idaho adult chinook salmon monitoring... · 2018. 10. 31. · idaho adult chinook salmon...

IDAHO ADULT CHINOOK SALMON MONITORING

2017 ANNUAL REPORT

Photo: Eli Felts

Prepared by:

Eli A. Felts, Fisheries Biologist

Bruce Barnett, Fisheries Data Coordinator Micah Davison, Supervisory Fisheries Biologist

Matthew J. Belnap, Fisheries Biologist Kimberly A. Apperson, Fisheries Biologist

Robert Hand, Fisheries Biologist Mike Peterson, Fisheries Biologist

Evan Brown, Sr. Fisheries Data Coordinator

IDFG Report Number 18-08 March 2018

Idaho Adult Chinook Salmon Monitoring

2017 Annual Report

By

Eli A. Felts Bruce Barnett Micah Davison

Matthew J. Belnap Kimberly A. Apperson

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 18-08 March 2018

THIS PAGE IS INTENTIONALLY BLANK

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ACKNOWLEDGEMENTS

Report Authors: Eli A. Felts Micah Davison Bruce Barnett Matthew J. Belnap

Kimberly A. Apperson

Robert Hand Mike Peterson Evan Brown

Report Contributors: Data and Field Work IDFG Southwest Region (Nampa) • Jared Kunz • Kayla Kinkead • Wyatt Tropea • Mike Peterson 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 • Matt Amick • Sarah Foster • Tristen Kienenberger • Chris Gratton • Matt Lyon IDFG Clearwater Region • Cody Black • Brett Bowersox • Marika Dobos • Jason Fortier • Brent Haverkamp • Brian Knoth • Scott Putnam • Jennifer Renner

• Adam Scheirer • Michael Soukup • Grant Truskowski • Clayton Waller IDFG Nampa Research • Micah Davison • Megan Heller • Dave Venditti • Bruce Barnett • Carlos Camacho • Keala Pelekai • William Massie • Corey Dondero • Eric Stark 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 • 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 • Idaho Power Company, Hells Canyon Mitigation • National Marine Fisheries Service, Pacific Coast Salmon Recovery Funds • National Marine Fisheries Service Pacific Salmon Treaty • 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) • Keala Pelekai (IDFG), William Massie (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) 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: Felts, E. A., B. Barnett, M. Davison, M. J. Belnap, K. A. Apperson, R. Hand, M. Peterson, and E.

Brown. 2018. Idaho adult Chinook Salmon monitoring. Annual report 2017. Idaho Department of Fish and Game Report 18-08.

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ABBREVIATIONS AND ACRONYMS

BPA Bonneville Power Administration

BY Brood Year

CWT Coded Wire Tag

DPS Distinct Population Segment

ESA Endangered Species Act

ESU Evolutionarily Significant Unit

FCRPS Federal Columbia River Power System

FINS Fish Inventory System Hatchery Database

GPS Global Positioning System

ICBTRT Interior Columbia Basin Technical Recovery Team

IFWIS Idaho Fish and Wildlife Information System

IDFG Idaho Department of Fish and Game

INPMEP Idaho Natural Production Monitoring and Evaluation Project

MPG Major Population Group

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

NPCC Northwest Power and Conservation Council

NPT Nez Perce Tribe

NRAAL Nampa Research Anadromous Ageing Laboratory

NWFSC Northwest Fisheries Science Center

PA Percent Agreement

PDO Pacific Decadal Oscillation

PIT Passive Integrated Transponder

PCSRF Pacific Coast Salmon Recovery Funds

PSMFC Pacific States Marine Fisheries Commission

RMSE Root Mean Squared Error

SAR Smolt-to-adult Return Rate

SBT Shoshone-Bannock Tribes

SGS Spawning Ground Survey

SGSA Spawning Ground Survey Application

UAV Unmanned Aerial Vehicle

USFS U.S. Forest Service

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TABLE OF CONTENTS Page

ACKNOWLEDGEMENTS ............................................................................................................ i ABBREVIATIONS AND ACRONYMS ......................................................................................... v CHAPTER 1 – PROJECT OVERVIEW ....................................................................................... 1 REPORT TOPICS ....................................................................................................................... 2 DATA MANAGEMENT AND ACCESS ........................................................................................ 2 LITERATURE CITED .................................................................................................................. 4 TABLES ...................................................................................................................................... 5 FIGURES .................................................................................................................................... 7 CHAPTER 2 – RELATIVE ABUNDANCE AND PRODUCTIVITY IN IDAHO

POPULATIONS OF SPRING/SUMMER CHINOOK SALMON .............................................. 9 ABSTRACT ................................................................................................................................. 9 INTRODUCTION ...................................................................................................................... 10 METHODS ................................................................................................................................ 10

Study Design ......................................................................................................................... 10 Data Collection....................................................................................................................... 11 Data Analysis ......................................................................................................................... 12

RESULTS ................................................................................................................................. 13 DISCUSSION............................................................................................................................ 16 RECOMMENDATIONS ............................................................................................................. 18 LITERATURE CITED ................................................................................................................ 19 TABLES .................................................................................................................................... 22 FIGURES .................................................................................................................................. 32 CHAPTER 3 – EVALUATION OF INDEX REDD COUNTS USING MULTIPLE PASS

REDD COUNTS AND MARK-RECAPTURE ESTIMATES .................................................. 49 ABSTRACT ............................................................................................................................... 49 INTRODUCTION ...................................................................................................................... 50 METHODS ................................................................................................................................ 50

Study Design ......................................................................................................................... 50 Data Collection....................................................................................................................... 50 Data Analysis ......................................................................................................................... 51

RESULTS ................................................................................................................................. 51 DISCUSSION............................................................................................................................ 52 LITERATURE CITED ................................................................................................................ 53 TABLES .................................................................................................................................... 54 FIGURES .................................................................................................................................. 56 APPENDIX ................................................................................................................................ 65

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LIST OF TABLES Page

Table 1.1. Interior Columbia Basin Technical Recovery Team population names and

associated abbreviations used in this report. ........................................................ 6 Table 2.1. List of Idaho spring/summer Chinook Salmon trend transects and 2017

sampling information. List is organized by Major Population Group and population. NS = Not Surveyed, NA = Not Applicable, NT= No trend transects identified, NPT = Nez-Perce Tribe, SBT = Shoshone-Bannock Tribe, UAV = Unmanned Aerial Vehicle. ............................................................ 23

Table 2.2. Chinook Salmon redds counted in Idaho trend transects in the Salmon River and Clearwater River basins during 2017 by major population group and population. .................................................................................................. 26

Table 2.3. Spring/summer Chinook Salmon carcasses collected during spawning ground surveys in Idaho during 2017. Surveys are organized by major population group (MPG). F = female; M = male; U = unknown sex. Hatchery fraction is the number of hatchery-origin carcasses divided by the number of known-origin carcasses. Asterisks indicate values assumed or calculated from previous brood cycle for productivity analysis. ........................... 28

Table 2.4. Age composition of natural-origin spring/summer Chinook Salmon carcasses collected during spawning ground surveys in Idaho during 2017. Populations are organized by major population group (MPG). ........................... 30

Table 2.5. Parameter estimates and pseudo-r2 values for Beverton-Holt stock-recruit models fitted to observed data from Idaho populations of spring/summer Chinook Salmon................................................................................................. 31

Table 3.1. Multiple-pass redd count census surveys that were conducted for spring-summer Chinook Salmon in Idaho during 2017. Surveys are organized by major population group (MPG). .......................................................................... 55

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LIST OF FIGURES Page

Figure 1.1. Spring/summer Chinook Salmon populations and major population groups

(MPGs) in the Snake River evolutionary significant unit (ESU). Red dots represent impassable dams. ................................................................................ 8

Figure 2.1. Number of spring/summer Chinook Salmon redds counted in trend transects of Idaho populations of the Snake River ESU during 2017. Populations shaded white were not surveyed. ................................................... 33

Figure 2.2. Number of spring/summer Chinook Salmon redds counted in trend transects of the Clearwater and Salmon River basins, 2012-2017. Note different y-axis scales. ....................................................................................... 34

Figure 2.3. Number of spring/summer Chinook Salmon redds counted in trend transects for populations of the South Fork Salmon River MPG, 2012-2017. Solid reference lines represent pre-1970 range, and dashed reference line represents pre-1970 geometric mean. Note different y-axis scales. ................... 35

Figure 2.4. Number of spring/summer Chinook Salmon redds counted in trend transects for populations of the Middle Fork Salmon River MPG, 2012-2017. Solid reference lines represent pre-1970 range, and dashed reference line represents pre-1970 geometric mean. Note different y-axis scales. ............................................................................................................... 36

Figure 2.5. Number of spring/summer Chinook Salmon redds counted in trend transects for populations of the Upper Salmon River MPG, 2012-2017. Solid reference lines represent pre-1970 range, and dashed reference line represents pre-1970 geometric mean. Note different y-axis scales. ................... 37

Figure 2.6. Number of spring/summer Chinook Salmon redds counted in trend transects for populations of the Wet Clearwater MPG, 2012-2017. .................... 38

Figure 2.7. Number of spring/summer Chinook Salmon redds counted in trend transects of the Upper South Fork Clearwater, which was the only population surveyed in the Dry Clearwater MPG, 2012-2017. ............................ 39

Figure 2.8. Age bias plot depicting relationship between age estimates obtained from spring/summer Chinook Salmon fin rays and known age for known-age fish collected in 2017. RMSE = root mean squared error, PA = percent agreement, and n = the number of known-age fish. ........................................... 40

Figure 2.9. Length frequency distribution by age class (estimated from fin rays) for natural-origin spring/summer Chinook salmon carcasses (n = 288) collected in 2017. ............................................................................................... 41

Figure 2.10. Productivity (returned redds per spawned redds) of Idaho populations of spring/summer Chinook Salmon for brood years 2001-2012. Dashed line represents 1:1 replacement line. ........................................................................ 42

Figure 2.11. Relationship between stock (brood year redds) and recruits (returned natural-origin redds) in South Fork Salmon River MPG populations of summer Chinook Salmon for brood years 1995-2012 for which complete data were available. Dashed line represents 1:1 replacement line. .................... 43

Figure 2.12. Relationship between stock (brood year redds) and recruits (returned natural-origin redds) in Middle Fork Salmon River MPG populations of spring/summer Chinook Salmon for brood years 1995-2012 for which complete data were available. Dashed line represents 1:1 replacement line. .................................................................................................................... 44

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Figure 2.13. Relationship between stock (brood year redds) and recruits (returned natural-origin redds) in Upper Salmon River MPG populations of spring/summer Chinook Salmon for brood years 1995-2012 for which complete data were available. Dashed line represents 1:1 replacement line. .................................................................................................................... 45

Figure 2.14. Productivity (natural-origin redds per spawned redd) of South Fork Salmon River MPG populations of spring/summer Chinook Salmon for brood years 2001-2012. Select brood years omitted due to incomplete data. Dashed line represents 1:1 replacement line................................................................... 46

Figure 2.15. Productivity (natural-origin redds per spawned redd) of Middle Fork Salmon River MPG populations of spring/summer Chinook Salmon for brood years 2001-2012. Select brood years omitted due to incomplete data. Dashed line represents 1:1 replacement line................................................................... 47

Figure 2.16. Productivity (natural-origin redds per spawned redd) of Upper Salmon River MPG populations of spring/summer Chinook Salmon for brood years 2001-2012. Select brood years omitted due to incomplete data. Dashed line represents 1:1 replacement line................................................................... 48

Figure 3.1. Relationship between trend count (line) and multiple pass estimate of total redd abundance (bars) for the Marsh Creek spring Chinook Salmon population, 1998-2017. ...................................................................................... 57

Figure 3.2. Relationship between total redd abundance and percent of total redd abundance represented by trend count for the Marsh Creek spring Chinook Salmon population, 1998-2017. Points are represented as text indicating year of observation. ........................................................................................... 58

Figure 3.3. Relationship between trend count (line) and multiple pass estimate of total redd abundance (bars) for the Lemhi River spring Chinook Salmon population, 2000-2017. ...................................................................................... 59

Figure 3.4. Relationship between total redd abundance and percent of total redd abundance represented by trend count for the Lemhi River spring Chinook Salmon population, 2000-2017. Points are represented as text indicating year of observation. ........................................................................................... 60

Figure 3.5. Relationship between trend count (line) and multiple pass estimate of total redd abundance (bars) for transect NS-16 in the Salmon River upper mainstem above Redfish Lake spring Chinook Salmon population, 2015-2017. .................................................................................................................. 61

Figure 3.6. Relationship between total redd abundance and percent of total redd abundance represented by trend count for the Salmon River upper mainstem above Redfish Lake spring Chinook Salmon population, 1998-2017. Points are represented as text indicating year of observation. .................. 62

Figure 3.7. Relationship between trend count (line) and mark-recapture estimate of female abundance (bars) for the portion of the Salmon River upper mainstem above Redfish Lake Creek spring Chinook Salmon population located above Sawtooth weir, 1998-2017. ......................................................... 63

Figure 3.8. Relationship between female abundance and percent of female abundance represented by trend redd count for the portion of the Salmon River upper mainstem above Redfish Lake Creek spring Chinook Salmon population located above Sawtooth weir, 1998-2017. Points are represented as text indicating year of observation............................................................................. 64

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LIST OF APPENDICES Page

Appendix A. Additional information collected on spawning ground surveys in 2017. .............. 66

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CHAPTER 1 – PROJECT OVERVIEW

Historically, Idaho waters supported abundant, naturally reproducing Chinook Salmon Oncorhynchus tshawytscha runs, which represented an important cultural, economic, and recreational resource within the state (Fulton 1968; Chapman 1986). Adult spring/summer-run and fall-run Chinook Salmon migrate through the Columbia River and enter Idaho via the Snake River. Fall-run Chinook Salmon are monitored in Idaho by Idaho Power and the Nez-Perce Tribe. As such, this report is exclusively focused on spring/summer Chinook Salmon. Spring/summer Chinook Salmon historically spawned in much of the Salmon River and Clearwater River basins. Population abundance in these two basins has declined from historical levels but their history and current status are quite different.

Snake River spring/summer Chinook Salmon runs were historically supported by

populations that spawned in Salmon River and Clearwater River basins of Idaho. The Salmon River basin has long been recognized as the most productive spawning area for spring/summer Chinook Salmon in the entire Columbia River basin (Fulton 1968). During the late 1950s, an estimated 44 percent of the spring and summer runs in the Columbia River, and 83 percent in the Snake River, were destined for the Salmon River basin (Fulton 1968). The Clearwater River basin represented an important spawning area for Snake River spring/summer Chinook Salmon until 1927 when the construction of Lewiston Dam, located 6 km upstream of the Clearwater River confluence with the Snake River, prevented passage and functionally extirpated all populations in this basin (Fulton 1968). Lewiston Dam was removed in 1973 to accommodate other projects taking place as part of the Federal Columbia River Power System (FCRPS). Dworshak Dam, located on the North Fork Clearwater River 5 km upstream of the confluence with the Clearwater River, was completed in 1973 and currently prevents Chinook Salmon passage into previously productive spawning ground (Fulton 1968).

Snake River spring/summer Chinook Salmon abundance displayed an overall decline

from the early 1960s into the 1990s (Raymond 1988), which ultimately resulted in their listing as threatened under the Endangered Species Act (ESA) in 1992 (NWFSC 2015). Abundance has been variable since the initial 1992 listing but observed increases have not been sufficient for delisting (NWFSC 2015). The factors most often attributed to these declines include decreased survival of juvenile Chinook Salmon emigrating through the Snake River following the construction of four lower Snake River Dams in the late 1960s and 1970s (Raymond 1988), and a shift in ocean climatic regime to an unfavorable state for productivity of all Columbia River salmonid stocks (Mantua et al. 1977).

Current monitoring of spring/summer Chinook recovery is framed by population boundaries established by the Interior Columbia Basin Technical Recovery Team (ICBTRT 2005) following ESA guidance. The ESA defines species to include subspecies and distinct population segments (DPS) of vertebrate species. Policy guiding identification of DPS for salmon species directs the National Marine Fisheries Service (NMFS) to identify population groups that are evolutionarily significant units (ESU) within their species (NMFS 2016). NMFS considers a group of populations an ESU “if it is substantially reproductively isolated from other populations, and represents an important component in the evolutionary legacy of the biological species” (NMFS 2016). Evolutionarily Significant Units are divided into two hierarchical levels including Major Population Groups (MPGs), which are further divided into populations (ICBTRT 2005; McElhany et al. 2000). The 1992 ESA listing identified Snake River spring/summer Chinook Salmon as an ESU which is further organized into seven MPGs, five of which are in Idaho (Figure 1.1, ICBTRT 2005). Three MPGs in the Salmon River basin of Idaho are considered extant by the ESA, whereas the two MPGs located within the Clearwater River basin are considered extirpated.

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The Idaho Natural Production Monitoring and Evaluation Project (INPMEP) is designed to

collect information necessary to assess the status of Idaho’s Chinook Salmon populations. Status of Pacific Salmonids listed under the ESA is assessed by NMFS using viability criteria which are related to trends and status in abundance, productivity, spatial structure, and diversity (McElhany et al. 2000). Data collected from this project are provided to NMFS for status review of extant MPGs of the Snake River spring/summer Chinook salmon ESU. The overall objective of this report is to document status and trends in all naturally reproducing spring/summer Chinook Salmon populations in Idaho.

REPORT TOPICS

The primary objective of this annual report is to document abundance and productivity of spring/summer Chinook Salmon using data collected on Idaho’s spawning grounds. Abundance of spawning salmon can fluctuate greatly and must be related to historic observations for proper interpretation. Therefore, one specific objective is to report annual redd counts at trend transects surveyed during the historical peak spawning period, and to relate these observations to long-term data. In addition to abundance, adult-to-adult productivity, or replacement rate, is essential to evaluate population status. Thus, a second specific objective is to report spawner composition metrics necessary to quantify productivity (i.e. age composition, hatchery fraction), and use that information to quantify adult-to-adult productivity through the most recently completely brood year.

In addition to annual IDFG reports, trend counts are used for ESA status evaluations which

require estimates to be expressed in units of total spawner abundance. Trend counts must be expanded to meet these requirements. An additional objective of this report is to use intensive monitoring data, such as multiple pass redd counts and mark-recapture studies, to evaluate expansion methods used to expand trend redd counts to estimates of total spawner abundance.

Additional data not related to specific objectives are often collected during spawning

ground surveys and this report also serves to document those collection efforts annually.

DATA MANAGEMENT AND ACCESS

Throughout this report we refer to populations designated by the Interior Columbia Basin Technical Recovery Team (ICBTRT 2005); as some of these names are quite long, we frequently use abbreviations (Table 1.1) to describe populations in tables and figures.

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 (GPS) devices. Waypoints are captured for new redds, carcasses, and survey boundaries using standardized naming conventions. Personnel from IDFG and the Shoshone-Bannock Tribes enter index and non-index survey data into a local Spawning Ground Survey application (SGSA), and the GPS 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

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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 (1993; 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 with permission from Idaho Department of Fish and Game (IDFG) 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 the 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 Estimate Total Age field in the SGS database.

For this report, all index and census redd survey data were entered into preformatted

tables by biologists responsible for their collection. Length and fin ray age data were downloaded from the BioSamples database on 8 Mar 2018. Adult weir and trap data are stored in and accessed from the Fish Inventory System Hatchery Database (FINS; https://www.fishnet.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 13 January 2018.

Summaries of the data sets used for this report are available at the IDFG Follow Idaho

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

https://fishandgame.idaho.gov/ifwis/portal

https://www.fishnet.org/

http://216.206.157.62/idaho/web/apps/index_main.php

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LITERATURE CITED

Chapman, D. W. 1986. Salmon and steelhead abundance in the Columbia River in the nineteenth century. Transactions of the American Fisheries Society 115: 662-670.

Fulton, L. A., 1968. Spawning areas and abundance of Chinook Salmon (Oncorhynchus

tshawytscha) in the Columbia River basin – past and present. United States Fish and Wildlife Service Special Scientific Report – Fisheries No. 571, Washington D.C.

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

redds. Idaho Department of Fish and Game, Boise. 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.

Mantua, N. J., S. R. Hare, Y. Zhang, J. M. Wallace, R. C. Francis. 1997. A Pacific interdecadal

climate oscillation with impacts on salmon production. Bulletin of the American Meteorological Society 78: 1069-1079.

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). 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.

NWFSC (Northwest Fisheries Science Center). 2015. Status review update for Pacific salmon

and steelhead listed under the Endangered Species Act: Pacific Northwest. 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.

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TABLES

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Table 1.1. Interior Columbia Basin Technical Recovery Team population names and associated abbreviations used in this report.

Population Name Abbreviation Big Creek BIG Bear Valley Creek BVC Camas Creek CAM Chamberlain Creek CHC East Fork Salmon River EFSR East Fork South Fork Salmon River EFSFSR Lapwai/Big Canyon LAP Lawyer Creek LAW Lemhi River LEM Little Salmon River LSR Lochsa River LOC Lolo Creek LOLO Loon Creek LOON Lower North Fork Clearwater River LNFC Marsh Creek MAR Meadow Creek MED Middle Fork Salmon River above and including Indian Creek MFSRU Middle Fork Salmon River below Indian Creek MFSRL Moose Creek MOO North Fork Salmon River NFSR Pahsimeroi River PAH Panther Creek PAN Potlatch River POT Secesh River SEC South Fork Salmon River mainstem SFSR Sulphur Creek SUL Salmon River Upper Mainstem below Redfish Lake Creek USRL Salmon River Upper Mainstem above Redfish Lake Creek USRU Upper North Fork Clearwater River UNFC Upper Selway River SEL Upper South Fork Clearwater River USFC Valley Creek VAL Yankee Fork Salmon River YFK

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FIGURES

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Figure 1.1. Spring/summer Chinook Salmon populations and major population groups (MPGs)

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

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CHAPTER 2 – RELATIVE ABUNDANCE AND PRODUCTIVITY IN IDAHO POPULATIONS OF SPRING/SUMMER CHINOOK SALMON

ABSTRACT

The Idaho Natural Production Monitoring and Evaluation Project monitors the status of Snake River spring/summer Chinook Salmon Oncorhynchus tshawytscha populations in the Salmon River and Clearwater River basins. Single-pass redd counts and carcass surveys are conducted annually at trend transects and provide estimates of relative abundance and productivity of Chinook Salmon. In 2017, 949 redds were counted at 90 transects covering 1,060 km, 24 populations, and 5 major population groups. Relative abundance of Chinook Salmon in 2017 was lower than recent years and historical observations across all Idaho populations. Relative abundance of Chinook Salmon has decreased in many Idaho populations since a relatively large return in 2014. Brood Year 2013, represented by age-4 fish on the spawning grounds, had the highest relative frequency among age classes. Brood year 2012 productivity estimates were low (<1 returned redd per spawned redd) for nearly every population. Productivity has declined in recent years in all populations, which has contributed to decreasing abundance. Stock-recruitment analysis found the Beverton-Holt model to be a poor fit to observed data for brood years 1995-2012, indicating density independent factors have been the major driver of adult-to-adult productivity trends over that period.

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INTRODUCTION

Abundance is an essential metric in monitoring fish populations as it represents the end product of the interplay between three processes (recruitment, growth, and mortality) considered to be the pillars of fisheries management (Allen and Hightower 2010). Population status is often assessed by using current abundance estimates to predict extinction risk and future trends (McElhany et al. 2000). The direct link between population processes and patterns in abundance have led to its designation as a critical metric in assessing viability of salmonid populations (ICBTRT 2005).

Understanding the relationship between spawner abundance and recruitment of a new

generation of spawners is imperative to managing fish populations. In semelparous fishes such as Chinook Salmon Oncorhynchus tshawytscha, estimation of adult-to-adult productivity is relatively straightforward if abundance and age composition of spawners is quantified annually (Myers et al. 1999). This metric represents the integrated effects of factors such as population density, environmental conditions, and ecological conditions throughout the entire life cycle (McElhany et al. 2000). Adult-to-adult productivity offers an indication of population trends that is robust to annual fluctuations in spawner abundance. If population abundance is below a desired threshold, as is the case for all spring/summer Chinook Salmon populations in Idaho (NMFS 2016), it must, on average, display productivity exceeding replacement to increase. As such, adult-to-adult productivity (along with abundance) is given the highest priority in assessing viability of salmonid populations (McElhany et al. 2000, ICBTRT 2005).

In this report, we summarize relative abundance of the 2017 spring/summer Chinook

Salmon escapement to Idaho using single-pass redd counts. We also used continuous standardized redd count data to compare the 2017 relative abundance to recent and historical observations. The broad geographic coverage of redd counts in Idaho allowed for comparison of relative abundance among 24 populations from 5 major population groups (MPG) in Idaho. Continuous monitoring of abundance and age composition also permitted estimation of recent productivity trends in 18 populations. Specific objectives were to:

1) Index spawner abundance for Idaho populations of spring/summer Chinook Salmon in

2017. 2) Compare 2017 spawner abundance to recent and historical spawner abundance of

Idaho spring/summer Chinook Salmon populations. 3) Quantify and assess recent trends in productivity for completed brood years of Idaho

spring/summer Chinook Salmon populations.

METHODS

Study Design

Stream transects targeted for redd counts in 2017 were selected based on long-term trend monitoring conducted by IDFG and collaborators. Transects are located within Idaho populations of the Snake River Spring/Summer Chinook Salmon ESU. Standardized sampling of trend transects began as early as 1957 (Hassemer 1993). Trend transects were selected to represent important production areas containing a large portion of available spawning habitat (Hassemer 1993). Trend transects have been added periodically over the course of the program’s history so

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the amount of habitat surveyed has increased over time (Hassemer 1993). Surveys were timed to coincide with the period of maximum spawning activity on a particular stream as estimated from historical observations (Hassemer 1993).

Data Collection

Redd counts were conducted by trained observers who attended a training workshop hosted by IDFG in Stanley, Idaho on August 8, 2017. Training occurs annually to standardize the criteria by which Chinook Salmon redds are identified across Idaho. Workshop attendees were trained to identify redds by the presence of two features: 1) a “pit” resulting from excavation of the redd and covering of the eggs, and 2) tailspill, which is defined by the presence of loose substrate immediately downstream of the excavated pit (Hassemer 1993). Training emphasizes the “four D’s” (disturbance, digging, definition, and deposition) as criteria indicating a completed redd.

Trend surveys were conducted by walking or flying a single pass along the designated

transect and examining the streambed for redds. Aerial surveys were conducted with either low-flying helicopter or unmanned aerial vehicles (UAV). All redds were enumerated and georeferenced using GPS units.

Chinook Salmon carcasses encountered during ground redd counts were sampled to

determine origin, to estimate age composition, and to collect tissue for genetic analysis. Each carcass was inspected for marks and tags, measured for fork length (mm), and examined to determine sex. Dorsal fin ray and tissues samples were taken from a subsample of carcasses. Four to five fin rays were collected, placed in a coin envelope, and frozen. Tissue samples were 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 (NRAAL) located in Nampa, Idaho. Additional surveys were conducted for the sole purpose of collecting biological information from Chinook Salmon carcasses.

Carcasses were identified as either natural- or hatchery-origin based on where they were

produced as indicated by marks and tags. Natural-origin fish are those produced outside of a hatchery (i.e., fish that emerged from the gravel), whereas hatchery-origin fish are those produced in a hatchery. Both “segregated” and “integrated” hatchery-origin Chinook Salmon are present in Idaho. Segregated hatchery-origin Chinook Salmon are those produced from crosses of hatchery fish only, whereas integrated hatchery-origin fish are produced from crosses of either two natural-origin parents or crosses of one natural- and one hatchery-origin parent. Most segregated and integrated fish are marked as smolts. All segregated fish in the Salmon River basin are marked with an adipose fin clip, and a subsample is marked with an internal coded wire tag (CWT) and an internal passive integrated transponder (PIT) tag. In the Clearwater River basin there are unmarked, segregated hatchery fish. In the Salmon River, integrated fish are marked with an internal CWT, and a subsample is marked with an internal PIT tag. There are no integrated Chinook Salmon releases in the Clearwater River. All carcasses encountered were visually inspected for an adipose fin clip, scanned for a CWT, and scanned for an internal PIT tag. Carcasses with an adipose fin clip were considered segregated hatchery-origin. Carcasses with CWT and an intact adipose fin were considered integrated hatchery-origin. In the Salmon River basin where all hatchery fish are marked, unmarked fish and fish with a PIT tag and no other mark were considered natural-origin, whereas origin of unmarked fish in the Clearwater River basin was considered unknown. All whole carcasses were treated as described above, and partial carcasses were treated similarly as far as was feasible.

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Once delivered to NRAAL, dorsal fin rays were processed and assigned a saltwater age. Fin rays were dried, set in epoxy resin, cut into cross sections with a bone saw, and mounted on microscope slides. Mounted fin rays were read independently by two trained readers and discrepancies were re-examined in a referee session until both readers and a third party came to a consensus. If a consensus could not be reached, the sample was removed from analysis. Total age was estimated by adding two to saltwater age. To assess accuracy of age estimates, fin ray samples from known-age fish were mixed into the overall sample. Hatchery fish marked with PIT tags and CWTs during spawning operations were considered known-age.

Data Analysis

The number of redds counted in trend transects was summarized by population and compared to recent (previous 6 years) and historical observations. Geometric mean, minimum, and maximum number of redds during years surveyed from 1957-1969 were calculated for historical comparison. This period corresponds to the “pre-dam era” described in the Comparative Survival Studies (McCann et al. 2017). The spatial distribution of redds among populations was summarized graphically by constructing maps displaying population polygons shaded in proportion to relative abundance. Spatial data were analyzed using the dplyr (Wickham et al. 2017), rgdal (Bivand et al. 2017), and sp (Pebesma and Bivand 2005) packages in program R (R Core team 2017). Maps were constructed using the ggplot2 (Wickham 2009) and viridis (Garnier 2017) packages in program R (R Core Team 2017).

Population-specific age composition for 2017 was calculated using total age estimates

from populations, or from an MPG aggregate, depending on the number of carcasses directly aged within a given population. If at least 20 carcasses in a population were assigned an age based on fin ray estimation, then age composition was estimated by calculating the proportion of each age class within the sample. If at least 20 carcasses in a population were assigned an age based on fin ray estimation, and additional carcasses were measured for fork length but not assigned an age based on fin ray estimation, then an age-length key was constructed using methods described by Isley and Grabowski (2007) to assign age based on length for the additional carcasses. In these scenarios, the combined sample of fish assigned ages based on fin ray estimation and from an age-length key was used to calculate age composition. If less than 20 carcasses in a population were assigned an age based on fin ray estimation, then the aggregate age composition for that population’s MPG was taken to represent age composition. Age composition at the MPG-level was calculated using the same methods described for populations. In addition to overall age composition, mature age composition was calculated as the proportion of each age class within the sample of fish estimated to be greater than total age 3.

Performance of NRAAL age estimation from fin rays was evaluated using a combination

of metrics and graphical assessment. Accuracy was assessed using root mean squared error (RMSE), percent agreement (PA) between estimated and known age, and age bias plots. RMSE was calculated as the square root of the mean squared difference between the estimated age (Ae) and the known age (Ak):

𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅 = �𝐴𝐴𝑒𝑒 − 𝐴𝐴𝑘𝑘2

Percent agreement was calculated as the number of samples for which estimated age was equal to known age divided by the total number of known-age samples, then multiplied by 100. An age bias plot was constructed to depict the relationship between known age and estimated age for a

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group of samples. Accuracy metrics and age bias plots were computed using the base and ggplot2 (Wickham 2009) packages in Program R (R Core Team 2017).

Redd to redd productivity was quantified with stock-recruitment analysis and was updated

through brood year 2012 for this report. The number of redds counted during a given brood year was taken as a measure of “stock.” Adult returns (“recruits”) were calculated by estimating the number of natural-origin redds produced from a brood year at age 4, 5, and 6:

𝑅𝑅𝑗𝑗 = �𝑎𝑎𝑎𝑎𝑎𝑎4𝑝𝑝𝑝𝑝𝑝𝑝𝑝𝑝𝑗𝑗+4 ∗ 𝑤𝑤𝑝𝑝𝑗𝑗+4� + �𝑎𝑎𝑎𝑎𝑎𝑎5𝑝𝑝𝑝𝑝𝑝𝑝𝑝𝑝𝑗𝑗+5 ∗ 𝑤𝑤𝑝𝑝𝑗𝑗+5� + �𝑎𝑎𝑎𝑎𝑎𝑎6𝑝𝑝𝑝𝑝𝑝𝑝𝑝𝑝𝑗𝑗+6 ∗ 𝑤𝑤𝑝𝑝𝑗𝑗+6�

where Rj is recruits (natural-origin redds) from brood year j, ageXprop is the proportion of mature fish which were age X, and wr is the estimated number of natural-origin redds. Natural-origin redds was estimated by multiplying wild fraction (1-hatchery fraction) by the total number of redds counted in trend transects within populations. Mature age composition was applied because age-3 fish, which were primarily males, were assumed to have no effect on redd abundance (Quinn 2005). Age composition dating back to brood year 1995 was calculated using the methods described above for the current year’s age composition. This time series was selected to align with the period during which age estimation methods became standardized and widespread in Idaho. The estimated number of natural-origin redds was used for returning redds because we were primarily interested in how many returning redds were produced by natural-origin Chinook Salmon. Trends in productivity were documented by calculating the number of returning redds per spawned redd for available brood years.

The stock-recruit relationship was modeled using a loge transformed Beverton-Holt (Beverton and Holt 1957) model:

𝑙𝑙𝑝𝑝𝑎𝑎𝚎𝚎[𝑅𝑅] = log ((log(𝛼𝛼 ∗ 𝑅𝑅))(1 + 𝛽𝛽 ∗ 𝑅𝑅) )

where recruits (estimated number of returned natural-origin redds; R) is a function of stock (Number of redds during the brood year; S), α is the slope at the origin and can be interpreted directly as the maximum adult-to-adult productivity at low spawner abundance, and β is the level of density dependence (Myers et al. 1999, Myers 2001, Rose et al. 2001). Model pseudo-r2 values were computed by regressing the predicted recruits from the fitted Beverton-Holt model against observed recruits. Productivity analysis was restricted to populations for which redd counts were conducted continuously within a fixed amount of habitat from 1995-2017, which allowed for analysis of brood years 1995-2012. The Chamberlain Creek population was included, although it was not sampled during 2017, so analysis was limited to brood years 1995-2011. Although fish from brood year 2012 may return as age-6 fish in 2018, the proportion of age-6 fish has been sufficiently low across all years and populations to assume that results will not change significantly with the addition of the age-6 returns (Copeland et al. 2006). Nonlinear regression analysis was conducted using the nlstools package (Baty et al. 2015) in Program R (R Core Team 2017).

RESULTS

During August and September 2017, 90 transects covering 1,060 km of stream in Idaho were surveyed for Chinook Salmon redds (Table 2.1). Fifteen trend transects were not surveyed during 2017 due to wildfire and other factors. A total of 949 Chinook Salmon redds were counted in trend transects across 5 MPGs and 24 populations in the Salmon and Clearwater river basins

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during 2017. The majority of redds (88%) were counted in the Salmon River basin (Table 2.1, Figure 2.1). Relative abundance of Chinook Salmon was highest in the Upper Salmon River above Redfish Lake Creek, South Fork Salmon River mainstem, East Fork Salmon River, Bear Valley Creek, and Upper South Fork Clearwater populations (Table 2.1). However, hatchery fraction was high in the Upper Salmon River above Redfish Lake Creek (0.79), South Fork Salmon River (0.82), and Upper South Fork Clearwater (0.92) populations (Table 2.2). Relative abundance of Chinook Salmon in 2017 was the lowest in the last 6 years across basins and within all populations, although the magnitude of decrease from recent years was variable (Figures 2.2-2.7).

All trend transects in the South Fork Salmon River MPG were surveyed, which included

123.6 km of current Chinook Salmon spawning habitat. The greatest amount (70.1 km) surveyed was in the South Fork Salmon River mainstem population. The total number of redds counted in 2017 in populations of the South Fork Salmon River MPG was low compared to recent and historical observations (Figure 2.3), and ranged from a low of 1 in the Little Salmon River population to a high of 180 in the South Fork Salmon River mainstem population (Table 2.1). The 2017 trend count was lower than the minimum observed during the historical period in the East Fork South Fork Salmon River and South Fork Salmon River mainstem populations (Figure 2.3). The absolute decrease of redds from historical observations was greatest in the South Fork Salmon River mainstem population where the 2017 count (180 redds) represented an 84% decrease from the historical geometric mean (1,107 redds; Figure 2.3). Hatchery-origin fish composed all carcasses collected in the Little Salmon River and the majority in the South Fork Salmon River mainstem (82% hatchery-origin) and East Fork South Fork Salmon River (55% hatchery-origin), whereas hatchery-origin fish represented a small portion of carcasses collected in the Secesh River (9% hatchery-origin; Table 2.2).

All except for two trend transects in the Middle Fork Salmon River MPG were surveyed,

which included 364.7 km of current Chinook Salmon spawning habitat. Trend transects in the Chamberlain Creek population (WS-1, WS-1a) were not surveyed in 2017 due to fire. The greatest amount (72.9 km) surveyed was in the Middle Fork Salmon River below Indian Creek population (Table 2.1). The total number of redds counted in 2017 in populations of the Middle Fork Salmon River MPG was low compared to recent and historical observations (Figure 2.4) and ranged from a low of 1 in the Middle Fork Salmon River below Indian Creek population to a high of 72 in the Bear Valley Creek population (Table 2.1). The 2017 trend count was lower than the minimum observed during the historical period in all surveyed populations (Figure 2.4). The absolute decrease of redds from historical observations was greatest in the Bear Valley Creek population where the 2017 count (72 redds) represented a 92% decrease from the historical geometric mean (881 redds; Figure 2.4). The Marsh Creek population was slightly below the historical geometric mean (352 redds) in 2014 (331 redds) but has declined consistently over the last three years, and the 2017 count (37 redds) represented an 89% decrease from the historical geometric mean (Figure 2.4). Nearly all carcasses collected were natural-origin in populations of the Middle Fork Salmon River MPG, although some hatchery-origin carcasses were collected in the Bear Valley Creek and Middle Fork Salmon River below Indian Creek populations (Table 2.2).

All trend transects in the Upper Salmon River MPG were surveyed, which included 525.3

km of current Chinook Salmon spawning habitat. The greatest amount (214.1 km) surveyed was in the Upper Salmon River mainstem below Redfish Lake population (Table 2.1). The total number of redds counted in 2017 in populations of the Upper Salmon River MPG was low compared to recent and historical observations (Figure 2.5) and ranged from a low of 2 in the North Fork Salmon River population to a high of 192 in the Upper Salmon River mainstem above Redfish Lake population (Table 2.1). The 2017 trend count was below or slightly greater than the minimum

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observed during the historical period among all populations (Figure 2.5). The absolute decrease of redds from historical observations was greatest in the Lemhi River population where the 2017 count (29 redds) represented a 96% decrease from the historical geometric mean (699 redds; Figure 2.5). Trend counts in the East Fork Salmon River and Lemhi River populations have been below the minimum observed during the historical period in each of the last 6 years (Figure 2.5). Hatchery-origin fish composed the majority of the spawners in the Upper Salmon River mainstem below Redfish Lake and the Upper Salmon River mainstem above Redfish Lake populations (Table 2.2). Natural-origin fish composed the majority of carcasses collected in the Lemhi River (Table 2.2).

Six of 15 trend transects in the Wet Clearwater MPG were surveyed, which included 60.9

km of current Chinook Salmon spawning habitat. The greatest amount (32.2 km) was surveyed in the Lochsa River population (Table 2.1). Transect NC-13 in the Lochsa River population and transects WC-3a and WC-3b in the Moose Creek population were not surveyed due to fire. Six transects in the Upper Selway River population were not surveyed in 2017 and have not been surveyed since 2010 due to discontinued helicopter use. Total number of index redds counted in 2017 in populations of the Wet Clearwater MPG was low compared to recent observations (Figure 2.6), and ranged from a low of 2 in the Upper Selway River population to a high of 23 in the Lochsa River population (Table 2.1).

All except one trend transect in the Dry Clearwater MPG were surveyed, and 80.9 km of

current Chinook Salmon spawning habitat was surveyed (Table 2.1). Sixty-nine redds were counted in the one population (Upper South Fork Clearwater) sampled in the Dry Clearwater MPG (Table 2.1), which represented a 75% reduction from the 2014 count (Figure 2.7).

In total, 288 natural-origin spring/summer Chinook Salmon carcasses were collected and

assigned an age using fin ray estimation in 2017 (Table 2.3). Sample size was low in most populations, with 77% of age estimates coming from only 4 populations including the Secesh River, East Fork South Fork Salmon River, Marsh Creek, and Salmon River upper mainstem above Redfish Lake populations (Table 2.3). Fewer than 20 carcasses were collected and assigned an age in all other populations, so age composition used in productivity analysis was taken from the MPG aggregate in most cases. Age estimates matched known age for 92.4% of known-age samples (n = 157) and there were no apparent biases among age-classes, indicating age estimates were accurate (Figure 2.8). Brood Year 2013, represented by age-4 fish on the spawning grounds, had the highest relative frequency in age samples within MPGs (Table 2.4) and across all samples (Figure 2.9). Brood year 2012 (age-5) and 2014 (age-3) were also represented (Figure 2.9).

Productivity was estimated for 18 populations from the South Fork Salmon River, Middle

Fork Salmon River, and Upper Salmon River MPGs. All other populations were excluded because they lacked continuous sampling within a fixed amount of habitat. Temporal trends in productivity (returned redds per spawned redd) tracked similarly among populations over recent years (Figure 2.10). Productivity was below replacement in all but one population (Pahsimeroi River) for brood years 2001-2002 and below replacement in all populations for brood year 2003. Productivity was above replacement in all populations for brood years 2006 and 2007, and was higher on average than in all other years considered. Productivity of most populations was near replacement for brood years 2008-2011 and dropped below replacement in nearly all populations for brood year 2012. Fitted Beverton-Holt stock-recruit curves were poor predictors of brood year return across 16 populations for which the analysis was conducted (Table 2.5). Pseudo-r2 ranged from 0.003 to 0.573, and was less than 0.3 for all but one population (Table 2.5). Stock-recruit data organized

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by populations within MPGs are presented in Figures 2.11-2.13. Below we summarize productivity results within individual MPGs.

Trends dating back to 2001 were limited to five brood years within two populations of the

South Fork Salmon River MPG due to either years lacking redd counts or variability in amount of habitat surveyed. Productivity during recent brood years was below replacement in the Secesh River and South Fork Salmon River mainstem populations (Figure 2.14). Additionally, productivity decreased throughout the most recent brood cycle in the South Fork Salmon River mainstem population and was lower than in the Secesh River within years (Figure 2.14).

Productivity trends dating back to 2001 indicated a peak in productivity during brood years

2006-2007 for all populations in the Middle Fork Salmon River MPG except Loon Creek and Camas Creek (Figure 2.15). Productivity for Loon Creek and Camas Creek was highest for brood year 2011. For all other populations, productivity has declined since the peak in brood years 2006-2007. Productivity was below replacement in all populations for brood year 2012 (Figure 2.15).

Productivity trends dating back to 2001 were less consistent across populations in the

Upper Salmon River MPG than others. The East Fork Salmon River, Lemhi River, North Fork Salmon River, and Valley Creek each displayed peaks in productivity of 3.0 to 13.4 redds per redd during brood years 2006-2007 (Figure 2.16). The Salmon River lower mainstem below Redfish Lake and Salmon River upper mainstem above Redfish Lake populations also displayed a relative peak in productivity during brood years 2006-2007, but this peak was lower than other populations within the MPG, with a maximum of 1.9 redds per redd (Figure 2.16). Productivity was relatively low in all populations for brood year 2012 and was above replacement in only the Lemhi River (1.1) and Panther Creek (1.8) populations.

DISCUSSION

Relative abundance of spring/summer Chinook Salmon redds was low compared to recent years across all Idaho populations. Relative abundance has steadily declined in nearly all populations since a relatively strong run in 2014. Although the magnitude of decrease in abundance was variable, smaller decreases were generally observed in populations such as Camas Creek and Loon Creek, which displayed relatively low numbers of redds in trend areas during recent years. Larger decreases were observed in populations such as East Fork South Fork Salmon River, Bear Valley Creek, Marsh Creek, and East Fork Salmon River, which displayed relatively high numbers of redds in trend areas during recent years. Relative abundance in 2017 and recent years was very low in comparison to historical observations.

Variation in the amount and quality of habitat sampled complicates comparisons of relative

abundance among populations and over time. In general, trend transects were selected because they were important spawning areas (Hassemer 1993), so in many cases more habitat was sampled in certain populations because there was truly more habitat present. However, other factors such as accessibility and the importance of a population influence the extent of sampling. Easily accessible populations which are considered disproportionately important to recovery at the MPG and ESU scale are sampled more intensively and will display greater numbers of redds within trend transects than less intensively surveyed populations because a greater amount of habitat is surveyed.

Monitoring in the Clearwater River basin is important in understanding reintroduction of

Chinook Salmon to habitats from which the species was previously extirpated but current survey

17

efforts and management practices limit inferences regarding natural production. Populations in the Clearwater River basin are classified as extirpated (ICBTRT 2005) and are therefore not considered in ESA status assessments. This has led to low sampling effort in these populations relative to those in the Salmon River basin. Widespread releases of hatchery fish with intact adipose fins makes it difficult or impossible to determine origin and quantify natural production. Future evaluations of Chinook Salmon natural production in the Clearwater River basin would benefit from efforts to reduce overlap between hatchery releases and areas suspected to support natural production. Additionally, methods such as parental-based tagging could be used to determine origin of ad-intact fish.

Age estimates were accurate and unbiased for the relatively low number of carcasses

collected in 2017. The number of carcasses collected is likely directly related to spawner abundance, so it is unsurprising that relatively few carcasses were collected in 2017, given the low number of spawners. Population-level age composition was assumed from the MPG aggregate for most populations due to low sample size, which assumes the MPG aggregate is representative of those populations. We speculate productivity estimates are robust to violations of this assumption as the proportion of spawners by age is not highly variable within brood years. Also, the application of the MPG aggregate tends to occur in years with low spawner abundance, meaning that errors in age proportion lead to relatively small errors in estimates of returned redds and corresponding productivity estimates. Our long-term data set offers the opportunity to rigorously evaluate these assumptions.

Productivity of brood year 2012 was below replacement in almost all populations.

Productivity has been near or below replacement across most populations since 2007, indicating stable to decreasing population growth. Stock-recruit analysis using brood years 1998-2012 found spawner abundance to be a poor predictor of recruit abundance across all populations, indicating that density independent factors have been the primary drivers of spawner abundance over that period. Smolt-to-adult return rate (SAR) explained much of the variation in population productivity for Snake River spring/summer Chinook Salmon, after controlling for density dependence (McCann et al. 2017)

Low productivity has contributed to declines in relative abundance of spring/summer

Chinook Salmon in Idaho since 2014, and stock-recruitment analysis indicates this is likely a result of density independent factors. Broad variation in spawner abundance across populations coupled with synchronicity in population productivity trends also indicates that density independent factors have been driving recent trends in productivity. Population synchrony is often a result of spatially correlated environmental influences (Moran 1953). Climatic factors affecting Chinook Salmon juvenile production may be correlated across Idaho populations such that productivity is synchronized; however, juvenile production has been regulated by density-dependence in at least some of Idaho’s populations in the same period analyzed for this report (Walters et al. 2013, Apperson et al. 2017). Therefore, we suspect density independent factors affecting survival through the hydrosystem and ocean, which are similar among Idaho’s spring/summer Chinook Salmon populations, have driven recent productivity trends.

Numerous density independent factors such as hydrosystem (FCRPS) operation during

emigration (Raymond 1979, 1988; Schoeneman et al. 1961), ocean condition upon arrival and throughout the ocean phase (Mantua et al. 1997), predation rate (Keefer et al. 2012), and angling mortality (Crozier et al. 2017) affect Chinook Salmon survival during the smolt to adult phase of their life cycle. Interannual variation in these factors is likely to result in concurrent variability in productivity. Each of these factors has displayed interannual variation across the life cycle of

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recent brood years, but ocean climatic conditions since 2013 have been especially abnormal and are suspected to have had a negative impact on productivity of Pacific Northwest salmon.

Ocean climatic conditions and their cascading effects on food web ecology are related to

salmon landings from the Pacific Northwest (Mantua et al. 1997), and have exhibited shifts during the period examined for this report. One index of ocean climatic condition, called the Pacific Decadal Oscillation (PDO), is quantified by multivariate analysis of monthly sea surface temperature variability and is commonly referred to in terms of cold and warm “phases.” In general, cold phases are associated with enhanced ocean productivity off the West Coast of the contiguous United States, which is thought to contribute to increased production of Columbia River basin Chinook Salmon populations, whereas warm phases are associated with the exact opposite pattern (Mantua et al. 1997). The PDO has been in a warm phase during recent migration years (Peterson et al. 2017). Additionally, a large area of abnormally warm water nicknamed the “blob” stretched from the coast of Alaska to Baja California in the northeastern Pacific from late 2013 until late 2015 (Cavole et al. 2016). The elevated sea surface temperatures associated with the “blob” reduced phytoplankton availability and caused several food web changes thought to reduce prey quality for Chinook Salmon (Cavole et al. 2016). We posit that ocean climatic conditions are most likely the leading cause of decreased productivity in recent years.

Results from 2017 monitoring efforts indicate Idaho populations of spring/summer Chinook

Salmon are functioning at low abundance relative to historical observations and recovery goals. The most recent status review for the Snake River spring/summer Chinook Salmon ESU concluded the majority of populations in the ESU were at high overall risk and recommended no change in status (NMFS 2016). Low productivity has been observed since the 2015 status assessment, resulting in decreased abundance throughout the ESU. Poor ocean conditions have likely been a major driver of recent trends, and abundance is unlikely to increase to desired levels without favorable ocean conditions. Chinook Salmon have a high maximum annual reproductive rate (Myers et al. 1999), meaning populations can quickly increase in abundance when exposed to favorable conditions. If current trends continue, Idaho populations of spring/summer Chinook Salmon will remain at low abundance, and ESA-listed populations will continue to be considered at high overall risk. However, changes in density independent factors which affect productivity could quickly reverse recent trends.

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. 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.

3. Quantify variability in spawner age proportion within brood years and evaluate sensitivity

of productivity to those estimates.

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Zoology 1: 291-298. Myers, R. A., 2001. Stock and recruitment: generalizations about maximum reproductive rate,

density dependence, and variability using meta-analytic approaches. ICES Journal of Marine Science 58: 937-951.

Myers, R. A., K. G. Bowen, and N. J. Barrowman. 1999. Maximum reproductive rate of fish at low

population sizes. Canadian Journal of Fisheries and Aquatic Sciences 56: 2404-2419. 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.

Pebesma, E. J., and R. S. Bivand. 2005. Classes and methods for spatial data in R. R News 5

(2). https://CRAN.R-project.org/doc/Rnews/. Peterson, W. T., J. L. Fisher, C. A. Morgan, B. J. Burke, S. M. Zeman, and K. C. Jacobson. 2017.

Ocean ecosystem indicators of salmon marine survival in the northern California current. Northwest Fisheries Science Center, Newport.

Quinn, T. P. 2005. The behavior and ecology of Pacific salmon and trout. American Fisheries

Society, Bethesda. R Core Team. 2017. R: A language and environment for statistical computing. R Foundation for

Statistical Computing. Vienna, Austria. http://www.R-project.org. Raymond, H. L. 1979. Effects of dams and impoundments on migrations of juvenile Chinook

Salmon and Steelhead from the Snake River, 1966 to 1975. Transactions of the American Fisheries Society 108: 505-529.

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

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

https://cran.r-project.org/doc/Rnews/

http://www.r-project.org/

21

Rose, K. A, J. H. Cowan Jr., K. O, Winemiller, R. A. Myers, and R. Hilborn. 2001. Compensatory density dependence in fish populations: importance, controversy, understanding and prognosis. Fish and Fisheries 2: 293-327.

Schoeneman, D. E., R. T. Pressey, and C. O Junge Jr. 1961. Mortalities of downstream migrant

salmon at McNary Dam. Transactions of the American Fisheries Society 90: 58-72. Walters, A. W., T. Copeland, and D. A. Venditti. 2013. The density dilemma: limitations on juvenile

production in threatened salmon populations. Ecology of Freshwater Fish 22: 508-519. Wickham, H. 2009. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag, New York. Wickham, H, R. Francois, L. Henry, and Kirill Müller. 2017. dplyr: A Grammar of Data

Manipulation. R package version 0.7.4. https://CRAN.R-project.org/package=dplyr.

https://cran.r-project.org/package=dplyr

22

TABLES

23

Table 2.1. List of Idaho spring/summer Chinook Salmon trend transects and 2017 sampling information. List is organized by Major Population Group and population. NS = Not Surveyed, NA = Not Applicable, NT= No trend transects identified, NPT = Nez-Perce Tribe, SBT = Shoshone-Bannock Tribe, UAV = Unmanned Aerial Vehicle.

Population Transect ID Target Survey Date Actual Survey Date Method Agencies

South Fork Salmon River MPG LSR NS-34 9/5-9/10 9/6 Ground IDFG

SFSR NS-26 9/5 8/31 Ground IDFG NS-27 9/5 9/5-9/12 Ground NPT, IDFG NS-28 9/5 9/5-9/6 Ground NPT, IDFG NS-29 9/5 9/4 Ground IDFG

SEC WS-16 8/25-9/1 8/24 Ground IDFG WS-17 8/25-9/1 8/24 Ground IDFG WS-18 8/25 8/24 Ground IDFG WS-19 8/25 8/24 Ground IDFG WS-20 8/25 8/24 Ground IDFG

EFSFSR NS-30 9/1-9/5 8/31 Ground NPT NS-31 9/1-9/5 9/14 Ground NPT

Middle Fork Salmon River MPG

CHC WS-1 8/25 NS NA NA WS-1a 8/25 NS NA NA MFSRL WS-15 9/5-9/12 9/8-9/9 Aerial IDFG BIG WS-13 9/5 8/30 Ground IDFG WS-14a 9/5 8/30 Ground IDFG WS-14b 9/5 9/9 Aerial IDFG WS-14c 9/5 9/9 Aerial IDFG WS-14d 9/5 9/9 Aerial IDFG CAM WS-8 8/25-9/5 9/8 Aerial IDFG LOON WS-6 8/25-9/5 9/8 Aerial IDFG WS-7 8/25-9/5 9/8 Aerial IDFG MFSRU NT NA NA NA NA SUL OS-4 8/21 8/21 Ground IDFG WS-12 8/21 8/21 Ground IDFG BVC WS-9a 8/27 8/22 Ground IDFG WS-9b 8/27 8/22 Ground IDFG WS-9c 8/27 8/22 Ground IDFG WS-9d 8/27 8/22 Ground IDFG WS-10a 8/27 8/22 Ground IDFG WS-10b 8/27 8/22 Ground IDFG WS-11a 8/27 8/22 Ground IDFG WS-11b 8/27 8/22 Ground IDFG

24

Table 2.1. Continued


Middle Fork Salmon River MPG Continued

BVC WS-11c 8/27 8/22 Ground IDFG MAR WS-2a 8/18 8/18 Ground IDFG WS-2b 8/18 8/18 Ground IDFG WS-3 8/17 8/20 Ground IDFG WS-4 8/19 8/21 Ground IDFG WS-5 8/16 8/19 Ground IDFG

Upper Salmon River MPG

PAN NS-11a 9/8 9/2 UAV IDFG NS-11b 9/8 9/2 UAV IDFG NS-11c 9/8 9/2 UAV IDFG NFSR NS-25a 9/8 9/5 Ground IDFG NS-25b 9/8 9/5 Ground IDFG NS-25c 9/8 9/6 Ground IDFG LEM NS-9 9/8 9/3 UAV IDFG NS-10 9/8 9/3 UAV IDFG USRL NS-17 9/8 9/4 Aerial IDFG NS-18 9/8 9/4 Aerial IDFG NS-19 9/8 9/4 Aerial IDFG NS-20 9/8 9/4 Aerial IDFG NS-21 9/8 9/4 Aerial IDFG NS-22 9/8 9/4 Aerial IDFG NS-23 9/8 9/4 Aerial IDFG NS-24 9/8 9/4 Aerial IDFG PAH NS-33a 9/8 9/23 Aerial IDFG EFSR NS-1a 9/8 9/4 Aerial IDFG NS-1b 9/8 9/4 Aerial IDFG NS-2a 9/8 9/4 Aerial IDFG NS-2b 9/8 9/4 Aerial IDFG NS-2c 9/8 9/4 Ground SBT YFK NS-5 9/8 9/8 Ground SBT NS-6 9/8 9/8 Ground SBT NS-7 9/8 9/8 Ground SBT NS-8 9/8 9/8 Ground SBT VAL NS-3a 9/8 9/4 Aerial IDFG NS-3b 9/8 9/4 Aerial IDFG NS-4 9/8 9/4 Aerial IDFG USRU NS-12 8/31-9/5 9/4 Aerial IDFG NS-13a 9/8 9/4 Aerial IDFG NS-13b 9/8 9/4 Aerial IDFG NS-15a 9/8 9/4 Aerial IDFG NS-15b 9/8 9/4 Aerial IDFG

25



Upper Salmon River MPG Continued

USRU NS-16 9/8 9/4 Aerial IDFG OS-1 8/31-9/5 9/4 Ground IDFG OS-2 8/31-9/5 9/4 Ground IDFG OS-3 8/31-9/5 9/4 Ground IDFG OS-5 9/8 9/4 Aerial IDFG OS-6 9/8 9/4 Ground IDFG

Dry Clearwater MPG

LAP NT NA NA NA NA POT NT NA NA NA NA LAW NT NA NA NA NA USFC NC-1 9/3 9/5-9/6 Ground IDFG

NC-2a 9/3 9/4 Ground IDFG

NC-2b 9/3 9/5-9/6 Ground IDFG

NC-3 9/3 NS NA NA

NC-4 9/1-9/5 9/6 Ground IDFG

NC-6 9/3 9/15-9/19 Ground IDFG

NC-8 9/3 9/7 Ground NPT, IDFG

Wet Clearwater MPG LOLO NC-14 9/3 9/5 Ground NPT, IDFG LOC NC-10 9/3 9/6 Ground IDFG NC-11 9/3 9/2 Ground IDFG NC-13 9/3 9/6 Ground IDFG MED NT NA NA NA NA MOO WC-3c 9/8 NS NA NA WC-3d 9/8 NS NA NA SEL WC-1 9/8 NS NA NA WC-2 9/8 9/27 Ground IDFG WC-4a 9/8 NS NA NA WC-4b 9/8 NS NA NA WC-5 9/8 NS NA NA WC-6 9/8 NS NA NA WC-7 9/8 9/5 Ground IDFG WC-8 9/8 NS NA NA WC-9 9/8 NS NA NA

26

Table 2.2. Chinook Salmon redds counted in Idaho trend transects in the Salmon River and Clearwater River basins during 2017 by major population group and population.

Population Length

(km) Redds Hatchery Fraction

South Fork Salmon River MPG LSR 15 1 0 SFSR 70.1 180 0.82 SEC 28.1 61 0.09 EFSFSR 10.5 39 0.55

MPG Total 123.7 281


CHC NSa NSa NSa MFSRL 72.9 1 0 BIG 63.7 22 0 CAM 9.9 10 0 LOON 25.1 4 0 MFSRU NSb NSb NSb SUL 7.9 3 0 BVC 63 72 0.07 MAR 26.7 37 0

MPG Total 269.2 149


PAN 20.3 5 0 NFSR 29.3 2 0 LEM 38.2 29 0 USRL 214.1 18 0.82 PAH 27.9 39 0.13 EFSR 56.7 82 0 YFK 41.4 13 0.12 VAL 28.3 29 0 USRU 69 192 0.79

MPG Total 525.2 409

Salmon Basin Total 918.1 839

Dry Clearwater MPG

LAP NSb NSb NSb

POT NSb NSb NSb

LAW NSb NSb NSb USFC 80.9 69 0.92

MPG Total 80.9 69

27


Population Length (km) Redds Hatchery

Fraction

Wet Clearwater MPG LOLO 17.6 16 0.32 LOC 32.2 23 0.73 MED NSb NSb NSb MOO NSc NSc NSc SEL 11.1 2 0.12

MPG Total 60.9 41

Clearwater Basin Total 141.8 110

Idaho Total 1059.9 949 a = Not sampled due to fire. b = No trend transect established. c = Trend transect monitoring discontinued.

28

Table 2.3. Spring/summer Chinook Salmon carcasses collected during spawning ground surveys in Idaho during 2017. Surveys are organized by major population group (MPG). F = female; M = male; U = unknown sex. Hatchery fraction is the number of hatchery-origin carcasses divided by the number of known-origin carcasses. Asterisks indicate values assumed or calculated from previous brood cycle for productivity analysis.

Segregated Hatchery Integrated Hatchery Natural Unknown Total

Population F M U F M U F M U F M U All Known-origin Wild Wild Fraction

South Fork Salmon River MPG

LSR 1 15 0 0 0 0 0 0 0 0 0 0 16 16 0 0 SFSR downstream of weir (a) 3 1 0 1 0 0 2 3 0 0 1 0 11 10 5 0.50 SFSR upstream of weir (a) 0 0 0 18 35 3 0 8 0 0 0 2 66 64 8 0.13

SEC 5 0 0 0 2 0 29 43 0 1 0 1 81 79 72 0.91

EFSFSR 4 0 0 2 34 0 12 21 0 3 3 0 79 73 33 0.45

Total MPG 13 16 0 21 71 3 43 75 0 4 4 3 253 242 118 0.49


MFSRU 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.0*

MFSRL(b) 1 1 0 0 0 0 3 2 0 0 0 0 7 7 5 1.0*

BIG 0 0 0 0 0 0 0 1 0 1 1 0 3 1 1 1.0*

CAM 0 0 0 0 0 0 0 1 0 0 0 0 1 1 1 1.0*

LOON 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 1.0*

SUL 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.0*

BVC(c) 1 0 0 0 0 0 8 6 0 0 0 0 15 15 14 0.93

MAR 0 0 0 0 0 0 15 8 1 0 0 0 24 24 24 1.0

Total MPG 2 1 0 0 0 0 27 18 1 1 1 0 51 49 46 0.94


PAN(d) 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 1.0*

NFSR 1 0 0 0 0 0 1 1 0 0 0 0 3 3 2 1.0*

LEM 0 0 0 0 0 0 8 1 1 0 0 0 10 10 10 1.0

USRL 12 31 0 1 1 0 3 7 0 0 0 0 55 55 10 0.18 PAH downstream of weir 0 0 0 0 0 0 0 2 0 0 0 0 2 2 1 1.0

29


Segregated

Hatchery Integrated Hatchery Natural Unknown Total

Population F M U F M U F M U F M U All Known-origin Wild Wild Fraction

Upper Salmon River MPG Continued PAH upstream of weir 1 1 0 0 0 0 1 0 0 0 0 0 3 3 1 0.33

EFSR 0 0 0 0 0 0 5 3 1 0 0 0 9 9 9 1.0*

YFK(d) 1 1 0 0 0 0 1 1 0 1 0 0 5 4 2 0.88*

VAL(d) 0 0 0 0 0 0 3 0 0 0 0 0 3 3 3 1.0* USRU downstream of weir 81 42 0 5 5 0 29 20 0 0 0 0 182 182 49 0.27 USRU upstream of weir 75 116 2 6 20 0 10 38 0 0 0 0 267 267 48 0.18

Total MPG 172 188 2 12 29 0 61 73 2 1 0 0 540 539 136 0.25

Dry Clearwater MPG

USFC(a) 40 83 19 1 0 0 0 0 0 5 8 3 159 143 Unknown Unknown

Total MPG 40 83 19 1 0 0 0 0 0 5 8 3 159 143 Unknown Unknown

Wet Clearwater MPG

LOC(a) 5 1 2 0 0 0 0 0 0 0 3 0 11 8 Unknown Unknown

LOLO(e) 0 0 0 0 0 0 0 0 0 3 3 0 6 0 Unknown Unknown

SEL(a) 0 0 0 0 0 0 0 1 1 0 2 0 Unknown Unknown

Total MPG 5 1 2 0 0 0 0 0 0 4 7 0 19 8 Unknown Unknown

a Staff from the Nez Perce Tribe and Idaho Department of Fish and Game collected and provided information. a Staff from U.S. Forest Service collected and provided information. b Staff from the Shoshone-Bannock Tribes and Idaho Department of Fish and Game collected and provided information. c Staff from the Shoshone-Bannock Tribes collected and provided information. d Staff from the Nez Perce Tribe collected and provided information.

30

Table 2.4. Age composition of natural-origin spring/summer Chinook Salmon carcasses collected during spawning ground surveys in Idaho during 2017. Populations are organized by major population group (MPG).

Freshwater.Ocean Age (Total

Age)

Population Carcasses Assigned Age From Fin

Ray 2.1 (3) 2.2 (4) 2.3 (5) 2.4 (6) South Fork Salmon River MPG

LSR 0 0 0 0 0 SFSR(a) 8 1 4 3 0 SEC 71 21 37 13 0 EFSFSR 36 16 12 8 0 MPG Total 115 38 53 24 0

Middle Fork Salmon River MPG MFSRL 4 0 3 1 0 BIG 3 2 0 1 0 CAM 0 0 0 0 0 LOON 1 0 0 1 0 MFSRU 0 0 0 0 0 SUL 0 0 0 0 0 BVC(b) 13 0 7 6 0 MAR 22 2 13 7 0 MPG Total 43 4 23 16 0

Upper Salmon River MPG PAN(c) 0 0 0 0 0 NFSR 0 0 0 0 0 LEM 6 1 4 1 0 USRL 10 1 5 4 0 PAH 3 1 2 0 0 EFSR 6 0 2 4 0 YKF(c) 0 0 0 0 0 VAL 3 0 2 1 0 USRU 92 19 41 32 0 MPG Total 120 22 56 42 0

Dry Clearwater River MPG USFC 5 1 4 0 0 MPG Total 5 1 4 0 0

Wet Clearwater River MPG LOLO 0 0 0 0 0 LOC 3 1 2 0 0 SEL 2 0 2 0 0 MPG Total 5 1 4 0 0

31

Table 2.5. Parameter estimates and pseudo-r2 values for Beverton-Holt stock-recruit models fitted to observed data from Idaho populations of spring/summer Chinook Salmon.

Population α β pseudo-r2

SFSR 17.8 0.1 0.004 SEC 7.3 0.0 0.179 CHC No convergence BIG 21.3 0.2 0.071 CAM 12.8 0.1 0.130 LOON No convergence SUL 2.08 0.03 0.574 BVC 10.14 0.03 0.196 MAR 10.60 0.08 0.049 NFSR No convergence LEM 30.5 0.5 0.01 USRL No convergence PAH 3.9 0.1 0.126 EFSR 18.2 0.1 0.168 VAL 9.1 0.1 0.300 USRU 17.7 0.1 0.215

32

FIGURES

33

Figure 2.1. Number of spring/summer Chinook Salmon redds counted in trend transects of Idaho populations of the Snake River ESU during 2017. Populations shaded white were not surveyed.

34

Figure 2.2. Number of spring/summer Chinook Salmon redds counted in trend transects of the

Clearwater and Salmon River basins, 2012-2017. Note different y-axis scales.

35

Figure 2.3. Number of spring/summer Chinook Salmon redds counted in trend transects for

populations of the South Fork Salmon River MPG, 2012-2017. Solid reference lines represent pre-1970 range, and dashed reference line represents pre-1970 geometric mean. Note different y-axis scales.

36


populations of the Middle Fork Salmon River MPG, 2012-2017. Solid reference lines represent pre-1970 range, and dashed reference line represents pre-1970 geometric mean. Note different y-axis scales.

37


populations of the Upper Salmon River MPG, 2012-2017. Solid reference lines represent pre-1970 range, and dashed reference line represents pre-1970 geometric mean. Note different y-axis scales.

38


populations of the Wet Clearwater MPG, 2012-2017.

39

Figure 2.7. Number of spring/summer Chinook Salmon redds counted in trend transects of the

Upper South Fork Clearwater, which was the only population surveyed in the Dry Clearwater MPG, 2012-2017.

40

Figure 2.8. Age bias plot depicting relationship between age estimates obtained from

spring/summer Chinook Salmon fin rays and known age for known-age fish collected in 2017. RMSE = root mean squared error, PA = percent agreement, and n = the number of known-age fish.

41

Figure 2.9. Length frequency distribution by age class (estimated from fin rays) for natural-

origin spring/summer Chinook salmon carcasses (n = 288) collected in 2017.

42

Figure 2.10. Productivity (returned redds per spawned redds) of Idaho populations of

spring/summer Chinook Salmon for brood years 2001-2012. Dashed line represents 1:1 replacement line.

43

Figure 2.11. Relationship between stock (brood year redds) and recruits (returned natural-

origin redds) in South Fork Salmon River MPG populations of summer Chinook Salmon for brood years 1995-2012 for which complete data were available. Dashed line represents 1:1 replacement line.

44


origin redds) in Middle Fork Salmon River MPG populations of spring/summer Chinook Salmon for brood years 1995-2012 for which complete data were available. Dashed line represents 1:1 replacement line.

45


origin redds) in Upper Salmon River MPG populations of spring/summer Chinook Salmon for brood years 1995-2012 for which complete data were available. Dashed line represents 1:1 replacement line.

46

Figure 2.14. Productivity (natural-origin redds per spawned redd) of South Fork Salmon River

MPG populations of spring/summer Chinook Salmon for brood years 2001-2012. Select brood years omitted due to incomplete data. Dashed line represents 1:1 replacement line.

47

Figure 2.15. Productivity (natural-origin redds per spawned redd) of Middle Fork Salmon River

MPG populations of spring/summer Chinook Salmon for brood years 2001-2012. Select brood years omitted due to incomplete data. Dashed line represents 1:1 replacement line.

48

Figure 2.16. Productivity (natural-origin redds per spawned redd) of Upper Salmon River MPG

populations of spring/summer Chinook Salmon for brood years 2001-2012. Select brood years omitted due to incomplete data. Dashed line represents 1:1 replacement line.

49

CHAPTER 3 – EVALUATION OF INDEX REDD COUNTS USING MULTIPLE PASS REDD COUNTS AND MARK-RECAPTURE ESTIMATES

ABSTRACT

Single-pass index redd counts are the cornerstone of status assessment for spring/summer Chinook Salmon Oncorhynchus tshawytscha populations in Idaho. These surveys are assumed to be proportional to spawner abundance. We used paired samples of single-pass index redd counts and abundance estimates from either multiple pass redd counts or mark-recapture surveys to evaluate this assumed proportionality. We found high correlation (r2 = 0.81 – 0.99) between index redd counts and abundance estimates but additional analysis is needed to evaluate whether index redd counts are proportional to abundance.

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INTRODUCTION

Estimating numerical abundance of fish populations requires a large amount of time and money and due to these constraints indices are often used to monitor relative abundance (Hubert and Fabrizio 2007). Typically, relative abundance is taken as a measure of catch divided by some unit of effort such as the duration of sampling or the amount of habitat sampled (Hubert and Fabrizio 2007). A good index of relative abundance is proportional to abundance (Harley et al. 2001).

Abundance of salmonids is commonly quantified or indexed by counting the number of

redds within a population’s spawning area. Redds are gravel nests in which eggs are deposited and buried by female salmonids (Quinn 2005). Redds are readily identifiable by observers as their construction disturbs the streambed producing a characteristic pit and tailspill (Quinn 2005). Female Chinook Salmon Oncorhynchus tshawytscha very rarely construct more than one redd so redd counts have often been used to index adult population size (Dauble and Watson 1997) and may also serve as an index of effective population size (Meffe 1986).

The Idaho Department of Fish and Game (IDFG) has conducted counts of spring/summer

Chinook Salmon redds at standardized trend sites annually for as long as 60 years (Hassemer 1993). Redd counts from trend transects are assumed to be an index of spawner abundance within many of Idaho’s spring/summer Chinook Salmon populations. In this section we utilize estimates of total redd or total female abundance from intensively monitored Chinook Salmon populations with the objective of evaluating the assumption that trend sites serve as valid indices of spawner abundance.

METHODS

Study Design

Multiple pass redd counts were used to estimate total redds within two populations and one specific transect. Multiple pass redd counts have been conducted since the early 1990s within two populations: Marsh Creek and the Lemhi River. One transect (NS-16) in the Salmon River upper mainstem above Redfish Lake population has been targeted for multiple pass redd counts since 2015 due to increased interest in a developing, high-density spawning aggregation and as part of the Integrated Broodstock Evaluation conducted by IDFG. This transect encompasses the area of the population below the Sawtooth Hatchery weir. Multiple pass surveys were designed to begin with the start of spawning activity, with subsequent surveys conducted weekly until the end of spawning activity.

Mark-recapture methods were used to estimate total female abundance in the portion of

the Salmon River upper mainstem above Redfish Lake population above Sawtooth weir. The Sawtooth Hatchery weir in the Salmon River upper mainstem above Redfish Lake population was constructed to collect brood stock. The Sawtooth weir is operated from mid-June until the end of spawning activity.

Data Collection

Stream transects in the Marsh Creek and Lemhi River populations, and at transect NS-16 in the Salmon River upper mainstem above Redfish Lake population were surveyed three or more times with ground counts following methods described in Part 2. On each pass, newly observed

51

redds were flagged, assigned a unique number, and georeferenced using GPS units. At Sawtooth weir, fish passed above the weir were counted, examined for sex determination, and marked with an operculum punch. All carcasses recovered during spawning ground surveys above the weir were examined for an operculum punch. Single pass index trend counts were ground counts in the Marsh Creek population, and a mix of low-flying helicopter and ground counts in the Lemhi River and Salmon River upper mainstem above Redfish Lake populations. Index trend counts in transect NS-16 were conducted using low-flying helicopter.

Data Analysis

Total number of redds was calculated as the sum of all new redds observed for multiple pass surveys. Female abundance above Sawtooth weir was estimated using the Chapman modification of the Lincoln-Petersen method (Chapman 1951, Seber 1982):

𝑁𝑁� = (𝑅𝑅 + 1)(𝐶𝐶 + 1)

(𝑅𝑅 + 1)− 1

where M is the number of females marked at the weir, C is the number of female carcasses recovered above the weir, and R is the number of marked female carcasses recovered above the weir.

The relationship between trend counts and estimates derived from multiple pass counts and weir passage was assessed using correlation analysis. We calculated Pearson’s correlation coefficient among index redd counts and either the estimated total number of redds, or estimated female abundance. We also calculated the percentage of the total number of redds or female spawners represented by the index count. Analysis was conducted in the base package of program R and plots were generated using the ggplot2 package (Wickham 2009) in program R (R Core Team 2017).

RESULTS

Single-pass and multiple-pass counts at trend transects in the Marsh Creek population from 1998 through 2017 were correlated (r2 = 0.94) with total redd abundance estimated from multiple pass surveys (Figure 3.1). The 2017 trend count was 37 redds, which was 69% of the total redd estimate. Trend counts represented 40% to 90% of total redd abundance but ranged from 65% to 85% in most years (Figure 3.2).

Single-pass and multiple-pass counts at trend transects in the Lemhi River population from

2000 through 2017 were correlated (r2 = 0.81) with total redd abundance estimated from multiple pass surveys (Figure 3.3). The 2017 trend count was 29 redds, which was 50% of the total redd estimate. Trend counts represented 36% to 147% of total redd abundance, but ranged from 44% to 84% in most years (Figure 3.4). Trend counts overestimated abundance (>100% of total redd abundance) in three years when total redd abundance was low (Figure 3.4).

Single-pass and multiple-pass counts at transect NS-16 in the Salmon River upper

mainstem above Redfish Lake population from 2015 through 2017 were correlated (r2 = 0.99) with total redd abundance estimated from multiple pass surveys (Figure 3.5). The 2017 trend count was 131 redds, which was 86% of the total redd estimate. Trend counts represented 55% to 86% of total redd abundance (Figure 3.6). Over the three observed years, percent of total redd abundance represented by the trend count decreased with an increase in total redds (Figure 3.6).

52

Counts at trend transects above the Sawtooth weir in the Salmon River upper mainstem

above Redfish Lake population from 1998 through 2017 were correlated (r2 = 0.94) with female abundance estimated from mark-recapture (Figure 3.7).The 2017 trend count was 62 redds, which was 35% of the female abundance estimate. Trend counts represented 35% to 166% of female abundance estimates, but ranged from 48% to 87% most years (Figure 3.8). There may be a negative relationship between female abundance and percent represented by the trend count (Figure 3.8).

DISCUSSION

Trend counts were positively related to total redd abundance estimates across a range of habitats and stream sizes within Idaho. Catch-per-unit effort may not be a good index of abundance if sampling efficiency decreases at high abundance (Harley et al. 2001; Hansen et al. 2004), but ground-based redd counts may be robust to such effects because the units being counted are immobile and gear saturation is unlikely to occur except at very high densities. However, aerial redd counts may suffer from gear saturation, as high-density aggregations of redds may be difficult to count accurately in the relatively short amount of time in which observers must detect redds. Conversely, aerial redd counts in the Lemhi River apparently suffered from errors of commission in select years of this analysis, resulting in single-pass counts greater than multipass counts. These errors were most likely a result of inexperienced aerial observers mistakenly identifying hydraulic stream features as redds (D. Venditti, personal communication).

Overall, single-pass peak redd counts are clearly correlated with total spring/summer

Chinook Salmon spawner abundance in Idaho and are at the very least a reliable indicator of trends in spawner abundance. Additional analysis is necessary to evaluate the degree to which single-pass peak redd counts are proportional to total redd abundance, and whether this relationship holds for both ground-based and aerial methods.

53

LITERATURE CITED

Chapman, D. G. 1951. Some properties of the hypergeometric distribution with applications to zoological censuses. University of California Publications in Statistics 1: 131-160.

Dauble, D. D., and D. G. Watson. 1997. Status of fall Chinook Salmon populations in the mid-

Columbia River, 1948-1992. North American Journal of Fisheries Management 17: 283-300.

Hansen, M. J., S. P. Newman, and C. J. Edwards. 2004. A reexamination of the relationship

between electrofishing catch rate and age-0 walleye density in northern Wisconsin lakes. North American Journal of Fisheries Management 24: 429-439.

Harley, S. J., R. A. Myers, and A. Dunn. 2001. Is catch-per-unit-effort proportional to abundance?

Canadian Journal of Fisheries and Aquatic Sciences 58:1760-1772. Hassemer, P. 1993. Draft manual of standardized procedures for counting Chinook Salmon

redds. Idaho Department of Fish and Game, Boise. Hubert, W. A., and M. C. Fabrizio. 2007. Relative abundance and catch per unit effort. Pages

279-326 in Guy, C. S., and M. L Brown, editors. Analysis and Interpretation of Freshwater Fisheries Data, Bethesda.

Meffe, G. K. 1986. Conservation genetics and the management of endangered fishes. Fisheries

11: 14-23. Quinn, T. P. 2005. The behavior and ecology of Pacific salmon and trout. American Fisheries

Society, Bethesda. R Core Team. 2017. R: A language and environment for statistical computing. R Foundation for

Statistical Computing. Vienna, Austria. http://www.R-project.org/. Seber, G. A. F. 1982. The estimation of animal abundance and related parameters. Edward

Arnold, London. Wickham, H. 2009. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag, New York.

http://www.r-project.org/

54

TABLES

55

Table 3.1. Multiple-pass redd count census surveys that were conducted for spring-summer Chinook Salmon in Idaho during 2017. 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 8/4 & 8/10 4 8/19 7 8/29 1 9/6 1 9/13 0 13 Banner Creek 8/13 1 8/20 0 8/30 0 9/8 0 n/c n/c 1 Cape Horn Creek 8/2 & 8/13 1 & 5 8/20 7 8/30 0 9/8 0 9/12 0 13 Knapp Creek 8/12 0 8/21 0 n/c n/c(b) 9/5 1 n/c n/c 1 Marsh Creek 8/3 & 8/11 2 & 6 8/18 11 8/28 7 9/7 0 9/14 0 26

Total 19 25 8 2 0 54

Upper Salmon River MPG Lemhi River Bear Valley Creek 8/22 0 8/29 0 9/6 2 9/12 0 n/c n/c 2 Big Springs Creek n/c n/c n/c n/c n/c n/c n/c n/c 9/27 3 3 Big Timber Creek 8/23 0 8/30 0 9/7 0 9/13 0 n/c n/c 0 Canyon Creek 8/23 0 8/30 0 9/7 0 9/13 0 n/c n/c 0 Hayden Creek 8/21-23 0 8/27-29 1 9/5-6 8 9/11-12 1 n/c n/c 10 Lemhi River n/c n/c 8/30-31 19 9/7-8 14 9/13-14 9 9/20-21 1 43 Little Springs Creek 8/24 0 8/30 0 9/7 0 9/13 0 n/c n/c 0

Total 0 20 24 10 4 58

Salmon River Upper Mainstem Above Redfish Lake

Redfish Lake Creek upstream to Sawtooth Weir 8/22 26 8/27 47 9/3 57 9/11 16 9/18 5 151

Total

a Downloaded from the SGS database on 03/16/18. b Not completed = n/c. c Surveys were from the Hwy 28 Fishing Access upstream; an additional 2 redds were recorded on 9/3 in the aerial index from the Cottam Lane Bridge

downstream to the Lemhi River mouth.

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FIGURES

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Figure 3.1. Relationship between trend count (line) and multiple pass estimate of total redd

abundance (bars) for the Marsh Creek spring Chinook Salmon population, 1998-2017.

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Figure 3.2. Relationship between total redd abundance and percent of total redd abundance

represented by trend count for the Marsh Creek spring Chinook Salmon population, 1998-2017. Points are represented as text indicating year of observation.

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Figure 3.3. Relationship between trend count (line) and multiple pass estimate of total redd abundance (bars) for the Lemhi River spring Chinook Salmon population, 2000-2017.

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represented by trend count for the Lemhi River spring Chinook Salmon population, 2000-2017. Points are represented as text indicating year of observation.

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Figure 3.5. Relationship between trend count (line) and multiple pass estimate of total redd

abundance (bars) for transect NS-16 in the Salmon River upper mainstem above Redfish Lake spring Chinook Salmon population, 2015-2017.

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represented by trend count for the Salmon River upper mainstem above Redfish Lake spring Chinook Salmon population, 1998-2017. Points are represented as text indicating year of observation.

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Figure 3.7. Relationship between trend count (line) and mark-recapture estimate of female

abundance (bars) for the portion of the Salmon River upper mainstem above Redfish Lake Creek spring Chinook Salmon population located above Sawtooth weir, 1998-2017.

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Figure 3.8. Relationship between female abundance and percent of female abundance

represented by trend redd count for the portion of the Salmon River upper mainstem above Redfish Lake Creek spring Chinook Salmon population located above Sawtooth weir, 1998-2017. Points are represented as text indicating year of observation.

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APPENDIX

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Appendix A. Additional information collected on spawning ground surveys in 2017.

INTRODUCTION

Chinook Salmon spawning ground surveys are primarily designed to index trends in abundance and productivity within and among Idaho populations. However, some additional data are collected in order to monitor more intensively at smaller scales and to address ancillary objectives. These data are either not comparable on the broad scale that (need a comma after “scale” to use “which” or no comma and use “that” is the focus of this report, or do not fit into the specific objectives of this report. In most cases, these data will eventually be used in completion reports on projects such as habitat effectiveness monitoring and genetic diversity monitoring, but are not reported annually in relation to those objectives. The purpose of this appendix is to report the annual collection of these data.

METHODS

Additional Redd Count Surveys Additional redd surveys were conducted in various streams of the Clearwater River basin

to address specific questions regarding spawner abundance, spatial distribution, and spawn timing. Two passes, separated by one to two weeks, were made at each transect. One of the dates corresponded with the target date for a peak count and that pass was considered the trend. Survey methods were identical to those described for multiple pass surveys in chapter 3 of this report.

Genetics Samples at Weirs and Traps All adult Chinook Salmon captured at IDFG weirs or traps had the following data recorded:

origin (natural or hatchery), any marks or tags, fork length, and sex. We refer the reader to hatchery reports and to the Fish Inventory System Hatchery Database (FINS; http://www.fishnet.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 were stored on Whatman sheets and delivered to the IDFG Eagle Fish Genetics Laboratory located in Eagle, Idaho.

RESULTS

Additional Redd Count Surveys In 2017, additional redd count surveys were conducted in American River and Red River

of the Upper South Fork Clearwater River Population, and in the Upper Selway River population (Table 1). Two passes were conducted at each transect. Staff counted a total of 8 redds in American River, 75 redds in Red River, and 2 redds in the Upper Selway River.

Genetics Samples at Weirs and Traps A total of 1,058 tissue samples were collected from wild and integrated hatchery adult

Chinook Salmon released at IDFG hatchery weirs, hatchery traps, and research weirs during 2017 (Figure 1). Most samples (n = 389) 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 2017

http://www.fishnet.org/

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and no samples were collected. Chinook Salmon are incidental catch at the Fish Creek research weir, which is operated for steelhead Oncorhynchus mykiss.

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Appendix A Table 1. Additional redd count surveys that were conducted for spring-summer Chinook Salmon in Idaho during 2017. Surveys are organized by major population group (MPG).

(a) Data from Robert Hand of Clearwater Region in Lewiston, Idaho. Downloaded from SGS database on 3/16/18. (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 Limber Luke Creek

9/6 5 9/18-19 3 n/c n/c 8 A

Red River Mouth upstream to

Shissler Bridge 9/4-6 62 9/16-18 13 n/c n/c 75 A

Total 67 16 83

Wet Clearwater MPG Upper Selway River

Selway River Little Clearwater upstream to Magruder Crossing

9/5 2 9/12 0 n/c n/c 2 A,B

Total 2 0 2

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Appendix Figure 1. Number of genetics samples collected from wild and integrated hatchery

adult Chinook Salmon released at IDFG hatchery weirs (dots) and research weirs (triangles), 2013-2017. Crooked River samples for 2014 (n = 44) have not been located.

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Prepared by: Approved by: IDAHO DEPARTMENT OF FISH AND GAME Eli A. Felts J. Lance Hebdon Fisheries Biologist Anadromous Fisheries Manager Bruce Barnett James P. Fredericks, Chief Fisheries Data Coordinator Bureau of Fisheries Micah Davison Supervisory Fisheries Biologist Matthew J. Belnap Fisheries Biologist Kimberly A. Apperson Fisheries Biologist Robert Hand Fisheries Biologist Mike Peterson Fisheries Biologist Evan Brown Sr. Fisheries Data Coordinator

idaho adult chinook salmon monitoring... · 2018. 10. 31. · idaho adult chinook salmon...

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