Analyze Chinook Salmon Spatial and Temporal Dynamics and Persistence proposal 199902000

FY07-09 proposal 199902000

Section 1. Administrative

Proposal title	Analyze Chinook Salmon Spatial and Temporal Dynamics and Persistence
Proposal ID	199902000
Organization	US Forest Service (USFS) - Rocky Mt Research Station
Short description	We propose continuation of research applying a continuous, spatially explicit, and temporally extensive redd database to advance understanding of the spatial and temporal dynamics and factors influencing persistence of wild Chinook salmon populations.
Information transfer	Studies have and will continue to result in publishable contributions to the fields of fish biology and management, ecology, population biology, and conservation biology. Information will be distributed via contract reports; peer-reviewed publications in professional journals; oral papers presented at professional meetings, technical conferences, and workshops; in response to information requests; and at informal meetings with state and federal agencies, tribes, and university scientists involved in co-management of Snake River Chinook salmon.
Proposal contact person or principal investigator

Contacts

Contact	Organization	Email
Form submitter
Russell Thurow	USDA Forest Service: Rocky Mt. Research Station	rthurow@fs.fed.us
All assigned contacts
Russell Thurow	USDA Forest Service: Rocky Mt. Research Station	rthurow@fs.fed.us
Russell Thurow	USDA Forest Service: Rocky Mt. Research Station	rthurow@fs.fed.us
Russell Thurow	USDA Forest Service: Rocky Mt. Research Station	rthurow@fs.fed.us

Section 2. Locations

Province / subbasin: Mountain Snake / Salmon

Latitude	Longitude	Waterbody	Description
N45-00-00	W114-45-00	Middle Fork Salmon River	Middle Fork Salmon River drainage, entire drainage centered on the listed Lat.-Long. 4th Code Hydrologic Units #17060205 (Upper Middle Fork Salmon) and #17060206 (Lower Middle Fork Salmon)
		Middle Fork Salmon River	Entire Middle Fork Salmon River drainage

Section 3. Focal species

primary: Chinook Snake River Spring/Summer ESU

Section 4. Past accomplishments

Year	Accomplishments
2005	We completed the continuous redd survey for the 11th year. Crews measured spawning area characteristics. GIS files were created and shared. Results were presented in 1 paper and 3 posters at professional meetings and in a peer-review publication.
2004	We completed the continuous redd survey for the 10th year. Crews measured spawning area characteristics and hydraulic features. GIS files were created and shared. Results were presented in 5 papers at prof. meetings and at an international symposium.
2003	We completed the continuous redd survey. Crews measured spawning area characteristics and hydraulic features. GIS files were created and shared. Results were presented in 6 papers at professional meetings and in a peer-reviewed publication.
2002	We completed the continuous redd survey. Crews measured spawning area characteristics and hydraulic features. GIS files were created and shared. Results were presented in 2 papers at professional meetings.
2001	We completed the continuous redd survey. Crews measured spawning area characteristics. GIS files were created and shared. A within-year increase initiated redd validation research. We also began research to assess geomorphic controls on spawning sites.
2000	We completed a continuous survey and georeferenced salmon redds across 800 km of the MFSR drainage. Crews measured spawning area characteristics. GIS files were created and data summaries were shared with collaborators.
1999	We completed a continuous survey and georeferenced salmon redds across 800 km of the MFSR drainage. Crews measured spawning area characteristics. GIS files were created and shared with collaborators. Results were presented and published at a Prof meeting.

Section 5. Relationships to other projects

Funding source	Related ID	Related title	Relationship
BPA	198909800	Salmon Studies Id Rvrs IDFG	Project 199902000 fully compliments IDFG salmon redd counts in index areas within the MFSR.
BPA	199107300	Idaho Natural Production Monit	Project 199902000 provides the ability to relate index area redd counts to a total basin-wide count.
BPA	199405000	Salmon River Habitat Enhance	Project 199902000 compliments Shoshone-Bannock Tribe assessment of habitat enhancement in Bear Valley Cr.
BPA	198909803	Salmon Studies Id Rvrs SBT	Project 199902000 fully compliments Shoshone-Bannock Tribe salmon redd counts in Bear Valley Cr within the MFSR.
BPA	198909600	Genetic M&E Prog For Sal/Steel	Project 199902000 fully compliments NOAA genetic monitoring via collection of salmon carcass tissues in the MFSR drainage.
BPA	200303600	CBFWA Monitor/Eval Program	Project 199902000 provides data being applied in the system wide monitoring and evaluation program.
Other: NOAA Fisheries	NFFP7100-5-0004	Interior Columbia R Basin Technical Recovery Team	Project 199902000 provides data to the TRT that is being applied in recovery planning.
BPA	200301700	Integrated Status/Effect Progr	Project 199902000 provides data to the Northwest Fisheries Science Center that is being applied to a host of recovery planning, status, and monitoring questions.
Other: PSC	NA77FP0455	Salmon spawning ground surveys	Project 199902000 fully compliments IDFG salmon redd counts in index areas within the MFSR.

Section 6. Biological objectives

Biological objectives	Full description	Associated subbasin plan	Strategy
Understand population dynamics & persistence	We propose continuation of research funded by BPA since 1999 to describe the spatial and temporal dynamics and factors influencing the persistence of wild Chinook salmon (Oncorhynchus tshawytscha). A multitude of regional program documents emphasize the need for long-term monitoring and analysis of the spatial structure of Snake River Chinook salmon. Effective salmon conservation and restoration strategies will ultimately depend on information collected at relevant spatial and temporal scales. Since 1995, we have georeferenced salmon redds in more than 800 km of the Middle Fork Salmon River drainage. The resulting continuous, spatially explicit, and temporally extensive dataset is unique within the Columbia River Basin. We are using this dataset to: perform a detailed analysis of population spatial structure, assess distributional shifts at various escapement levels, identify core areas, validate redd sampling designs, develop population monitoring programs, validate physical models to predict suitable spawning habitats, and integrate demographic and genetic information to assess fine-scale population structure. This research is also advancing our understanding of the relationship between landscape characteristics and the distribution, pattern, and persistence of Chinook salmon. Our results illustrate that salmon spawning distributions are dynamic in both space and time, particularly as population abundance changes. Cumulative redd distribution curves suggest spawning aggregates contract into core areas during periods of very low escapement and key core areas persist across years. Gradients exist in the strength of spatial and temporal structuring of redd distributions. Although we have focused on larger scale spatial questions addressing population persistence, this research has simultaneously provided data for intensively monitoring an ESA listed Chinook salmon stock as well as assessing population responses to various mitigation and restoration efforts. Eleven years of data have been gathered since project inception in 1995. By censusing redds in additonal years, we will build upon this unique and valuable dataset and continue key analyses of wild Chinook salmon temporal and spatial dynamics.	Salmon	Aquatic Objective 2A: Strategy 2A1. monitor abundance and productivity of wild stocks
Understand population dynamics & persistence	see above	Salmon	Aquatic Objective 2A: Strategy 2A2. identify where there is a lack of knowledge pertaining to the population size of anadromous species
Understand population dynamics & persistence	see above	Salmon	Aquatic Objective 2A: Strategy 2A7. evaluate effectiveness of ongoing programs
Understand population dynamics & persistence	see above	Salmon	Aquatic Objective 3C: Strategy 3C1. quantify population specific adult abundance
Understand population dynamics & persistence	see above	Salmon	Aquatic Objective 3C: Strategy 3C3. determine population productivity
Understand population dynamics & persistence	see above	Salmon	Aquatic Objective 1A: Strategy 1A2. develop historic run reconstruction data
Understand population dynamics & persistence	see above	Salmon	Objective 2A: improve understanding and definition of small populations

Section 7. Work elements (coming back to this)

Work element name	Work element title	Description	Start date	End date	Est budget
Produce Environmental Compliance Documentation	Produce environmental compliance documentation	This element covers work to acquire or prepare documents in support of obtaining environmental compliance from BPA. Past inquiries for Project #199902000 indicate it does not require any NEPA documents since we are not manipulating habitat or installing any structures. Two other types of permits are required for working with ESA listed salmon, however. First, permission is required from NOAA Fisheries to enable us to count redds from the air and ground. In the past NOAA has determined that our redd counts are acceptable as long as they are completed by trained personnel who avoid disturbing live fish. Second, we collaborate with the Idaho Department of Fish and Game (IDFG) to collect tissue salmon from salmon carcasses. We annually obtain permission from IDFG to collect tissue samples as approved members of the NOAA permit they are issued which allows IDFG and us to collect tissue samples.	1/3/2007	9/25/2009	$0
Biological objectives Understand population dynamics & persistence			Metrics
Manage and Administer Projects	Manage and Administer Projects	The principle investigator defines the most relevant and productive research areas, formulates research hypotheses, plans the research approach, and executes the studies. He is responsible for management of the budget, personnel, contracts, and equipment. Within his own agency, he manages research joint venture agreements with university cooperators, subcontracts to accomplish helicopter surveys and fixed-wing flights, and temporary employee contracts. He assumes full responsibility for bringing research to completion and for coping with problems encountered during the course of the work. He assumes full responsibility for completing BPA's programmatic requirements for development of annual SOW packages (SOW, Budget, Spending Plan, Work Schedule, etc.), tracking budget expenditures, and accrual reporting. He submits proposal and materials to secure funding for continuation of key aspects of the research program. This Element will be accomplished by RMRS permanent personnel at no cost to BPA.	1/3/2007	9/25/2009	$0
Biological objectives Understand population dynamics & persistence			Metrics
Produce/Submit Scientific Findings Report	Report research results	This element covers preparation of reports as well as manuscripts to be submitted to peer-reviewed fisheries journals. The process typically includes completion of specific facets of the research that enable us to test hypotheses with rigorous statistical analysis. After the initial preparation, manuscripts are sent to reviewers and revised, and the resulting manuscript is submitted to a journal. The journal sends the manuscript to additional reviewers who judge its scientific merit. The journal eventually returns the manuscript for revision and re-submission. We anticipate drafting and submitting several manuscripts for publication during this contract period.	1/3/2007	9/25/2009	$4,500
Biological objectives Understand population dynamics & persistence			Metrics
Analyze/Interpret Data	Determine the spatial structure and influence of environmental factors on Chinook salmon populations	This research will explore the effect of spatial habitat complexity on Chinook salmon population response. More specifically, the intent is to understand which environmental variables and spatial configurations promote population attributes that contribute to the maintenance of biodiversity. We propose two complementary analyses; a basin-scale, correlative analysis that links habitat attributes to biological responses and cross-wavelet analyses, which is capable of elucidating the spatial domains over which different environmental factors structure Chinook salmon populations. Deliverables: Basinscale models that predict measures of Chinook salmon population performance, including occurrence, extinction/colonization, and productivity (recruits/spawner) from environmental covariates. Deliverables will be shared with collaborators and developed as manuscripts for publication in peer-reviewed journals.	1/3/2007	9/25/2009	$0
Biological objectives Understand population dynamics & persistence			Metrics Focal Area: Tributary basin, Emerging issues Primary R, M, and E Type: Status and trend monitoring Primary R, M, and E Type: Critical uncertainties research
Collect/Generate/Validate Field and Lab Data	Advance understanding of fine-scale population structure via collection of genetic samples from Chinook salmon carcasses	In association with collaborators at the University of Nevada-Reno, we have initiated work to understand fine-scale genetic population structure in MFSR Chinook salmon (Neville et al., submitted). Because we already possess extensive data on redd distributions, the addition of genetic information from the MFSR offers a unique opportunity to integrate demographic, ecological, and genetic information In collaboration with IDFG and tribal co-managers, more than 1,500 tissue samples have been collected since 1998, with georeferencing of these samples initiated in 2002. Continued collection of these samples will allow the locations of progeny from 2002 and subsequent spawner years to be linked to parent locations. Direct estimates of dispersal distance may then be estimable. Deliverables: A more robust sample of wild Chinook salmon tissue samples with broader coverage of potential genetic material and the ability to look at spatial patterns in parent-progeny relationships.	1/3/2007	9/25/2009	$87,150
Biological objectives Understand population dynamics & persistence			Metrics Focal Area: Tributary basin, Emerging issues Primary R, M, and E Type: Status and trend monitoring Primary R, M, and E Type: Critical uncertainties research
Collect/Generate/Validate Field and Lab Data	Map the annual distribution of Chinook salmon redds	Returns of adult Chinook salmon are influenced by a variety of factors so redd counts will fluctuate annually. As a result of this variation, multiple years of redd counts resulting from several generations of fish are essential for assessing population performance. Spring and summer Chinook salmon that spawn in the Middle Fork Salmon River (MFSR) have a strong 3-ocean component (IDFG et al. 1990) so one generation typically encompasses 5-6 years. Our assumptions are that trained observers will be capable of distinguishing redds and that annual water conditions will be suitable for a complete inventory of all redds in the drainage. These assumptions have been verified during the eleven year history of this project. Because Chinook salmon have specific spawning area requirements, not all areas of the Middle Fork Salmon River (MFSR) have the potential to support spawning fish. We selected potential study areas by reviewing past redd survey records, reviewing anecdotal accounts of redds and spawners, personal communications with biologists familiar with the drainage, and by reviewing records of juvenile Chinook salmon occurrence. Existing information suggests a total of 12 tributaries and the mainstem MFSR have the potential to support populations of Chinook salmon. The primary survey method will be redd observations from low-level helicopter flights. For consistency, the principle investigator will conduct all aerial redd counts. We will fly all accessible stream reaches (about 800 km) after Chinook salmon have completed spawning and while redds are visible. Typically Chinook salmon have completed spawning by early September so the primary redd survey will be conducted during the second week in September. We will use results of IDFG index area surveys and our own research surveys to determine when spawning is completed. Redd locations will be specifically located with the aide of a GPS unit mounted on the helicopter. Some areas of the streams may not be adequately surveyed from a helicopter. Small streams with a large amount of riparian vegetation or shading may be unsuitable for aerial surveys. The observer will record those areas that were judged to be unsuitable for aerial surveys. We will re-survey those areas with ground-based counts. In 2003, we documented a segment of the Chinook salmon population that spawned in late September, approximately two weeks after our primary redd survey. Since the primary redd survey would fail to detect these redds, we will conduct a secondary survey to re-survey the lower 48 km of the mainstem MFSR and lower reaches of Big Creek up to Cave Cr. This secondary survey is necessary to account for the later spawning segment of the spawning run. Failure to survey all spawning segments will result in an incomplete database to describe redd locations and occupied patches. Deliverables: A complete annual count and continuous database of spatially located wild Chinook salmon redds across a large basin.	1/3/2007	9/25/2009	$186,024
Biological objectives Understand population dynamics & persistence			Metrics Focal Area: Tributary basin. Emerging issues Primary R, M, and E Type: Status and trend monitoring Primary R, M, and E Type: Critical uncertainties research

Section 8. Budgets

Itemized estimated budget

Item	Note	FY07	FY08	FY09
Personnel	Temporary salaries	$17,230	$18,091	$18,996
Fringe Benefits	For temporary salaries	$3,540	$3,717	$3,903
Supplies	Misc field gear	$300	$315	$330
Travel	Vehicle costs, fixed-wing flights, per diem	$8,500	$8,925	$9,371
Other	Contract for redd count helicopter flights	$51,750	$54,337	$57,054
Overhead	Estimated Rate of 17.8 %	$5,334	$5,600	$5,881
Other	Journal publishing costs	$1,500	$1,500	$1,500
Totals		$88,154	$92,485	$97,035

Total estimated FY 2007-2009 budgets

Total itemized budget:	$277,674
Total work element budget:	$277,674

Cost sharing

Funding source/org	Item or service provided	FY 07 est value ($)	FY 08 est value ($)	FY 09 est value ($)	Cash or in-kind?	Status
US Forest Service: Rocky Mt. Research Station	PI salary for 3 mos.	$28,404	$29,824	$31,315	Cash	Confirmed
US Forest Service: Rocky Mt. Research Station	Support Biologist salary for 5 mos.	$27,000	$28,350	$29,767	Cash	Confirmed
US Forest Service: Rocky Mt. Research Station	Support PostDoc salary for 3 mos.	$18,000	$18,900	$19,845	Cash	Confirmed
US Forest Service: Rocky Mt. Research Station	Office space and administrative support	$10,000	$10,500	$11,025	In-Kind	Confirmed
US Forest Service: Rocky Mt. Research Station	Computer hardware and software	$8,000	$8,400	$8,820	In-Kind	Confirmed
US Forest Service: Rocky Mt. Research Station	Survey-grade GPS unit and software	$13,000	$13,650	$14,332	In-Kind	Confirmed
Totals		$104,404	$109,624	$115,104

Section 9. Project future

FY 2010 estimated budget: $101,732
FY 2011 estimated budget: $101,732

Comments: Future estimates are based on a 5% per year increase in costs

Future O&M costs: Virtually all costs are allocated to operations: specifically for field work by temporary crews and costs for aerial redd surveys via helicopter.

Termination date:
Comments: As noted in earlier sections of this application, we began this research in 1995. The resulting continuous, spatially explicit, and temporally extensive dataset is unique within the Columbia River Basin. We are applying this robust dataset to: perform a detailed analysis of population spatial structure, assess distributional shifts at various escapement levels, identify core areas, validate redd sampling designs, develop population monitoring programs, and validate physical models to predict suitable spawning habitats. As a result, by censusing redds in additonal years (i.e. for at least another decade), we will build upon this unique and valuable dataset and continue key analyses of wild Chinook salmon temporal and spatial dynamics.

Final deliverables: This research has and will continue to result in publishable contributions to the fields of fish biology and management, ecology, population biology, and conservation biology. Information will be distributed via contract reports; peer-reviewed publications in professional journals; oral papers presented at professional meetings, technical conferences, and workshops; in response to information requests; and at informal meetings with state and federal agencies, tribes, and university scientists involved in management of Snake River chinook salmon. In addition, we will continue to build upon and share a very valuable and versatile dataset that is unique within the Columbia River drainage.

Section 10. Narrative and other documents

Reviews and recommendations

FY07 budget	FY08 budget	FY09 budget	Total budget	Type	Category	Recommendation
NPCC FINAL FUNDING RECOMMENDATIONS (Oct 23, 2006) [full Council recs]
$88,154	$92,485	$97,035	$277,674	Expense	Basinwide	Fund
NPCC DRAFT FUNDING RECOMMENDATIONS (Sep 15, 2006) [full Council recs]
$88,154	$88,154	$88,154	$0		ProvinceExpense
Comments: Also reviewed by MSRT
NPCC DRAFT FUNDING RECOMMENDATIONS (Sep 15, 2006) [full Council recs]
$88,154	$92,485	$97,035	$0		Basinwide

ISRP PRELIMINARY REVIEW (Jun 2, 2006)

Recommendation: Fundable (Qualified)

NPCC comments: The sponsors propose to continue aerial surveys of the Middle Fork Salmon River to fully census spring and summer Chinook salmon redds, collect tissue from spawning Chinook in remote areas to add to tissue collections used to produce genotypic data, and perform correlative and cross-wavelet analysis of the relationship between the location of Chinook salmon redds and landscape features. The quality of the work and publication trail is excellent. The data on the spatial and temporal variation in Chinook salmon redds is used in recovery planning by State, Federal, and Tribal agencies. The analysis of the relationship between environmental factors and spatial and temporal variation in redd (Chinook) abundance will add to the basic understanding of the persistence of Chinook salmon metapopulations. On this basis the ISRP believes this effort is justified. At this time, the ISRP also qualifies the support for this activity. Specifically, there is a merging of research (the analysis of relationships between habitat conditions and redd abundance, and comparisons of index versus full census of redd counts) and annual trend monitoring of adult Chinook abundance via redd counts. These two functions of this proposal need to be clearly identified, and the research component needs to be justified in the future based on its broader application to the Snake and/or Salmon River systems. The project’s publication record is excellent, but there is a lack of evidence that what is being learned is being translated into either modified sampling schemes, innovative analyses of persistence by TRTs, or modified land use management in other watersheds. There is a point of diminishing returns in any research effort. The level of effort for the trend monitoring and for the research components in the future needs to reflect data needs and the incorporation of the research products into management actions. There are still vast amounts of spatial information collected on Chinook redds (in relation to habitat factors) to analyze and publish, so it is difficult to justify collecting even more. Managers might be consulted to determine the aspects of the data they are particularly interested in. Finally, the next generation of space imagery may provide sufficient resolution to count redds, and this might be useful as a tool in sampling and monitoring salmon populations. This technology would greatly improve the efficiency and effectiveness of sampling and monitoring salmon populations.

ISRP FINAL REVIEW (Aug 31, 2006)

Recommendation: Fundable (Qualified)