Research Project Description
Chinook salmon (Oncorhynchus tshawytscha) stocks in the Snake River have been listed under the Endangered Species Act (ESA) since 1992. In response to declining populations and ESA requirements, agencies have adopted policies that attempt to conserve and restore remaining Chinook salmon populations. These efforts have included measures to maintain genetic integrity of remaining wild stocks, reduce passage mortality by improving conditions in the downstream migration corridor, reduce the effects of exotics, restrict sport and commercial harvest, and conserve or restore remaining critical habitats (Lee et al. 1997; NWPPC 2000; IDFG 2001). The conventional approach to managing critical habitat has been focused on the quality of remaining habitats; i.e. conserving and restoring those habitats considered necessary for Chinook salmon to complete their complex life cycle from incubating eggs to mature fish depositing eggs in natal spawning areas. While the quality of critical habitats is essential, there is growing concern that the geometry (i.e. size, spacing, and connectivity) of habitats also needs to be considered (Krohn 1992). Simberloff (1988) suggested that effective conservation may require maintaining or restoring a critical amount or mosaic of habitat, as well as habitat of certain quality.
Emerging conservation theory further suggests that recolonization and persistence of widely ranging species may be strongly influenced by the spatial geometry of remaining habitats. The relevance of these concepts to the persistence of declining stocks of Chinook salmon is unknown. If patterns in the distribution and spatial structure of Chinook salmon populations are important to their persistence in stochastic environments, effective conservation may imply maintaining or restoring a critical amount or mosaic of habitat as well as smaller scale habitat characteristics. This research will describe factors influencing the spatial distribution and persistence of wild Chinook salmon. Results are advancing current understanding of the relationship between landscape characteristics and the distribution, pattern, and persistence of Chinook salmon. Such information could be key for development of conservation and restoration strategies. While this research will focus on larger scale spatial questions about persistence, it is simultaneously provides information useful for intensively monitoring an ESA listed Chinook salmon stock. Our annual estimates of wild Chinook salmon redds enable managers to estimate total annual redds in order to monitor stock status and evaluate the influences of various mitigation and restoration efforts.

I. Project Significance
This research addresses at least three critical needs identified in Regional Program documents: 1.) the need for long-term information to assess trends in wild Chinook salmon populations; 2) the need for evaluation of broad scale population sampling and inventory methods; and 3) the need for analysis of the spatial structure of wild Chinook salmon populations.

Long-term trend information
The July, 2010 Council Draft Monitoring Evaluation and Research Reporting Plan (MERR) which is referred in the instructions above, states that high priority status will be given to “relevant high level population status and trend data”. Earlier documents including the Power Planning Council’s Fish and Wildlife Program (NWPPC 2000), the Salmon Subbasin summary (Servheen et al. 2001), the National Marine Fisheries Service Biological Opinion (NMFS 2000), and IDFG (2001) all emphasize the need for long-term monitoring and acquisition of life history information for Chinook salmon. These and other Regional Program documents emphasize the need for efforts to gather data on wild and naturally occurring spawning stocks. The Biological Opinion (NMFS 2000) also notes that a comprehensive monitoring and evaluation program will be required to meet RPA (reasonable and prudent alternatives). Our research objectives are very consistent with guidelines outlined by NMFS (2001) that call for “critical monitoring/evaluation components” which will be integral to measuring recovery performance standards. The Columbia Basin Fish and Wildlife Authority (CBFWA) notes that a primary function of species monitoring and evaluation components is to measure progress toward achieving conservation and recovery objectives (NWPPC 2000). Since the project inception in 1995, this research has provided information critical to intensively monitoring an ESA listed Chinook salmon stock. Our annual estimates of wild Chinook salmon redds enable managers to estimate total annual redd numbers in order to monitor stock status and evaluate the influences of various mitigation and restoration efforts.  

Broad scale sampling
The Salmon Subbasin summary, specifically calls for research to provide validation of broad scale population sampling and inventory methods (Serhveen et al. 2001). The Biological Opinion (NMFS 2000) calls for monitoring population status by assessing population abundance, trends, distribution, and variation. Prior to this project, Chinook salmon were inventoried only in “index” areas of the MFSR drainage. This research represents the first comprehensive survey of spawning areas and redds in the basin and provides key information on overall distribution of redds and spawning fish. Further, the data enables a comparison of population trends between “index” areas and the complete inventories.

Spatial structure
The Biological Opinion (NMFS 2000) and the Salmon Subbasin summary (Serhveen et al. 2001) both call for an analysis of the spatial structure of wild Chinook salmon populations. The CBFWA similarly notes that monitoring programs need to be expanded as necessary to reduce critical uncertainties (NWPPC 2000). As noted above, in response to declining populations, ESA requirements, and regional monitoring efforts, agencies have adopted policies that attempt to conserve and restore remaining Chinook salmon populations. Considerable effort has been applied to conserve or restore the quality of habitats considered necessary for Chinook salmon to complete their complex life cycle. Although recolonization and persistence of Chinook salmon may be strongly influenced by the spatial geometry of remaining habitats, the relevance of these concepts to the persistence of declining stocks of salmon remains unknown. Yet, little effort has been directed toward evaluating whether patterns in the distribution and spatial structure of salmon populations are important to their persistence in stochastic environments. This research directly addresses those stated research priorities and management needs.

Columbia River Basin Research Plan
The 2006 Columbia River Basin Research Plan lists critical uncertainties that our research project directly addresses in three categories: A) Population Structure and Diversity, Pg 19, #1. population recovery approaches and their influence on meta population structure and diversity, #3. The relationship between genetic diversity and ecological and evolutionary performance; B) Climate Change, Pg 19, #1. our long-term data base has the potential to establish a baseline for assessing the effects of a changing climate on salmon populations; and C) Monitoring and Evaluation, Pg 22, #1. Can probabilistic sampling designs be developed?, #2. Application of remote sensing techniques, and #3. Application of empirical models. More specifically, the RM&E Table on pages 30-40 lists several data needs that our research project is contributing to: redd numbers, status, and trends; spawner age; habitat condition; water temperature; and habitat connectivity.      

In addition to providing long-term and broad scale information to monitor an ESA listed salmon population, our results will simultaneously advance current understanding of the relationship between landscape characteristics and the distribution, pattern, and persistence of Chinook salmon. Such information could be critical for development of conservation and restoration strategies. At a broad scale, emerging strategies to conserve and restore critical habitats and viable populations will be based on this and associated research.

Salmon Subbasin Plan Consistency
Research Project #199902000 provides a continuous, temporally robust (1995-2005), basin wide Chinook salmon redd count in the MFSR drainage that directly addresses the following Salmon Subbasin Plan Objectives and strategies:
Aquatic Objective 2A:
Strategy 2A1. monitor abundance and productivity of wild stocks- pg 23
Strategy 2A2. identify where there is a lack of knowledge pertaining to the population size of anadromous species- pg 24
Strategy 2A7. evaluate effectiveness of ongoing programs- pg 24
Aquatic Objective 3C:
Strategy 3C1. quantify population specific adult abundance- pg 25
Strategy 3C3. determine population productivity- pg 25

We incorporate historical (since 1957) as well as present salmon population data and also address:
Aquatic Objective 1A:
Strategy 1A2. develop historic run reconstruction data- pg 20

Our analysis is designed to assess the factors influencing the persistence of Chinook salmon populations so directly addresses:
Aquatic Objective 2A: improve understanding and definition of small populations- pg 23

This research directly addresses key performance measures cited as lacking for anadromous fish in the Salmon Subbasin, specifically: 1) addressing key BIOP questions for research, monitoring, and evaluation, 2) relating fish population data to habitat conditions, and 3) providing unbiased and precise estimators of abundance and productivity targets- pg 26.

Further, this research addresses identified research needs (pg 120) including performance measures of adult spawner spatial distribution and population growth rate (lambda).  

II. Project history and accomplishments
In 1995, we developed a study plan and coordinated with Idaho Department of Fish and Game (IDFG) and USDA-Forest Service biologists. We developed a Memorandum of Understanding (No.INT-95121-MOU) to coordinate our research with IDFG fisheries biologists and managers. We developed a cost-share agreement with the Payette National Forest to assist funding of a portion of the field work. From 1995 to 2013 we have annually completed surveys of the mainstem Middle Fork Salmon River and 12 tributaries and used a GPS (global positioning system) to map the location of Chinook salmon redds. Although the Project has been in progress since 1995, FY 1999 was the initial year of BPA funding and FY 2014 is the sixteenth year of BPA funding. Previous year costs were paid by RMRS with some assistance from cooperators. Nineteen years of data have been gathered to date.

     FY 1995-1998: Annually in September 1995-1998, we flew reaches of the mainstem MFSR and 12 tributaries and used a GPS to map the location of potential spawning areas and redds. We completed ground-based counts in four streams that were not visible from the air. GPS files were corrected and transferred into GIS for spatial analysis. Summaries of redd surveys were submitted to collaborators and other interested parties. From 1995 to 1998, annual redd counts ranged from 20 to 424.

     FY 1999-2013: Annual aerial redd counts were continued in September 1999-2013 within reaches of the mainstem MFSR and 12 tributaries. A GPS was used to map the location of potential spawning areas and redds. We completed ground-based counts in four streams that were not visible from the air. GPS files were corrected and transferred into GIS for spatial analysis. Summaries of redd surveys were submitted to collaborators and other interested parties. From 1999 to 2013, annual redd counts ranged from 110 to 2,271. In 1999 the principal investigator attended a technical conference, presented a paper, and published a companion paper in the conference proceedings (see Thurow 2000).

In FY 2001 we submitted and were granted a request for a within year increase in funds to evaluate the bias and precision of redd counts, our primary survey method. In 2002, we expanded the 2001 redd count bias and precision proposal and formally submitted it as proposal (#28001). The full proposal was funded to expand the redd count analysis research and became Project #2002-049-00.

In June 2001, we initiated a cooperative research agreement with the University of Idaho to examine geomorphic controls on the spatial distribution of spawning gravels in the MFSR. We constructed a digital elevation model of the basin, and predicted substrate size as a function of channel hydraulics (channel type and bankfull discharge). Pilot field studies were conducted to quantify reach-average channel type, substrate size, and channel dimensions (bankfull depth, width, and channel gradient). Some of these data were used to drive the hydraulic model, while others were used to validate our predictions of substrate size. Initial results illustrated a strong correspondence between predicted locations of suitable spawning gravels and observed locations of redds, indicating that much of the spatial pattern of Chinook spawning may be explained by the effects of channel hydraulics on substrate size. These findings were presented at the American Fisheries Society (AFS) Transboundary conference (Buffington et al. 2002). In June 2002, we continued to expand the geomorphic research to sample a broader range of locations and underlying geologies in the basin; over 120 stream reaches were sampled. We also initiated a pilot study to examine the effects of sediment supply on substrate size and quality. The 2002 field work was conducted with USFS and UI funding external to BPA. Additional results were presented as invited presentations to the National AFS meeting and the Fall American Geophysical Union meeting (Buffington et al. 2003a,b) as well as the Alaska Habitat Modeling Workshop sponsored by the Nature Conservancy and Alaska Department of Fish & Game (Buffington et al. 2006a,b).

We have continued to extend the analyses of annual patterns of spawning locations and density as well as assess population structure. In addition to publishing manuscripts, the principle investigator and collaborators have shared the results of this research at numerous technical conference and workshops. As examples, results have been presented at the AFS (American Fisheries Society)  Transboundary conference (Isaak and Thurow 2002), Colorado/Wyoming chapter AFS (Issak and Thurow 2003), Idaho chapter AFS meetings (Thurow and Isaak 2003, Isaak and Thurow 2003, Isaak et al. 2005, Isaak et al. 2006), AFS National meetings (Isaak et al. 2003, Thurow and Isaak 2004, Isaak and Thurow 2004, Isaak et al. 2005, Neville et al. 2005), Western Division AFS meetings (Thurow and Isaak 2004, Isaak and Thurow 2004, Thurow and Isaak 2006, Isaak et al. 2006), the North American Benthological Society meeting (Isaak and Thurow 2004), the Biobío River Scientific Forum, University of Concepción, Chile (Buffington et al. 2004), the Idaho State University Department of Biological Sciences Seminar Series (Buffington et al. 2005), the World Wilderness Congress (Thurow et al. 2005), the Big Creek Symposium (Thurow and Isaak 2006), the Oregon State University Science Seminar Series (Isaak 2006) the Region 1/Region 4 USDA-Forest Service Biologists Conferences (Isaak et al. 2006, Isaak et al. 2007) the National meeting of the American Geophysical Union (Thurow et al. 2008), the 40th Anniversary Celebration of the Wild and Scenic Rivers Act (Thurow 2008), and the Workshop: Exploring wilderness science in the interior West (Thurow 2009).  In May 2013, the principle investigator was invited to: a.) participate in an interview designed to assess issues related to Columbia River Basin long-term salmon and steelhead recovery processes. The assessment is being conducted by Oregon Consensus and the William D. Ruckelshaus Center; and b.) Assist the Salmon-Challis National Forest in development of a management and monitoring plan to assess the effects of recreational floating on spawning by ESA listed Chinook salmon in the Middle Fork Salmon River. Results of this research were also presented in a special symposium of seven papers for the April 2013 Western Division AFS Meeting entitled: “Wild Chinook Salmon in a Dynamic Wilderness Landscape: Informing Salmon Recovery by Understanding Ecosystem Processes and Biological Responses.”

In addition to the proceedings manuscript noted above, six other manuscripts have been published in peer reviewed journals (Isaak et al. 2003, Isaak and Thurow 2006, Neville et al. 2006, Isaak et al. 2007, Neville et al. 2007, Courbois et al. 2008), and one additional manuscript is in review and three are in preparation.
Since 1995, redds were observed at elevations between 1100m and 2100m with a majority were constructed between 1500m and >2000m. Chinook salmon spawned in both mainstem reaches of the Middle Fork Salmon River and tributaries with about 98.5% of the redds to date observed in tributaries. The MFSR Chinook salmon population spawns at the highest elevations of any spring/summer Chinook salmon population in the world (Crozier et al. 2008).

Additional years of data will allow us to build upon this unique redd dataset as we study multiple generations of wild salmon. This research represents the first comprehensive survey of spawning areas and redds in a large basin and provides key information on overall spawning escapements and the distribution of fish. Results are being used in recovery planning by State, Federal, and Tribal agencies. Our annual redd estimates also provide a foundation for evaluating the influences of various salmon mitigation and restoration efforts outside the MFSR and may represent a baseline for evaluating the effects of a changing climate on wild Chinook salmon.

As we expand our analysis of the spatial and temporal variability in Chinook salmon populations we have continued to collect and archive genetic samples and otoliths from MFSR Chinook salmon carcasses. Genetic samples will ultimately be used to expand our earlier Chinook salmon genetics research (Neville et al. 2006; Neville et al. 2007). Nearly 4,000 otoliths have been collected and archived between 1996 and 2013. We are exploring collaborative opportunities to develop direct measures of dispersal and descriptions of life history patterns through otolith microchemistry.

III. Location of Project:
We selected the Middle Fork Salmon River (MFSR) drainage as the study area (see Thurow 2000 and Servheen et al. 2001 for detailed descriptions). The study area was selected for several reasons: 1) Remaining Chinook salmon stocks are wild and indigenous, unaltered by hatchery supplementation. Consequently, the ability of the salmon population to respond to the quality and quantity of the available habitat has not been altered. Wild, indigenous, Chinook salmon populations like those in the MFSR are rare; Thurow et al. (2000) reported their presence in 4% of the potential historical range and 15% of the current range in the Columbia River basin and portions of the Klamath River basin. 2) Most of the drainage has been lightly disturbed by anthropogenic activities so habitat quality has not been substantially altered in most areas. Widespread degradation of habitat would be expected to confound a spatial analysis of freshwater habitat by influencing fish distribution and abundance. 3) The large area provides an opportunity for a large sample size. About 650 km of tributaries and 170 km of the mainstem are accessible to Chinook salmon (Mallet 1974; Thurow 1985). This increases the likelihood of a sample size large enough to complete a robust spatial analysis. 4) Opportunities exist for extensive collaboration with other agencies and tribes who are already conducting Chinook salmon redd counts in the drainage; and 5) the principal investigator has more than 30 years of experience working in this drainage and has an intimate knowledge of the MFSR and the spawning ecology of its Chinook salmon.

IV. Summary
This research continues to build a temporally robust dataset that is unique within the Columbia River basin by providing a georeferenced dataset of the network-scale distribution of Chinook salmon redds. Spatially continuous sampling designs, when temporally replicated as this one, provide tremendous analytical flexibility and are unmatched in their ability to provide a dynamic system view that is commensurate with the scales at which important biophysical processes operate. Additional years of redd data will enhance our ability to monitor multiple generations of wild salmon. This research represents the first comprehensive survey of spawning areas and redds in a large basin and provides key information on overall spawning escapements and the distribution of fish. In addition to their value for recovery planning, these data also provide a foundation for evaluating the influences of various salmon mitigation and restoration efforts outside the MFSR and they may represent a baseline for evaluating the effects of a changing climate on wild Chinook salmon.