Use of Mainstem Habitats by Juvenile Pacific Lamprey (Lampetra tridentata) proposal 200718700

FY07-09 proposal 200718700

Section 1. Administrative

Proposal title	Use of Mainstem Habitats by Juvenile Pacific Lamprey (Lampetra tridentata)
Proposal ID	200718700
Organization	Pacific Northwest National Laboratory
Short description	Characterize the use of mainstem Columbia and lower Snake river habitats by juvenile Pacific lamprey and identify river reaches with high potential for restoration or expanded use.
Information transfer	Reports, journal articles, workshops, and presentations.
Proposal contact person or principal investigator

Contacts

Contact	Organization	Email
Form submitter
Dennis Dauble	Pacific Northwest National Laboratory	dd.dauble@pnl.gov
All assigned contacts
Dennis Dauble	Pacific Northwest National Laboratory	dd.dauble@pnl.gov
Robert Mueller	Pacific Northwest National Laboratory	robert.mueller@pnl.gov

Section 2. Locations

Province / subbasin: Mainstem/Systemwide / Systemwide

Latitude	Longitude	Waterbody	Description
		Columbia River	Hanford Reach
		Columbia River	Wanapum Dam Tailrace
		Snake River	Little Goose Dam Tailrace
		Snake River	Lower Granite Dam Tailrace

Section 3. Focal species

primary: Pacific Lamprey

Section 4. Past accomplishments

Year	Accomplishments

Section 5. Relationships to other projects

Funding source	Related ID	Related title	Relationship
BPA	199402600	Pacific Lamprey Population Sta	Collaboration
BPA	200201600	Lamprey Abundance	[Relationship field left blank]
BPA	200307100	Eval Lamprey In Willamette Rvr	[Relationship field left blank]
BPA	200303800	Eval Restor of Snake R Chinook	Collaboration

Section 6. Biological objectives

Biological objectives	Full description	Associated subbasin plan	Strategy
Reduce Negative Causes	Restore Pacific lamprey populations. Attain self-sustaining natural production of Pacific lamprey that provides for fishing opportunities at traditional locations.	Lower Middle Columbia	[Strategy left blank]
Reduce Negative Causes	Minimize stranding.	Lower Middle Columbia	[Strategy left blank]

Section 7. Work elements (coming back to this)

Work element name	Work element title	Description	Start date	End date	Est budget
Collect/Generate/Validate Field and Lab Data	Identify habitat types and develop sampling strategy for the Hanford Reach of the Columbia River	The objective of the first year’s activities will be to identify habitat use areas for juvenile lamprey. There is a plethora of physical habitat data available from studies of fall chinook salmon in the Hanford Reach (e.g., Geist and Dauble 1998; Mueller and Geist 1999; Geist et al 1999; Geist 2000; Nugent et al. 2001). Existing aerial photographs, bathymetry, shoreline slope, and substrate characteristics will be used to segregate habitat types into those areas with high, medium, and low potential for use by juvenile Pacific lamprey. We will first categorize the shoreline area as high, medium, and low probability of use for rearing. This will establish the total area to be sampled by habitat type. We will then use aerial photographs and bathymetric data to further segregate each 500 m segment into 50 m units for surveying by electroshocker. Each segment will be given a unique number number and surveyed selected randomly with respect to time (two seasons) and space using a random numbers table. The spatial dimensions will then be further divided into 50 m units to obtain greater homogeneity.	10/1/2006	3/1/2007	$34,778
Biological objectives Reduce Negative Causes			Metrics Focal Area: Systemwide Primary R, M, and E Type: Uncertainties Research
Collect/Generate/Validate Field and Lab Data	Conduct larval lamprey surveys in the Hanford Reach of the Columbia River	Near-shore habitats will be surveyed during two intervals for the first year of the study: March-April or prior to the spring discharge peak, and September-October or during low fall flows. We will establish shoreline transects in locations with highest potential for burrowing lamprey to be found and sample these areas weekly using backpack (<1 m depth) and boat operated (>1 m depth) electroshocker. All locations will be mapped using GPS and reference photographs taken. Physical habitat features (i.e., bottom type or substrate, shoreline configuration, bank slope, water velocity, presence/absence of vegetation, vegetation type, and water depth) will be measured and documented at each sample station. Water surface elevation (pool level) will be obtained from dam operation records and discharges estimated using a stage/discharge model (Geist et al 2000). The Hanford Reach contains about 350 km of shoreline habitat (includes islands). Based on what we know about mainstem habitat used by juvenile lamprey for rearing, we estimate ~20% of this area or 70 km might be high potential for rearing. Thus 14 km would be surveyed if we subsampled 20% of the habitat. We plan to sample a lower proportion of low and medium potential habitat (e.g., up to 10% of available). The Advanced backpack II shocker (ABP-2) will be the principal method used to sample larvae. Settings on the ABP-2 will be 3 pulses per second at 25% duty cycle to remove larvae from substrate, then 30 pulses per second at 25% duty cycle to stun and capture. A constant burst pulse train of 3:1 will be applied at 125 volts. Catch per unit effort will be given as shocking time and shoreline distance sampled. Deeper areas (>3 ft) will be sampled by using a boat electroshocker set up for deep-water sampling. These methodologies have been shown to be effective for collecting juvenile Pacific lamprey from substrate burrows in tributary streams (Torgersen and Close 2003). All captured lamprey will be collected and placed in aerated, water-filled holding tanks for examination. Numbers, life stage, and size of all fish will be recorded and fish released at the capture site.	3/1/2007	9/30/2007	$57,964
Biological objectives Reduce Negative Causes			Metrics Primary R, M, and E Type: Uncertainties Research Focal Area: Systemwide
Analyze/Interpret Data	Determine larval lamprey distribution, abundance, and habitat relationships	We will use an Analysis of Variance (ANOVA) technique to assess relationships between physical habitat features and relative abundance of juvenile lamprey. If our assumption regarding finding lamprey at many sites is not met, we will use logistic regression of the habitat variables on the presence or absence of lamprey. Primary factors of interest in the analyses include habitat type or area and sampling interval. The product of this effort will be a description of all rearing areas and relative abundance (fish/m2 and no/sec) of juvenile lamprey by habitat type in the Hanford Reach.	3/1/2007	9/30/2007	$31,880
Biological objectives Reduce Negative Causes			Metrics Focal Area: Systemwide Primary R, M, and E Type: Uncertainties Research
Other	Produce Pisces Status Report - Project quarterly reports	Describe activities and progress towards objectives	10/1/2006	9/30/2007	$1,449
Biological objectives Reduce Negative Causes			Metrics
Other	Produce Annual Report - Project annual report	Summarize and describe data	9/1/2007	9/30/2007	$11,593
Biological objectives Reduce Negative Causes			Metrics
Manage and Administer Projects	Project contract administration	Coordination, budget/milestone tracking, oversight	10/1/2006	9/30/2007	$7,246
Biological objectives Reduce Negative Causes			Metrics
Collect/Generate/Validate Field and Lab Data	Identify habitat types and develop sampling strategy for the tailrace of Lower Granite, Little Goose, and Wanapum dams	A similar sampling and characterization approach will be employed for the second year of the study. We have previously developed physical habitat descriptions of the tailrace environment downstream of the four lower Snake River dams (Dauble et al. 1999), including substrate size, velocity, depth, and channel slope. Additional descriptions of physical habitat for the Columbia River basin are available from Battelle and USGS (2000). These “data layers” will be used to delineate habitat types downstream of the hydroelectric projects. The habitat maps will be refined prior to sampling based on results of year 1 studies. We will first categorize the shoreline area as high, medium, and low probability of use for rearing. This will establish the total area to be sampled by habitat type. We will then use aerial photographs and bathymetric data to further segregate each 500 m segment into 50 m units for surveying by electroshocker. Each segment will be given a unique number number and surveyed selected randomly with respect to time (two seasons) and space using a random numbers table. The spatial dimensions will then be further divided into 50 m units to obtain greater homogeneity.	10/1/2007	3/1/2008	$39,901
Biological objectives Reduce Negative Causes			Metrics Focal Area: Systemwide Primary R, M, and E Type: Uncertainties Research
Collect/Generate/Validate Field and Lab Data	Conduct larval lamprey surveys in the tailrace of Lower Granite, Little Goose, and Wanapum dams	Habitat surveys will emphasize a ~5-10 km section downstream of each hydroelectric project (i.e., Lower Granite, Little Goose, and Wanapum dams). Based on our experience, these areas should have the highest potential for use because of velocity and substrate characteristics present. Limited sampling will be conducted in upper reservoir habitats, again based on results of Hanford Reach surveys. Periods of low project discharge will be emphasized. Where juvenile lamprey are found, we will characterize the physical habitat (i.e., project discharge or water surface elevation, channel slope, substrate composition, water velocity, and depth) and record biological data (fish length and development state). Each of the three tailrace areas contains about 30 km of shoreline habitat. The amount of high potential rearing habitat is expected to be somewhat higher for these areas, possibly up to 50% or 45 km total. This would yield a similar amount of habitat (i.e., 14 km) sampled as per the Hanford Reach. Other methodology will be as described for FY2007 in the Hanford Reach.	3/1/2008	9/30/2008	$66,502
Biological objectives Reduce Negative Causes			Metrics Focal Area: Systemwide Primary R, M, and E Type: Uncertainties Research
Analyze/Interpret Data	Determine larval lamprey distribution, abundance, and habitat relationships	We will use an Analysis of Variance (ANOVA) technique to assess relationships between physical habitat features and relative abundance of juvenile lamprey. If our assumption regarding finding lamprey at many sites is not met, we will use logistic regression of the habitat variables on the presence of absence of lamprey. Primary factors of interest in the analyses include habitat type or area and sampling interval. The product of this effort will be a description of all rearing areas and relative abundance (fish/m2 and no/sec) of juvenile lamprey by habitat type in each of the three tailrace areas.	3/1/2008	9/30/2008	$36,576
Biological objectives Reduce Negative Causes			Metrics Focal Area: Systemwide Primary R, M, and E Type: Uncertainties Research
Other	Produce Pisces Status Report - Project quarterly reports	Describe activities and progress towards objectives	10/1/2007	9/30/2008	$1,663
Biological objectives Reduce Negative Causes			Metrics
Other	Produce annual report - Project annual report	Summarize and describe data	9/1/2008	9/30/2008	$13,300
Biological objectives Reduce Negative Causes			Metrics
Other	Manage and Administer Projects- Project contract administration	Coordination, budget/milestone tracking, oversight	10/1/2007	9/30/2008	$8,313
Biological objectives Reduce Negative Causes			Metrics
Analyze/Interpret Data	Conduct landscape-level classification of larval lamprey distribution, abundance, and habitat relationships	The objective of the third year will be to document current mainstem habitats for juvenile lamprey and to identify areas with the highest potential for restoration, should operational scenarios for mainstem hydroelectric projects (e.g., reservoir drawdown or dam removal) be changed. We will use the information collected on habitat use in the Hanford Reach and tailrace areas to define other river segments with highest potential for lamprey spawning and rearing. We have previously used this general approach (Battelle and USGS 2000) to rank the importance of mainstem habitat features to fall chinook salmon at both the site-level (1-10 m) and channel/reach-level (10-1,000 m). We will use channel plan form, longitudinal gradient, geologic features (i.e., geologic formation, rock type, age, major lithology, and bedrock/unclassified classification for each 500 m segment), and discharge for the entire study area already digitized and available as GIS map sets. The first step in our analysis will be to categorize 500 m segments of the four study sites (i.e., Hanford Reach and three tailrace areas) into potential rearing habitat using criteria developed for fall chinook salmon spawning (Battelle and USGS 2000). In brief, the segments must contain >50% unconsolidated sediment, contain channel bars/islands, and have <0.0005 units in longitudinal gradient. This will result in an initial reach-level classification of potential habitats. We will then use data from both historic-and present-use locations (i.e., those habitat data collected during our surveys of 50 m units) to confirm that the coarse-level classification correctly identifies known rearing locations and adjust the classification scheme, if necessary. The sampling design for individual sampling units will be based on substrate size. This will allow us to "scale up" to the geologic features classification, but with some loss of precision since our measurement scales obviously differ at each level of classification. Our geomorphic approach will also identify historical reaches where juvenile lamprey habitats likely occurred in addition to the current distribution. All data will be incorporated into a habitat model for each river reach sampled. The product will be a geo-referenced summary of all known (i.e., historical and current) mainstem habitats for juvenile Pacific lamprey and a description of locations with the highest potential for restoration.	10/1/2008	9/30/2009	$84,028
Biological objectives Reduce Negative Causes			Metrics Focal Area: Systemwide Primary R, M, and E Type: Uncertainties Research
Other	Produce Pisces Status Report - Project quarterly reports	Describe activities and progress towards objectives	10/1/2008	9/30/2009	$1,000
Biological objectives Reduce Negative Causes			Metrics
Other	Produce annual report - Project annual report	Summarize and describe data	9/1/2009	9/30/2009	$10,003
Biological objectives Reduce Negative Causes			Metrics
Other	Manage and Administer Projects - Project contract administration	Coordination, budget/milestone tracking, oversight	10/1/2008	9/30/2009	$5,002
Biological objectives Reduce Negative Causes			Metrics

Section 8. Budgets

Itemized estimated budget

Item	Note	FY07	FY08	FY09
Personnel	Research Scientist/Eng: FY07 .36 FTE, FY08 .40 FTE, FY09 .35 FTE; Administrative: FY07 .01, FY08 .01, FY09 .03; Technicians: FY07 .23, FY08 .23, FY09 .05; Clerical: FY07 .01, FY08 .01, FY09 .02	$33,746	$38,438	$34,624
Fringe Benefits	[blank]	$11,676	$12,993	$11,253
Supplies	Misc. Supplies	$540	$843	$540
Travel	Travel to Pendleton, OR and Lewiston, ID	$827	$5,654	$1,305
Overhead	[blank]	$64,362	$73,434	$52,289
Other	Student	$33,759	$34,893	$22
Totals		$144,910	$166,255	$100,033

Total estimated FY 2007-2009 budgets

Total itemized budget:	$411,198
Total work element budget:	$411,198

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
Totals		$0	$0	$0

Section 9. Project future

FY 2010 estimated budget: $0
FY 2011 estimated budget: $0

Comments: [Outyear comment field left blank]

Future O&M costs: Not Applicable

Termination date:
Comments:

Final deliverables:

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]
$0	$0	$0	$0	Expense	Basinwide	Do Not Fund
NPCC DRAFT FUNDING RECOMMENDATIONS (Sep 15, 2006) [full Council recs]
$0	$0	$0	$0		Basinwide

ISRP PRELIMINARY REVIEW (Jun 2, 2006)

Recommendation: Fundable

NPCC comments: Short-term hydropower operations may have discernable effects on abundance and reproduction of mainstem spawning lamprey, as it does with fall Chinook salmon. This project will provide much needed information on juvenile lamprey use of Columbia and Snake River mainstem habitats that could be used to identify the areas with highest potential for restoration of mainstem lamprey populations, and reduce risks from stranding of juveniles from hydropower operations. The objectives are clear and measurable. The approach is innovative and has been used successfully by the sponsors to identify potential fall Chinook mainstem habitat. This proposal received a fundable recommendation from the ISRP during the last review cycle. The ISRP continues to believe that this work will be an important component of lamprey recovery within the Columbia Basin. Technical and scientific background: The proposal clearly explains the need for a study of habitat utilization by lamprey in the mainstem Columbia and Snake. This study would be the first of its kind to characterize mainstem lamprey habitat. The sponsors propose to identify options for restoration of mainstem habitat and to reduce risk of stranding due to changes in water surface elevation. The narrative refers to Wydoski and Whitney (1979). This publication was updated in 2003 and includes many lamprey references that appeared after the first edition was published (Wydoski and Whitney 2003. Inland Fishes of Washington. American Fisheries Society and University of Washington Press.) Rationale and significance to subbasin plans and regional programs: Lamprey restoration is identified as a priority in several subbasin plans. Relationships to other projects: The proposal complements other ongoing studies that primarily address use of tributary habitat. The proposal also addresses critical uncertainties identified by the Columbia Basin Pacific Lamprey technical work group. The sponsors say they will employ approaches and performance measures similar to other lamprey projects to ensure consistency among projects. This is a new project, so active collaboration with other projects has not yet been undertaken. Objectives: Objectives are clearly defined and outcomes are measurable. A reasonable timeline is specified. The Hanford Reach will be the focus of the first years work because a great deal is known about its habitat characteristics. In the following years the work will shift to the tailraces of three dams. Tasks (work elements) and methods: For the most part the methods are adequately explained. The sponsors should give some thought to the following questions: 1. Has it been demonstrated that boat electroshocking is an effective means for sampling juvenile lamprey? 2. The sponsors state that the product of objectives 1 and 2 will be a description of all rearing areas and relative abundance of lamprey in the entire reach. How will the data from selected sampling sites within a reach be extrapolated to the entire reach, or is this product to be generated by the landscape modeling? 3. The sponsors state that a habitat model will be developed for each reach. They need to provide more detail about the model. Is it a statistical model, a GIS-based model? Monitoring and evaluation: The project results will allow for determination of success or failure, and will be applicable to other lamprey projects. Facilities, equipment, and personnel: The Pacific Northwest National Lab is a well-known research facility and the personnel are highly qualified for this work. Information transfer: The proposal promises quarterly and annual reports, but there is no mention of long-term storage of data or meta-data. The sponsors have a good record of peer-reviewed publication. There is every reason to expect they will publish the results of this work. Benefit to fish and wildlife: The project should provide long-term benefits for lamprey populations. The sponsors propose to identify options for restoration of lamprey in mainstem areas. The sponsors are aware that electroshocking could be deleterious to juvenile salmon using shallow water habitats. Their highly trained technical staff should minimize danger to non-focal species. The work could lead to improvements in mainstem habitat that could benefit non-focal vertebrate and invertebrate species.

ISRP FINAL REVIEW (Aug 31, 2006)

Recommendation: Fundable