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FISH PASSAGE CENTER 847 NE 19th Avenue, #250, Portland, OR 97232 Phone: (503) 833-3900 Fax: (503) 232-1259

www.fpc.org/ e-mail us at fpcstaff@fpc.org

MEMORANDUM TO: David Leonhardt Portland District Corps of Engineers Ritchie Graves NOAA Fisheries

FROM: Michele DeHart, Fish Passage Center DATE: October 16, 2015 RE: Data Analysis Workshop regarding methods and analysis of PIT-tag recoveries on

East Sand Island held on October 13, 2015 Fish Passage Center staff attended the Data Analyses Workshop held on October 13, 2015, to discuss methods and analyses of PIT-tag recoveries on East Sand Island. FPC appreciates the opportunity to hear the presentations and participate in the discussions. The FPC is involved in the implementation and analyses of the regional Comparative Survival Study (CSS) and the Smolt Monitoring Program (SMP). It is likely that a significant number of the PIT tags recovered at East Sand Island originate from CSS and SMP PIT-tag mark groups. We offer the following comments for your consideration as you develop further methods, data and analyses of East Sand Island PIT-tag recoveries. Our summarized recommendations from the meeting discussion, for future analyses of East Sand Island PIT-tag recoveries, are listed below, followed by a detailed discussion of each point. In addition, for context, a background discussion describing our interest in the assessment of avian predation is included. These comments and recommendations for future analyses of East Sand Island PIT-tag recoveries are submitted for your consideration, as they apply to questions of predation impacts and management actions to benefit adult salmon and steelhead.

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• One of our greatest concerns is that the complete PIT-tag recovery data is not available to fishery management agencies or the public. The PIT-tag recovery data from East Sand Island should be available to the public. It is not possible to validate or recreate the various analysis conducted by private contractors and NOAA Fisheries if the tag recovery data is not available. The attached letters, sent to NOAA Fisheries requesting the tag recovery data, were sent by registered letter in July and August of 2014. To date the data has not been provided.

• The level of compensatory mortality occurring in the Columbia River Estuary related to avian predation should be analytically estimated. “Compensatory Mortality” is a well-established life-cycle dynamic in the body of scientific work regarding ecosystem management, in particular with regard to the assessment of the effect of predation on a population. The East Sand Island PIT-tag recoveries are particularly applicable to analysis of compensatory mortality. The simple approach of, ‘birds eat salmon and steelhead smolts therefore they should be eliminated,’ does not reflect a rigorous scientific approach or understanding of the complex ecosystem of the Columbia River Estuary, and therefore does not provide robust support for management actions. This simple approach can result in misguided management actions that have little or no benefit to salmon and steelhead.

• The CSS life-cycle analyses using several data sets including PIT tags and run reconstruction data indicate that route of passage through the hydrosystem during the juvenile out-migration affects estuary and first year ocean survival and subsequent adult returns. The East Sand Island PIT-tag recoveries should be analyzed in terms of route of passage through the mainstem hydrosystem including smolt transportation.

• Detection probability analysis of East Sand Island tag recoveries requires more thorough analyses and perhaps consideration of other analytical approaches.

• Acoustic tagged salmon and steelhead may be more subject to mortality and bird predation, due to the handling, marking, and surgical procedure (Brown et al. 2013). Further, size requirements for acoustic tagging may result in a tag group that does not represent the run-at-large. Acoustic tagging fish to evaluate bird predation has little management application because results are likely biased by their increased susceptibility to avian predation.

• The CSS life-cycle analyses (all data and analyses available to the public at www.fpc.org) indicate that the most important environmental variables related to smolt-to-adult return rate in CSS mark groups of steelhead, Chinook and sockeye, are water travel time, (flow) spill, and removable spillway weirs (only for steelhead). The environmental variables considered relative to bird predation rates in the estuary should primarily consider local variables collected during time periods when fish are exposed to predation. An abundance of data exists on conditions in the estuary through the CSMEP project, which could be evaluated relative to bird predation.

• Review of the bioenergetics-based bird predation estimates in the COE EIS and in the 2014 Biological Opinion reveals concerns regarding the calculation of those estimates. The population estimates utilized in the calculation of predation impacts were not developed for use as a population estimate in this manner. The use of these estimates as a “count” without confidence intervals could be problematic and the assumption that these estimates have count-like accuracy is unproven.

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The Comparative Survival Study (CSS) is a Chinook, steelhead, and sockeye life-cycle monitoring program utilizing PIT tags. All CSS data and analysis are available to the public at www.fpc.org as well as the publicly accessible PTAGIS database. The Independent Scientific Advisory Board (ISAB) of the Northwest Power Planning Council reviews the CSS Annual Reports each year, providing extensive comments regarding data, methods and analyses and recommendations for further analyses. Since 2010 and each subsequent year, the ISAB has recommended that the CSS collaborate with other researchers on ecosystem issues, other species, food webs, and habitats to explore patterns in migration and survival through the life-cycle. The ISAB continues to recommend that the CSS improve scientific collaboration between CSS and estuary-ocean researchers to address migration and survival of Columbia River salmon and steelhead in the estuary and ocean. In addition on August 27, 2013, in response to requests from states fish and wildlife managers, the FPC staff presented CSS life-cycle analyses to a joint meeting of the Upper Columbia Habitat Conservation Committees and the Priest Rapids Coordinating Committee. At that meeting members of the upper Columbia technical committees commented that avian predation should be incorporated into the CSS life-cycle analyses as an environmental variable affecting smolt-to-adult return rates. The FPC staff agreed to explore available data defining the avian predation metric to include in CSS life-cycle analyses. Many of the PIT-tag recoveries from East Sand Island are from CSS mark groups. The analysis of East Sand Island PIT-tag recoveries, in addition to other analysis completed in the avian predation projects, provides an opportunity to pursue ISAB CSS recommendations to examine estuary ocean ecosystems in the salmon life cycle. PIT tag recovery data should be available to the public It has not been possible to recreate analyses completed by private contractors or NOAA Fisheries, because PIT-tag recovery data is not available to the public. The attached letters requesting the specific details of recovery data on East Sand Island were sent on July 9, 2014, and August 4, 2014, following e-mail requests. To date that data has not been provided. It is impossible to define an appropriate predation metric, to incorporate into life-cycle modelling as recommended by the ISAB, if the data are not available. Quantitative estimation of the level of compensatory mortality is possible. The level of compensatory mortality must be evaluated related to the impact of cormorant predation on listed salmon and steelhead. We strongly disagree with the statement made by consultants to the COE at the meeting, doubting that assessment of compensatory mortality was possible. Methods for quantitatively estimating the levels of compensatory versus additive mortality have been available for nearly 40 years (Anderson and Burnham 1976), with further improvements to methods and hypotheses provided by Burnham and Anderson (1984) and Nichols et al. (1984). A quantitative assessment of compensatory mortality is possible given available data and is a key component in any ecological system in which predator control is being considered. Methods for analysis and evaluation of compensatory mortality are established in a large body of scientific

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work. Assessment of compensatory mortality is necessary to determine whether or not predator controls will actually result in an increase of the population in question. As an example of the complexity of this ecosystem, PIT-tag data indicate that 4.8% of the PIT-tagged northern pikeminnow (another species that preys upon steelhead and a species that is the target of a long standing predator elimination program in the Columbia River) that were released below Bonneville Dam in 2010 were deposited and detected on the East Sand Island cormorant colony. Assuming the 51% deposition rate for steelhead is applicable to pikeminnow, this would indicate that cormorants removed 9.4% of the northern pikeminnow below Bonneville Dam in 2010. Single-species management actions that do not account for compensatory shifts in predator-prey relationships may not result in the anticipated effects because of compensatory responses (Ellis-Felege et al. 2012). For these reasons, a quantitative evaluation of compensation is warranted, and available methods and data allow for this evaluation to occur. Ecosystem management actions to increase populations of any particular species should be based on robust scientific analyses to avoid wasting effort and funding resources on actions that have little or no benefit.

Route of passage through the mainstem hydrosystem related to avian predation The CSS life-cycle analyses indicate that route of passage through the hydrosystem is related to estuary and first year ocean survival (Haeseker et al. 2012, Tuomikoski et al. 2010). East Sand Island PIT-tag recovery data should be analyzed in terms of passage history of each tag, including those juveniles that are transported. Delayed and latent mortality has been documented for juvenile salmon migrating through the mainstem hydrosystem as well as those that are transported.

Environmental variables hypothesized to affect bird predation rates in the estuary should primarily consider local variables collected during time periods when fish are exposed to predation, and logical mechanisms should be identified. The present analyses as described utilize broad scale environmental variables (e.g., PDO, ENSO, NPGO) without supporting hypothesis regarding underlying mechanisms. Future analyses should include variables supported by existing lines of evidence or plausible mechanisms. As an example, route of passage through the mainstem hydrosystem is related to smolt-to-adult returns (Tuomikoski 2010). Analysis completed in the CSS project indicate that juvenile salmon and steelhead that pass through powerhouses have higher post-Bonneville mortality and lower smolt-to-adult return rates, when compared to non-powerhouse or spillway passage routes. The operative variable that results in lower proportions of the smolt population to avoid powerhouse passage is spill. Therefore spill is a variable with a defined mechanism, which should be included as an environmental variable in future analyses. In addition, CSS analyses indicate that water transit time, or flow is an important variable in juvenile salmon and steelhead travel time and survival. Since water transit time (flow) affects fish travel time, it follows that this variable could affect exposure time to predation. With any of the environmental variables considered, researchers should define appropriate spatial and temporal scales for collecting the data that align with the spatial and temporal scales of predation impacts. Failure to do so will often result in spurious correlations that falsely identify the underlying processes that influence predation rates.

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Detection probability on East Sand Island According to the researchers at the meeting, PIT tags were “haphazardly applied” on East Sand Island to estimate detection probability. We recognize that detection probability is a key element of analyses. However, the methods for estimating detection probabilities should be carefully reviewed. As discussed at the October 13 meeting, detection probability is based on a pre-nesting estimate and a post-nesting estimate. Detection probability may be more complex and variable than a simple, extrapolated, straight line between two points. In addition, the detection probability estimates rely on the assumption that hand-sown tags reflect the on-island deposition and detection process. We suggest that researchers consider other mark-recapture models that do not rely on hand-sown tags to evaluate the assumption that hand-sown tags are consistent with the on-island deposition and detection process. For example, Frechette et al. (2012) used a mark-recapture model to estimate detection probabilities without reliance on hand-sown tags.

Acoustic tagging should not be used to evaluate bird predation as was discussed at the meeting. Acoustic tagging should not be utilized to evaluate bird predation. In comparisons of PIT-tagged and acoustic-tagged fish of the same size, acoustic-tagged fish had a higher mortality rate due to the handling, marking, and surgical procedure (Brown et al. 2013). Acoustic tagging could make fish more vulnerable to bird predation. In addition, fish size requirements for acoustic tagging bias mark groups to larger fish, which again could make acoustic-tagged fish more vulnerable to bird predation, therefore limiting the applicability of results to the run-at-large and subsequent management decisions.

Consideration of the population estimate below Bonneville, confidence bounds on that population estimates and the resulting impact on estimated predation rates. The bioenergetics-based estimates of bird predation are based upon a population estimate of fish below Bonneville Dam. These are derived estimates and not counts, yet they are utilized as counts. There are no confidence intervals calculated for these population estimates. Although this concern does not apply specifically to the future analyses of East Sand Island PIT-tag recoveries, the magnitude of this assumption should be kept in mind in future assessments and comparisons should be made between the bioenergetics-based and PIT-based consumption estimates. If the two sets of estimates are not consistent, discrepancies should be investigated to determine why they are not similar.

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References Anderson, D.R., and K.P. Burnham. 1976. Population ecology of the mallard: VI. The effect of exploitation on survival. Resource Publication 128. U.S. Fish and Wildlife Service 66 pp. Brown, R.S., E.W. Oldenburg, A.G. Seaburg, K.V. Cook, J.R. Skalski, M.B. Eppard, and K.A. Deters. 2013. Survival of seaward-migrating PIT and acoustic-tagged juvenile Chinook salmon in the Snake and Columbia Rivers: an evaluation of length-specific tagging effects. Animal Biotelemetry 2013 1:8. Burnham, K.P., and D.R. Anderson. 1984. Tests of compensatory vs. additive hypotheses of mortality in mallards. Ecology 65:105–112. Ellis-Felege, S.N., Conroy, M.J., Palmer, W.E., and Carroll, J.P. 2012. Predator reduction results in compensatory shifts in losses of avian ground nests. Journal of Applied Ecology 06/2012; 49(3):661–669. Frechette, D., A.M.K. Osterback, S.A. Hayes, M.H. Bond, J.W. Moore, S.A. Shaffer, and J.T. Harvey. 2012. Assessing avian predation on juvenile salmonids using passive integrated transponder tag recoveries and mark-recapture methods. North American Journal of Fisheries Management 32:1237–1250. Haeseker, S.L., J.M. McCann, J.E. Tuomikoski, and B. Chockley. 2012. Assessing freshwater and marine environmental influences on life-stage-specific survival rates of Snake River spring/summer Chinook salmon and steelhead. Transactions of the American Fisheries Society, 141:1, 121–138. Nichols, J.D., M.J. Conroy, D.R. Anderson, and K.P. Burnham. 1984. Compensatory mortality in waterfowl populations: a review of the evidence and implication for research and management. Transactions of the North American Wildlife and Natural Resources Conference 49:535–554. Tuomikoski, J., J. McCann, T. Berggren, H. Schaller, P. Wilson, S. Haeseker, J. Fryer, C. Petrosky, E. Tinus, T. Dalton, and R. Elke. 2010. Comparative Survival Study (CSS) of PIT-tagged Spring/Summer Chinook and Summer Steelhead, 2010 Annual Report. Project No. 199602000. http://www.fpc.org/documents/CSS/2010%20CSS%20Annual%20Report--Final.pdf

g:\staff\document\2014 documents\2014 files\90-14.doc

FISH PASSAGE CENTER 847 NE 19th Ave. Suite 250, Portland, OR 97232

Phone: (503) 833-3900 Fax: (503) 232-1259 http://www.fpc.org

e-mail us at fpcstaff@fpc.org

July 9, 2014 Dr. Rich Zabel NMFS, NWFSC Fish Ecology Division 2725 Montlake Blvd., East Seattle, WA 98112

Dear Dr. Zabel:

The East Sand Island Cormorant DRAFT Environmental Impact Statement is presently in the public review process. That document references specific publications such as Evans et al. (2012) and Zamon et al. (2013) which include analyses of PIT tag recaptures on East Sand Island that differentiate between PIT tags consumed by Terns and PIT tags consumed by Cormorants for the East Sand Island tag detections. The designation of Cormorant-consumed tags versus Tern-consumed tags for the East Sand Island detections is not included in the public PTAGIS data system.

After telephone discussions with Cynthia Studebaker, US Army Corps of Engineers; Daniel Roby, Oregon State University; Alan Evans, Realtime Research; and Jen Zamon, NOAA Fisheries; the Fish Passage Center (FPC) was advised that the Tern versus Cormorant consumption designation was generated by NOAA Fisheries and, although the data had been previously published in the public domain and included in the DRAFT EIS, a formal data request was required. The FPC submitted an e-mail formal specific data request to NOAA Fisheries on June 23, 2014. Following is the text of that request sent to NOAA on June 23, 2014.

“On Mon, Jun 23, 2014 at 10:51 AM, Michele Dehart <mdehart@fpc.org> wrote:

Jen Zamon, Daniel Roby, Cynthia Studebaker, Allen Evans:

Following our previous telephone conversations regarding data and methods referenced in the recent COE East Sand Island, Cormorant predation DRAFT EIS, we were advised by Jen Zamion, NOAA, that we need to submit a formal data

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request in order to review the raw tag detection data from East Sand Island. We presently have all of the publically available PIT tag detection data for East Sand Island. Apparently the Tern versus Cormorant designation for these tags is not included in the public data base.

Therefore we are submitting this formal data request for the basis (methods for determination) of and the specific colony designation (e.g., cormorant vs. tern) for all salmonid (species 1, 2, 3, 4) (and each PIT tag) PIT-tags that have been recovered at East Sand Island in all years. In addition, it is our understanding that those tags that have been designated as having been recovered in the cormorant colony, there is a secondary designation as to what species of cormorant. We are requesting this secondary designation as well.

We understand that this data base was the foundation for a portion of the DRAFT EIS, and has been incorporated into peer reviewed publications; therefore we assume that it is readily available in final form and will not require any additional work or time to provide in response to this request. Thank you in advance, for your help on this matter.”

Today on July 9, 2014, the FPC was advised by Kurt Fresh, NOAA Fisheries, that the subject data request must be submitted via a formal written letter to Rich Zabel, NOAA Fisheries. Therefore, the purpose of this letter is to once again formally request the Tern versus Cormorant consumption designation for each PIT tag recovered on East Sand Island as described in our June 23 e-mail request. Analyses of these data have been previously published in Evans et al. (2012) and Zamon et al. (2013) as well as included in the Draft Cormorant EIS.

To restate this data request:

The Fish Passage Center is requesting the NOAA generated Tern, Cormorant and Brandt Cormorant designation for each salmonid PIT tag [(Species (PTAGIS codes) = 1 (chinook), 2 (coho), 3 (Steelhead), or 4 (sockeye)] recovered on East Sand Island.

Because the public review period on the East Sand Island Cormorant DRAFT EIS is quickly passing, and because NOAA requirements for a formal data request letter has caused some delay, hopefully the NOAA response to this request will be timely.

Best Regards,

Michele DeHart, Manager The Fish Passage Center