest Service. (f) Surveyed by Shoshone-Bannock Tribes. (g) Partial survey. (h) Survey not conducted in 2016 due to fire (n/c = no count). (i) Transect is no longer surveyed due to discontinued helicopter use (n/c = no count). (j) New Transect boundaries: sections within WC-3b

25

Table 2. Multiple-pass redd count census surveys that were conducted for spring-summer Chinook Salmon in Idaho during 2016. Surveys are organized by major population group (MPG).

Population Waterbody Date New

redds(a) Date New

redds(a) Date New

redds(a) Date New

redds(a) Date New

redds(a) Total Middle Fork Salmon River MPG

Marsh Creek Beaver Creek 8/5 3 8/16 40 9/1 12 9/13 2 n/c n/c 57 Banner Creek n/c n/c 8/17 5 8/31 0 9/12 0 n/c n/c 5 Cape Horn Creek 8/6 5 8/17 23 8/31 7 9/12 0 n/c n/c 35 Knapp Creek n/c n/c 8/19 1 9/3 0 9/14 0 n/c n/c 1 Marsh Creek 8/4 9 8/18 96 9/2 22 9/16 1 n/c n/c 128

Total 17 165 41 3 226

Upper Salmon River MPG Lemhi River Bear Valley Creek 8/23 0 8/29 0 9/6 0 9/12 0 n/c n/c 0 Big Timber Creek 8/15 0 8/25 0 9/2 0 9/8 0 n/c n/c 0 Canyon Creek 8/15 0 8/25 0 9/2 0 n/c n/c n/c n/c 0 Hayden Creek 8/22-8/24 20 8/29-8/30 28 9/6-9/7 6 9/12-9/13 3 n/c n/c 57 Lemhi River 8/31-9/1 39 9/6 33 9/13-9/14 22 9/19-9/20 16 n/c n/c 110 Little Springs Creek 8/25 0 8/31 0 9/8 0 n/c n/c n/c n/c 0

Total 167

Salmon River Upper Mainstem Above Redfish Lake

Redfish Lake Creek upstream to Sawtooth Weir 8/30 190 9/6 216 9/15 32 9/19 10 9/23 0 448

Total 448 (a) Downloaded from the SGS database on 12/15/16. (b) Not completed = n/c. (c) Surveys were from the Lemhi store upstream.

26

Table 3. Additional redd count surveys that were conducted for spring-summer Chinook Salmon in Idaho during 2016. Surveys are organized by major population group (MPG).

(a) Data from Robert Hand of Clearwater Region in Lewiston, Idaho. (b) A = assessment of spawner abundance; B = assessment of spatial distribution; C = assessment of spawn timing. (c) Not completed = n/c.

Population Waterbody Transect Date New

redds(a) Date New

redds(a) Date New

redds(a) Total Purpose(b) Dry Clearwater River MPG

Upper South Fork Clearwater River

American River Mouth upstream to Kirks Fork

9/8 1 9/19 9 n/c n/c

10 A

American River Kirks Fork upstream to Lick Creek

9/8 0 9/19 1 n/c n/c

1 A

American River Lick Cr upstream to Limber Luke Creek

9/7 0 9/21 0 n/c n/c

0 A

Red River Campground

upstream to Shissler Bridge

9/7 7 9/20 0 n/c n/c

7 A

Red River Gibler upstream to

Dawson 9/7 5 9/13 0 n/c n/c

5 A

Red River Mouth upstream to

Shissler Bridge 9/7 66 9/13 11 n/c n/c

77 A

79 21 100 Total

Wet Clearwater MPG Upper Selway River

Selway River Little Clearwater upstream to Magruder Crossing

8/31 15 9/12 2 n/c n/c 17 A,B,C

Total 15 2 17

27

Table 4. Carcasses observed on spring-summer Chinook Salmon spawning grounds in Idaho by origin and sex during 2016. Surveys are organized by major population group (MPG). F = female; M = male; U = unknown sex. Hatchery fraction is sum of segregated hatchery and integrated hatchery divided by the sum of segregated hatchery, integrated hatchery, and wild carcasses.

Population

Segregated hatchery(a) Integrated hatchery(a) Wild(a) Unknown origin(a) Total

carcasses Hatchery

fraction F M U F M U F M U F M U South Fork Salmon River MPG

Little Salmon River(c,g) 1 3 0 0 1 0 1 0 0 1 0 0 7 83% South Fork Salmon River Mainstem downstream of weir(c)

47 34 0

17 11 0

29 24 0

2 0 1

165

67%

South Fork Salmon River Mainstem upstream of weir

0 0 0

64 79 2

13 26

1 0 1

186

78%

Secesh River(b) 1 2 0

0 0 0

104 69 1

6 4 1

188

2% East Fork South Fork Salmon River(b)

32 17 0

35 20 0

154 83 1

0 2 3

347

30%

Total MPG 81 56 0

116 111 2

301 202 2

10 6 6

893

42%

Middle Fork Salmon River MPG Chamberlain Creek 0 0 0

0 0 0

6 7 0

0 0 0

13

0%

Upper Middle Fork(e) 0 0 0 0 0 0 2 2 0 0 0 0 4 0% Lower Middle Fork(e) 0 0 0 0 0 0 1 1 0 0 0 2 4 0% Big Creek(b) 1 0 0

0 0 0

11 7 0

2 0 1

22

5%

Camas Creek 0 0 0

0 0 0

12 1 0

0 0 0

13

0% Loon Creek 0 0 0

0 0 0

8 2 1

0 0 0

11

0%

Sulphur Creek 0 0 0

0 0 0

5 7 1

0 0 0

13

0% Bear Valley Creek(d,e) 0 0 0

0 0 0

52 16 0

0 0 0

68

0%

Marsh Creek 0 0 0

0 0 0

88 27 2

0 0 0

117

0% Total MPG 1 0 0

0 0 0

185 70 4

2 0 3

265

<1%

Upper Salmon River MPG Panther Creek(f) 2 0 0

0 0 0

46 34 0

0 0 0

82

2%

North Fork Salmon River

0 0 0

0 0 0

3 1 0

0 0 0

4

0%

Lemhi River 0 0 0

0 0 0

38 9 2

0 0 0

49

0% Salmon River Lower Mainstem Below Redfish Lake

3 1 0

1 0 0

31 12 3

0 0 0

52

10%

28

Table 4. Continued.

Population

Segregated hatchery(a) Integrated hatchery(a) Wild(a) Unknown origin(a) Total

carcasses Hatchery

fraction F M U F M U F M U F M U Upper Salmon River MPG, continued

Pahsimeroi River downstream of weir

0 0 0

0 0 0

2 1 0

0 0 0

3

0%

Pahsimeroi River upstream of weir

0 0 0

2 0 0

21 6 0

0 0 0

29

4%

East Fork Salmon River

1 0 0 0 0 0 28 8 2 0 0 0 39 2%

Yankee Fork Salmon River(f)

0 10 0

1 0 0

20 23 2

0 0 1

57

19%

Valley Creek(f) 0 0 0

0 0 0

11 4 0

0 0 0

15

0% Salmon River Upper Mainstem Above Redfish Lake downstream of weir

216 108 1

53 24 0

148 105 0

0 0 0

655

46%

Salmon River Upper Mainstem Above Redfish Lake upstream of weir

3 13 0

75 63 0

34 34 1

0 0 0

223

69%

Total MPG 225 132 1

132 87 0

382 237 11

0 0 1

1,208

48%

Dry Clearwater River MPG Upper South Fork Clearwater River(c)

73 76 1

1 3 0

13 12 1

0 0 0

180

91%

Total MPG 73 76 1

1 3 0

13 12 1

0 0 0

180

91%

Wet Clearwater River MPG Lochsa River(c) 13 7 0

0 0 0

17 10 0

0 0 0

47

43%

Lolo Creek(b) 6 5 0

0 0 0

20 13 1

0 0 0

45

24% Upper Selway River(c) 0 0 0

0 0 0

7 3 0

0 0 0

10

0%

Total MPG 19 12 0

0 0 0

44 26 1

0 0 0

102

30%

(a) Downloaded from the SGS database on 12/1/16 except if provided otherwise. (b) Staff from the Nez Perce Tribe collected and provided information. (c) Staff from the Nez Perce Tribe and IDFG collected and provided information. (d) Staff from the Shoshone-Bannock Tribes and IDFG collected and provided information. (e) Staff from U.S. Forest Service and IDFG collected and provided information (f) Staff from the Shoshone-Bannock Tribes collected and provided information. (g) Boulder Creek and Slate Creek surveys.

29

Table 5. Brood year and age class frequencies of wild spring-summer Chinook Salmon carcasses sampled from Idaho spawning grounds during 2016. Samples are organized by major population group (MPG). Saltwater ages were derived from fin rays and freshwater ages (X) were assumed to be one year.

Population

Fin ray sample

target for 2016

Fin ray samples taken(a)

Total aged(a)

Brood year and age (freshwater.ocean)(a)

2013 2012 2011 2010 1.1 1.2 1.3 1.4

South Fork Salmon River MPG Little Salmon River 50 1 1 0 0 1 0 South Fork Salmon River Mainstem(b) 100 50 50 0 23 27 0 Secesh River(b) 150 172 171 6 128 37 0 East Fork South Fork Salmon River(b) 150 228 228 6 142 79 1

Total MPG 450 451 450 12 293 144 1

Middle Fork Salmon River MPG Chamberlain Creek 150 12 12 0 8 4 0 Middle Fork Salmon River Below Indian Creek

5 2 2 0 1 1 0

Big Creek 150 21 21 1 12 8 0 Camas Creek 150 13 13 0 7 6 0 Loon Creek 150 9 9 0 5 4 0 Middle Fork Salmon River Above and Including Indian Creek

10 4 4 0 1 3 0

Sulphur Creek 115 12 12 0 5 6 1 Bear Valley Creek(c) 0 0 0 n/a n/a n/a n/a Marsh Creek(c) 100 73 73 0 31 42 0

Total MPG 830 146 146 1 70 74 1

Upper Salmon River MPG Panther Creek(d) 100 46 46 0 18 28 0 North Fork Salmon River 100 4 4 0 1 3 0 Lemhi River 150 47 46 0 29 17 0 Salmon River Lower Mainstem Below Redfish Lake

150 45 45 0 26 19 0

Pahsimeroi River 100 30 30 1 18 11 0 East Fork Salmon River 150 2 2 0 1 1 0 Yankee Fork Salmon River(d) 150 22 22 3 15 6 0 Valley Creek 150 13 13 0 7 6 0 Salmon River Upper Mainstem Above Redfish Lake Creek(e)

150 83 83 0 43 40 0

Total MPG 1,200 292 291 4 158 131 0

Dry Clearwater River MPG Potlatch River(f) 0 0 0 n/a n/a n/a n/a Lapwai Creek(f) 0 0 0 n/a n/a n/a n/a Lawyer Creek(f) 0 0 0 n/a n/a n/a n/a Upper South Fork Clearwater River 150 19 19 1 12 6 0

Total MPG 150 19 19 1 12 6 0

Wet Clearwater River MPG Lolo Creek 75 30 30 1 26 3 0 Lochsa River 150 12 11 0 5 6 0 Meadow Creek 0 1 1 0 1 0 0 Moose Creek 0 0 0 0 0 0 0 Upper Selway River 0 8 8 0 5 3 0

Total MPG 225 51 50 1 37 12 0

30

Table 5. Continued.

Population

Fin ray sample

target for 2015

Fin ray samples taken(a)

Total aged(a)

Brood year and age (freshwater.ocean)(a)

2013 2012 2011 2010 1.1 1.2 1.3 1.4

Idaho Hatcheries Pahsimeroi(h) 0 29 29 0 17 12 0 Sawtooth(h) 0 70 70 0 37 12 0 McCall(h) 0 52 52 0 34 18 0 Johnson Creek(g,h) 0 66 66 0 37 29 0

Total Idaho Hatcheries 0 216 216 21 124 71 0 (a) Downloaded from the BioSamples database on 5/1/17. (b) Staff from the Nez Perce Tribe collects most or all of the samples and will analyze age composition using an age-length key derived from IDFG ageing data. (c) Age composition is analyzed using an age-length key derived from IDFG ageing data (see Tables 6 and 7). (d) Staff from the Shoshone-Bannock Tribes collects most or all of the samples. (e) Fin rays were not collected upstream of the Sawtooth hatchery weir. (f) No carcass surveys conducted in 2016 (g) Staff from the Nez Perce Tribe collects the samples. (h) Collected from wild fish at hatcheries.

31

Table 6. Marsh Creek spring-summer Chinook Salmon age-frequency distribution for 2016 as calclulated from an age-length key based on historic (1998-2016) Marsh Creek and Bear Valley Creek fin ray ages and carcass length (n = 2,730). This age-length key was applied to carcass lengths collected in Marsh Creek in 2016. (n = 115) to describe age composition (Schrader et al. 2016).

Length group (cm)

Number in 2016 length sample

Historic age-length key from Bear Valley Creek and Marsh Creek fin rays and carcasses

(1998-2016)

Marsh Creek 2016 sample allocation per age-group based on carcass

length

Age-3 Age-4 Age-5 Age-6 Age-3 Age-4 Age-5 Age-6 <60 - 88 4 - - - - - -

60-64 - 6 17 1 - - - - - 65-69 7 4 124 2 - - 7 - - 70-74 15 3 381 5 - - 15 - - 75-79 13 - 558 17 1 - 13 - - 80-84 16 - 248 63 1 - 13 3 - 85-89 23 - 83 289 9 - 6 17 - 90-94 26 - 13 368 7 - 1 25 - 95-99 8 - 2 222 8 - - 8 - ≥100 7 - - 196 10 - - 7 -

All 115 2,730 0 55 60 0

32

Table 7. Bear Valley spring-summer Chinook Salmon age-frequency distribution for 2016 as calclulated from an age-length key based on historic (1998-2016) Marsh Creek and Bear Valley Creek fin ray ages and carcasse length (n = 2,730). This age-length key was applied to carcass lengths collected in Bear Valley in 2016. (n = 68) to describe age composition (Schrader et al. 2016).

Length group (cm)

Number in 2016 length sample

Historic age-length key from Bear Valley Creek and Marsh Creek fin rays and carcasses

(1998-2016)

Bear Valley Creek 2016 sample allocation per age-group based on

carcass length

Age-3 Age-4 Age-5 Age-6 Age-3 Age-4 Age-5 Age-6 <60 - 88 4 - - - - - -

60-64 1 6 17 1 - - 1 - - 65-69 2 4 124 2 - - 2 - - 70-74 5 3 381 5 - - 5 - - 75-79 16 - 558 17 1 - 16 - - 80-84 10 - 248 63 1 - 8 2 - 85-89 17 - 83 289 9 - 4 13 - 90-94 13 - 13 368 7 - - 13 - 95-99 2 - 2 222 8 - - 2 - ≥100 2 - - 196 10 - - 2 -

All 68 2,730 - 35 33 -

33

Table 8. Mean length at age in cm for spring-summer Chinook Salmon in Idaho during 2016 from carcasses collected during spawning ground surveys. Ages were established from dorsal fin rays from post-spawn fish collected on the spawning grounds and at hatchery weirs. Samples are organized by major population group (MPG). Carcass length range is in parentheses.

Major population group

(MPG) Sample size(a)

Mean fork length (cm) at age(a) Age-3 Age-4 Age-5 Age-6

South Fork Salmon River 448 66.5 76.3 88.6 86.0(b)

(55-84) (54-96) (70-109) --

Middle Fork Salmon River 145 53.0(b) 75.0 87.6 92.0(b)

-- (66-88) (68-108) --

Upper Salmon River 246 62.8(d) 75.4 87.1 n/a(c)

(55-71) (62-108) (69-108) --

Dry Clearwater River 19 46(b) 68.8 84.0(d) n/a(c)

-- (60-72) (59-91) --

Wet Clearwater River 50 76(b) 72.3 87.4 n/a(c)

-- (55-95) (72-93) -- (a) Downloaded from the BioSamples database on 2/2/2017. (b) Only one sample. (c) No samples available (n/a) to estimate an average. (d) Fewer than ten samples available to estimate average.

34

FIGURES

35

Figure 1. Spring-summer Chinook Salmon populations and major population groups (MPGs)

in the Snake River evolutionary significant unit (ESU). Red dots represent impassable dams.

36

Figure 2. Location of spring-summer Chinook Salmon monitoring infrastructure used in

Idaho during 2016. Numbers correspond to IDFG infrastructure sites in the lower left inset. Major population groups are highlighted and independent populations are delineated.

37

Figure 3. Spring-summer Chinook Salmon index redd count trends in Idaho major population

groups (MPGs), 2011-2016. Numbers shown are raw counts entered by biologists responsible for respective counts. Missing index counts from population (year) include: East Fork South Fork Salmon River (Upper Salmon River MPG; 2011-2012); Yankee Fork Salmon River (Upper Salmon River MPG; 2012-2013); Lolo Creek (Wet Clearwater River MPG; 2011-2012); and Moose Creek (Wet Clearwater River MPG; 2011-2012).

992

674

558

1,139

680

824

966 937

624

1,270

825

643

863

947

544

1,277

895

1,141

264

160147

271

170

928442

127200

80139

0

200

400

600

800

1,000

1,200

1,400

2011 2012 2013 2014 2015 2016

Num

ber i

ndex

redd

s co

unte

d

South Fork Salmon River MPG Middle Fork Salmon River MPG

Upper Salmon River MPG Dry Clearwater River MPG

Wet Clearwater River MPG

38

Figure 4. Distribution of Spring-summer Chinook Salmon index redd counts completed by the Idaho Department of Fish and Game in the South Fork Salmon River in 2016.

39

Figure 5. Distribution of Spring-summer Chinook Salmon redds identified during index redd surveys completed by the Idaho Department of Fish and Game in Boulder Creek, a newly established transect in the Little Salmon River drainage in 2016.

40

Figure 6. Distribution of Spring-summer Chinook Salmon redds identified during index and census redd surveys completed by the Idaho Department of Fish and Game and the Rocky Mountain Research Station (RMRS; US Forest Service) in the Middle Fork Salmon River MPG in 2016. Survey methods were a combination of ground and aerial (helicopter).

41

Figure 7. Distribution of Spring-summer Chinook Salmon redds identified during index redd surveys completed by the Idaho Department of Fish and Game in Panther Creek, the North Fork Salmon River, and the mainstem Middle Salmon River below the Pahsimeroi River populations in 2016. Survey methods were a combination of ground and aerial (helicopter).

42

Figure 8. Distribution of Spring-summer Chinook Salmon redds identified during a

combination of ground index redd surveys and census surveys completed by the Idaho Department of Fish and Game in the Lemhi River and Hayden Creek in 2016. Pink lines denote areas where census surveys were completed, and blue lines indicate areas where an index survey was completed.

43

Figure 9. Distribution of Spring-summer Chinook Salmon redds identified during an aerial index count completed by the Idaho Department of Fish and Game in the Pahsimeroi River and Patterson/Big Springs Creek in 2016.

44

Figure 10. Distribution of Spring-summer Chinook Salmon redds identified during aerial index counts completed by the Idaho Department of Fish and Game in the Upper Salmon River, the East Fork Salmon River, and Valley Creek in 2016.

45

Figure 11. Relative length frequency distributions of the entire sample of wild spring-summer

Chinook Salmon carcasses (n=908) collected from in Idaho during 2016. Ages in this plot were estimated from fin rays collected from carcasses on the spawning grounds. Fish collected at hatchery traps, hatchery weirs, and research weirs for integrated broodstock were not included in proportions calculated here. The summation of all proportions irrespective of age is equal to 1. No age-length key data was included here. FL= Fork Length in centimeters (cm).

0.00

0.01

0.02

0.03

0.04

0.05

45 50 55 60 65 70 75 80 85 90 95 100 105 110

Prop

ortio

n

FL (cm)

Age-3

Age-4

Age-5

46

Figure 12. Age bias plot illustrating pairwise comparisons of fin ray determined age with

known age for spring-summer Chinook Salmon in Idaho, 2016. Idaho Fish and Game attempts to achieve a percent agreement of at least 90% and a CV less than 10%. The dashed line represents the 1:1 relationship. Error bars represent 95% confidence intervals around the mean fin ray assigned age for all fish of a given tag-assigned age. Mean coefficient of variation (CV) is over all individual CVs (n = 80). PA = percent agreement. Fin ray freshwater ages were assumed to be 1 year. This plot demonstrates that age data presented in this report were within IDFG’s accepted level of bias. Data were downloaded from the IDFG BioSamples database, fin ray data; PTAGIS database, PIT-tag data; Regional Mark Information System (RMIS database, CWT data)

0

1

2

3

4

5

6

0 1 2 3 4 5 6

Age

dete

rmin

ed fr

om fi

n ra

ys

Known age determined from tags

Mean CV = 2.3%PA = 90.0%n = 80

13

44

23

47

Figure 13. Number of genetics samples collected from wild and integrated hatchery adult

Chinook Salmon released at IDFG hatchery weirs (dots) and research weirs (triangles), 2012-2016. Crooked River samples for 2014 (n = 44) have not been located.

2012 (n =1,592)

2013 (n =1,494)

2014 (n =2,901)

2015 (n =1,865)

2016(n=1,696)

Salmon River (Sawtooth) 477 386 701 447 421E. F. Salmon River 244 260 322 0 0Pahsimeroi River 216 376 660 455 399S. F. Salmon River 429 332 990 696 709Rapid River 39 16 30 34 23Hells Canyon Dam 119 23 27 81 114Lochsa River (Powell) 7 23 8 0 10Fish Creek 14 0 6 3 3Crooked River 40 34 44 70 30Red River 87 55 67 36 31

0

100

200

300

400

500

600

700

800

900

1,000

Num

ber g

enet

ics s

ampl

es co

llect

edAdult Chinook Genetics at IDFG Weirs

48

Prepared by: Approved by: IDAHO DEPARTMENT OF FISH AND GAME Matthew J. Belnap J. Lance Hebdon Fisheries Biologist Anadromous Fisheries Manager Bruce Barnett James P. Fredericks, Chief Fisheries Data Coordinator Bureau of Fisheries Kimberly A. Apperson Fisheries Biologist Matt Amick Fisheries Technician I Carlos Camacho Fisheries Biologist Robert Hand Fisheries Biologist Mike Peterson Fisheries Biologist Evan Brown Sr. Fisheries Data Coordinator