Draft salmonid Monitoring Program for the 2-Gates Project
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- Study 1. Chinook Salmon Parr
- Study 2. Chinook Salmon Smolts
- Study 3. Mokelumne River Juvenile Steelhead
- Study 4. Mokelumne River Kelt Steelhead
| ATTACHMENT C.4
Mokelumne Salmonid Monitoring Plan for 2-Gates 
DRAFT Salmonid Monitoring Program for the 2-Gates Project Brad Cavallo (Previous versions co-authored by Joe Merz and EBMUD Fisheries Biologists) The focus of the 2-Gates Project is reducing entrainment of delta smelt at the Central Valley Project (CVP) & State Water Project (SWP) water export facilities. However, expected changes in central and southern Delta hydrodynamic conditions require an evaluation of Project effects on the survival, and migration duration and migration routes of juvenile salmonids emigrating through the Delta. Researchers have for many years studied salmon survival within the Delta in relation to location, temperature, flow, exports (Kjelson and Brandes 1989, Baker et al. 1995, Brandes and McLain 2001, Newman and Rice 2002, Newman 2003, Newman 2008, Kimmerer 2008, Newman and Brandes 2009), and more recently to migration pathways using acoustic tags (Vogel 2008, Perry et al. 2009). Acoustic tags are particularly useful because they allow recaptures at any desired location along a migration route by positioning one or more receivers; providing refined characterizations of fish migration and response to conditions along the migration route. Using acoustic tags, Perry et al. (2009) quantified the route-specific survival for Sacramento River Chinook salmon and measured by the proportion of smolts migrating through alternative Delta routes. Their study demonstrated how concurrent estimation of smolt distribution and survival among different migration routes is critical to understand the effect of water management actions on juvenile salmon survival. The application of acoustic tag-based salmonid migration research and monitoring in the Delta is presently very dynamic, with several studies recently completed, but where results are not yet available. Acoustic tag studies include general assessments of migration duration and mortality from various parts of the watershed, detailed examination of migration behavior at key channel junctions in the northern Delta, and assessments of emigration success under the Vernalis Adaptive Management Plan (VAMP) program (San Joaquin River Group Authority (SJRGA) 2009). In addition to ongoing acoustic tagging studies, Cavallo et al. (2009 in review) have developed a dynamic simulation modeling tool, the Delta Passage Model (DPM), which simulates migration and survival of juvenile Chinook salmon through the Delta. In the DPM, salmon survival through the Delta is estimated as a function of reach-specific flows, reach-specific salmon behavior and reach-specific survival. Probabilistic fish behavior and survival values rely on empirical data and previously published analyses of acoustic and coded wire tagging-based studies. Previous (and future) acoustic tag studies on salmon entering the Delta from the Sacramento River and the San Joaquin River are extremely useful for understanding general patterns of survival and route selection for upstream channel splits (e.g. Sutter Slough, Delta Cross Channel (DCC), Head of Old River). However, tagged fish released well upstream of the Delta will, due to high mortality and bifurcating Delta channels, tend to leave relatively few tagged fish within the central and southern Delta, the areas most affected by the 2-Gates Project. Furthermore, sensitivity analysis using the DPM suggests factors influencing salmon behavior and mortality within tidally-driven reaches of the central Delta are key uncertainties. As might be expected, a DPM-based evaluation of the 2-Gates Project found very minimal effects for Chinook salmon smolts entering the Delta from the Sacramento River. In order to properly evaluate the 2-Gates Project and to resolve key uncertainties in our current understanding of Delta salmon migration, we have developed an experimental design that specifically targets areas of the Delta, salmonid life stages and salmonid species which are likely to be effected by the Project but are unlikely to be adequately addressed by other acoustic tagging studies (VAMP, U.S. Fish and Wildlife Service (USFWS) experiments, National Marine Fisheries Service (NMFS) BiOp requirements). It is important to note that acoustic technology (passive tracking) is not available for juvenile salmonids smaller than ~105 mm FL. Therefore, we will rely on an innovative Passive integrated transponder (PIT) tagging study, where recoveries are provided by fixed-location trawl (operated on outgoing tides) fitted with a PIT tag detection antenna. Take associated with operation of the PIT tag detection trawl should be minimal given that no fish will be caught or physically handled. Our study emphasizes the use of both hatchery and natural origin juvenile Chinook salmon for PIT or acoustic tagging, as parr or smolts, respectively. In addition, hatchery and natural origin steelhead smolts and kelts will be implanted with VEMCO acoustic tags and tracked during their out-migration. This approach will provide detailed information at each life stage for hatchery and natural origin fish which should be representative for salmonids entering the Delta from either the Sacramento, the Mokelumne or the San Joaquin River. Information provided by this study is essential to evaluation of the 2-Gates Project, but will also help improve other aspects of Delta resource management, including exports, inflow, predators, and habitat enhancements. Study 1. Chinook Salmon Parr To test the hypothesis that the Project operations have no significant effect on migration timing and survival for Chinook salmon parr emigrating we will PIT tag hatchery and natural parr (> 55 mm FL) over 10 weeks, between 15 February and 30 April. To reduce costs and coordinate with on-going monitoring and studies, we will coordinate with California Department of Fish and Game (DFG) hatchery staff to tag fish during regular operation periods. We will also coordinate the tagging of natural fish to coincide with East Bay Municipal Utility District Fisheries (EBMUD) monitoring operations. Beginning in February, or as soon as appropriately sized salmon parr become available, we will begin weekly releases of PIT tagged smolts at three Delta locations: 1) the North Fork of the Mokelumne River (near Walnut Grove), 2) the South Fork of the Mokelume River (near Walnut Grove), and 3) the main stem San Joaquin (SJ) River upstream of Turner Cut. To recover PIT tagged fish we will operate a fixed location, open-ended trawl net outfitted with a PIT tag antenna coil and detector unit (Figure 1) near Jersey Point on the SJ River. The net will be will deployed four days per week on each outgoing tide (day and night). Details on the design and use of the PIT tag detection trawl are available in Ledgerwood et al. (2004). 
Figure 1. Sketch illustrating the mounting of the PIT tag receiver at the end of an open codend. Adapted from Jorgensen et al. (2003). Fish implanted with PIT tags will come from Feather River Hatchery, Mokelumne Fish Hatchery or from natural origin fish trapped during normal EBMUD salmonid trapping operations. Fish will be acclimated on site for three days prior to release. More detailed analysis will be required to determine the appropriate number of PIT tagged fish to be released each week. However, recovery probabilities are expected to be low (<1%) and thus a large number of PIT tagged individuals will be necessary to have sufficient statistical power to detect Project effects. PIT tags are relatively inexpensive ($3 per tag) and thus availability of hatchery and wild salmon parr is likely to be the limiting factor. As a high, but reasonable goal, 1,000 PIT tagged fish could be tagged and released per release site per week (30,000 PIT tagged fish over 10 weeks). Some PIT tagged fish (200 per day) will also be necessary to estimate sampling efficiencies for the PIT detection trawl.
To test the hypothesis that the 2-Gate Barrier operation has no significant effect on Mokelumne River Chinook salmon smolt migration routes, migration timing, or survival during the spring period, we will acoustically tag and release hatchery and natural smolts (> 105 mm FL) between 15 March and 31 May. The study will be coordinated with efforts of the VAMP group Salmon Smolt Survival Investigations, DFG operation of the Mokelumne River Fish Hatchery, and EBMUD fisheries monitoring program for the lower Mokelumne River. Study 2a- We will surgically implant tags in ~1000 Chinook salmon smolts from the Mokelumne River Fish Hatchery or Feather River Hatchery during the March through May period. Surgical procedures will be performed at the hatchery generally following the methods of Ross and Kleiner (1982), Summerfelt and Smith (1990), and Adams et al. (1998). Prior to surgery, fish will be deprived of food for 48 hours. These fish will then anesthetized in a bath of tricaine methanesulfonate (MS-222) at a concentration of 50 mg per liter of water. During surgery, fish will be held in a V-shaped aluminum or plastic trough lined with moistened foam rubber. To maintain fish anesthesia during the procedure, we will use a dilute (20 mg/L) solution of MS-222 to continuously irrigate the gills via a tube inserted in the mouth. To maintain aseptic conditions, we will disinfect all instruments with providone iodine (Swanberg et al. 1999). Infection will be minimized by pipetting oxytetracycline (50 mg per kilogram of fish body weight) into the abdomen before closing the incision with sterile surgical sutures. To minimize behavioral effects of the tags, tag weight will not exceed 4% of fish weight with the goal of 2%. Hatchery fish will be held for 48 hours, and then transported to each of three release locations: 1) New Hope landing upstream of the Mokelumne River Delta forks, 2) the SJ River upstream of Turner Cut, and 3) the SJ River downstream of Venice Cut. We will seek to release 50 acoustically tagged fish per release site per week (1,000 acoustic tagged fish over 10 weeks) Study 2b- We will capture up to 280 natural Mokelumne River Chinook salmon (60 – 150 mm FL) by boat electrofishing during the EBMUD Mokelumne River winter fish community survey. These fish will be transported to the Mokelumne River Fish Hatchery for controlled rearing. All fish will be grown to beyond the 105 mm FL size limit by April. We will surgically implant acoustic tags in to these fish and release them in the same location following the methods above. Analysis – Fish will be tracked remotely via portable Receiver. Fixed receiver data will be downloaded following VAMP protocols. Descriptive summaries (average and Standard Deviation (SD) of detections) for Project operations will be used to compare results for migration routes and migration timing. Analysis of variance will be used to test for statistically significant differences in migration rate. Recapture and survival probability at Chipps Island will be estimated using Jolly-Seber multiple mark recapture statistical model. The basic hypotheses for this Study 2 regarding 2-Gates Project effects are: Ho1: The Project has no significant effect on the migration pathways used by Chinook salmon smolts entering the central Delta from the forks of the Mokleumne or the SJ River. Ho2: The Project has no significant effect on the migration timing of Chinook salmon smolts entering the central Delta from the forks of the Mokleumne or the SJ River. Ho3: The Project has no significant effect on migration success (as indicated by estimated survival to Chipps Island) of Chinook salmon smolts entering the central Delta from the forks of the Mokleumne or the SJ River. Ho4: Natural-origin Chinook salmon exhibit similar migration behavior and survival relative to their hatchery surrogates. Study 3. Mokelumne River Juvenile Steelhead To test the hypothesis that the Project has no significant effect on Mokelumne River steelhead smolt emigration route, emigration rate or survival during the late winter and spring period, we will acoustically tag natural and hatchery steelhead smolts between March and May. To reduce costs and collaborate with on-going monitoring and studies, we will coordinate with DFG hatchery staff to tag fish during regular operation periods. We will also coordinate the tagging of natural fish to coincide with EBMUD monitoring operations. Fixed receiver locations will be downloaded and maintained in coordination with the Central Valley Fish Tracking Consortium. Study 3a- We will surgically implant VEMCO tags in ~320 steelhead smolts from the Mokelumne River Fish Hatchery during the April through June period. Surgical procedures will be performed at the hatchery generally following the methods described previously in Study 2. Study 3b- We will capture up to 200 natural Mokelumne River steelhead smolts by rotary screw traps (RST). We will surgically implant VEMCO tags into these fish and release them downstream of the traps. Analysis – Fish will be tracked remotely via a VEMCO Portable Receiver. Fixed receiver data will be downloaded in collaboration with the Central Valley Fish Tracking Consortium and information stored in their database. Descriptive summaries (average and SD of detections) related to Project operations will be used to compare results for migration routes and migration timing. Analysis of variance will be used to test for statistically significant differences in migration rate. Recapture and survival probability at Chipps Island will be estimated using Jolly-Seber multiple mark recapture statistical model. The basic hypotheses for this Study 3 regarding 2-Gates Project effects are: Ho1: The Project will have no effect on migration routes taken by emigrating Mokelumne steelhead smolts. Ho2: The Project will have no effect on survival of emigrating Mokelumne steelhead smolts. Ho3: The Project will have no effect on migration rates of emigrating Mokelumne steelhead smolts. Ho4: Natural-origin steelhead follow similar migration routes and migration rates to their hatchery surrogates. Study 4. Mokelumne River Kelt Steelhead We will surgically implant VEMCO tags in < 60 hatchery and natural steelhead kelts from the Mokelumne River Fish Hatchery and/or EBMUD winter fish community surveys during the February through May period. Surgical procedures and release strategies will follow the same methods as described above. Analysis – Fish will be tracked remotely via a VEMCO Portable Receiver. Fixed receiver data will be downloaded in collaboration with the Central Valley Fish Tracking Consortium and information stored in their database. Descriptive summaries (average and SD of detections) for gate-in and gate-out results will be used to compare results for migration routes and migration timing. Analysis of variance will be used to test for statistically significant differences in migration rate. Recapture and survival probability at Chipps Island will be estimated using Jolly-Seber multiple mark recapture statistical model. The basic hypotheses for this Study 4 regarding 2-Gates Project effects are: Ho1: The Project will have no effect on migration routes taken by emigrating Mokelumne steelhead kelts. Ho2: The Project will have no effect on survival of emigrating Mokelumne steelhead kelts. Ho3: The Project will have no effect on migration rates of emigrating Mokelumne steelhead kelts. Ho4: Natural-origin steelhead kelts follow similar migration routes and migration rates to their hatchery surrogates. ReferencesAdams, N.S., D.W. Rondorf, S.D. Evans, J.E. Kelly, and R.W. Perry. 1998. Effects of surgically and gastrically implanted radio transmitters on swimming performance and predator avoidance of juvenile Chinook salmon (Oncorhynchus tshawytscha). Canadian Journal of Fisheries and Aquatic Sciences 55:781-787. Baker, P. F., Speed, T. P. & Ligon, F. K. (1995). Estimating the influence of temperature on the survival of Chinook salmon smolts migrating through the Sacramento-San Joaquin River Delta of California. Canadian Journal of Fisheries and Aquatic Sciences 52, 855-863. Brandes, P. and J. Mclain. 2001. Juvenile Chinook salmon abundance and distribution, and survival in the Sacramento-San Joaquin Estuary. In: Brown RL, editor. Fish Bulletin 179: Contributions to the biology of Central Valley Salmonids. Volume 2. Sacramento (CA): California Department of Natural Resources. Cavallo, B., P. Bergman, C. Turner and J. Merz. 2009. A simulation tool for exploring and understanding juvenile salmon migration through the Sacramento-San Joaquin Delta. In review. Kimmerer, W.J. 2008. Losses of Sacramento River Chinook Salmon and Delta Smelt to Entrainment in Water Diversions in the Sacramento-San Joaquin Delta. San Francisco Estuary and Watershed Science [online serial] 6 (2): Article 2. Available at: http://repositories.cdlib.org/jmie/sfews Ledgerwood, R. and others. 2004. A Surface Trawl to Detect Migrating Juvenile Salmonids Tagged with Passive Integrated Transponder Tags. North American Journal of Fisheries Management 24:440–451, 2004. Newman, K. 2001. Analysis of the probability of detecting flow and export effects on juvenile Chinook salmon survival in the VAMP experiments. Report to USFWS. Newman, K. B. 2003. Modeling paired release-recovery data in the presence of survival and capture heterogeneity with application to marked juvenile salmon. Statistical Modeling 3, 157-177. Newman, K. B. & Rice, J. 2002. Modeling the survival of Chinook salmon smolts outmigrating through the lower Sacramento River system. Journal of the American Statistical Association 97, 983-993. Newman, K. B. 2008. An evaluation of four Sacramento-San Joaquin River Delta juvenile salmon survival studies. Project number SCI-06-G06-299. U.S. Fish and Wildlife Service, Stockton, CA. http://www.science.calwater.ca.gov/pdf/psp/PSP_2004_final/PSP_CalFed_FWS _salmon_studies_final_033108.pdf (November 2008). Newman, K. B. and P.L. Brandes. 2009. Hierarchical modeling of juvenile Chinook salmon survival as a function of Sacramento-San Joaquin Delta water exports. In review. Jørgensen, T, J. T. Øvredal and I. Huse. 2003. A new pass-through PIT tag detection system for marine use. Aquatic telemetry: advances and applications. Proceedings of the Fifth Conference on Fish Telemetry held in Europe. Ustica, Italy, 9-13 June 2003. Rome, FAO/COISPA. 2005. 295p. Kimmerer, W. 2008. Losses of Sacramento River Chinook salmon and delta smelt to entrainment in water diversions in the Sacramento-San Joaquin Delta. San Francisco Estuary and Watershed Science. 6(2). Kjelson, M. and P. Brandes. 1989. The use of smolt survival estimates to quantify the effects of habitat changes on salmonid stocks in the Sacramento San-Joaquin Rivers, California. In Levings C. et al., editors. Proceedings of the National Workshop on Effects of Habitat Alteration on Salmonid Stocks. Canadian Special Publication of Fisheries and Aquatic Sciences 105, pages 100-115. Lichatowich, J. A. 1999. Salmon without rivers: a history of the Pacific salmon crisis. Island Press, Washington, D.C. Perry, R. W., P.L. Brandes, P.T. Sandstrom, A. Amman, B. MacFarlane, A.P. Klimley and J. R. Skalski. 2009. Estimating survival and migration route probabilities of juvenile Chinook salmon in the Sacramento–San Joaquin River Delta. North American Journal of Fisheries Management. In Press. Ross, M. J., and C.F. Kleiner. 1982. Shielded-needle technique for surgically implanting radio-frequency transmitters in fish. Progressive Fish Culturist 44:41-43. San Joaquin River Group Authority. 2009. 2008 Annual Technical Report on implementation and monitoring of the San Joaquin River Agreement and Vernalis Adaptive Management Plan, January 2009. Summerfelt, R.C., and L.S. Smith. 1990. Anesthesia, surgery, and related techniques. Pages 213-272 in C.B. Schreck and P.B. Moyle, editors. Methods for fish biology. American Fisheries Society, Bethesda, Maryland. Swanberg, T.R., D.A. Schmetterling, and D.H. McEvoy. 1999. Comparison of surgical staples and silk sutures for closing incisions in rainbow trout. North American Journal of Fisheries Management 19:215-218. Vogel, D. 2008. Pilot study to evaluate acoustic-tagged juvenile Chinook salmon smolt migration in the northern Sacramento-San Joaquin Delta, 2006-2007. California Department of Natural Resources Report. Directory: assets assets -> Northern territory of australia assets -> Number: caveat in the [Will/Will and Codicil/Estate of] assets -> Invitation for Bid Calact/mbta for Standard Floor and Low Floor Rural Duty Vehicles ifb no. 12-03 November 14, 2012 assets -> 12 Step Retreats For Everyone in Twelve Step Recovery Ratner Fellowship assets -> 12 Step Retreats For Everyone in Twelve Step Recovery Ratner Fellowship assets -> Sigaccess annual Report assets -> Central Government is expected to ask the seventh pay commission to consider merging 50% dearness allowance assets -> List of accessible executive records assets -> Emergency telephone numbers Call toll-free from anywhere in France Download 32.98 Kb. Share with your friends:
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