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Stikine, Taku, and Alsek River Sockeye and Chinook Salmon Baseline DNA Profiles 2012

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Stikine, Taku, and Alsek River Sockeye and Chinook Salmon Baseline DNA Profiles 2012 Stikine, Taku, and Alsek River Sockeye and Chinook Salmon Baseline DNA Profiles 2012. (A study supported by the Northern Fund under the auspices of the Pacific Salmon Commission) Ian Boyce, Peter Etherton, and Bill Waugh Fisheries and Oceans Canada Suite 100, 419 Range Road Whitehorse, Yukon Territory Y1A 3V1 Executive Summary A total of $64,600 was set aside from the Northern Fund to support the collection of tissue samples from Stikine, Taku and Alsek river Chinook and sockeye salmon stocks in 2012, in order to continue development of DNA baselines for genetic stock identification purposes. A total of 26 Chinook salmon samples were collected from four spawning locations, and a total of 763 sockeye salmon samples were collected from 14 spawning locations. Sample collection took place from July to October. The locations sampled were remote and generally not accessible by road except to limited departure points (Dease Lake, Telegraph Creek, Atlin, and Haines Junction). Therefore access was primarily via helicopter or float-plane. Fish capture methodology included weirs, angling, gaffing, gillnetting and seine netting for post-spawn fish. i | P a g e 1.0 INTRODUCTION 1 2.0 OBJECTIVES 1 3.0 METHODS 1 4.0 RESULTS AND DISCUSSION 3 4.1 BUDGET AND PROJECT OPERATIONS 10 5.0 CONCLUSION 10 6.0 ACKNOWLEDGEMENTS 11 7.0 LITERATURE CITED 11 List of Tables Table 1. Chinook salmon samples collected in the Stikine River drainage 2007-2012. 4 Table 2. Sockeye salmon samples collected in the Stikine River drainage 2007-2012. 4 Table 3. Chinook salmon samples collected in the Taku River drainage 2007-2010. 5 Table 4. Sockeye salmon samples collected in the Taku River drainage 2007-2012. 5 Table 5. Chinook salmon samples collected in the Alsek River drainage 2007-2012. 6 Table 6. Sockeye salmon samples collected in the Alsek River drainage 2007-2012. 6 List of Figures Figure 1. Escapements of Chinook salmon to the Stikine River 1996-2012. 7 Figure 2. Escapements of sockeye salmon to the Stikine River, 1991-2012. (Note: Based on post season run size calculations exclusive of the Tahltan Lake stock.) 7 Figure 3. Escapements of Chinook salmon in the Taku River 1991-2012. 8 Figure 4. Escapements of sockeye salmon in the Taku River 1991-2012. 8 Figure 5. Escapements of Chinook salmon to the Klukshu River 1991-2012. 9 Figure 6. Escapements of sockeye salmon to the Klukshu River 1991-2012. 9 ii | P a g e List of Appendices Appendix 1. Transboundary Technical Committee Sample Targets 12 Appendix 2. Financial Summary 17 Appendix 3. Yeth Creek and Sutlahine River Report 20 INTRODUCTION 24 Rationale: .............................................................................................................................. 24 Project locations:.................................................................................................................. 24 Objectives: ............................................................................................................................ 24 METHODS 26 Yeth Creek: .......................................................................................................................... 26 Sutlahine River: ................................................................................................................... 26 RESULTS 26 Yeth Creek: .......................................................................................................................... 26 Sutlahine River: ................................................................................................................... 26 DISCUSSION 31 Yeth Creek: .......................................................................................................................... 31 Sutlahine River: ................................................................................................................... 31 RECOMMENDATIONS 32 Yeth Creek: .......................................................................................................................... 32 Sutlahine River: ................................................................................................................... 32 APPENDIX 1 – TABLES 33 APPENDIX 2 - PHOTOS 35 iii | P a g e 1.0 Introduction Improved inseason stock specific management of Transboundary River (Stikine, Taku and Alsek rivers) Chinook and sockeye salmon is required to meet stock specific spawning goals and harvest shares. Inseason catch estimates based on historical stock compositions (from scale pattern analysis i.e. SPA) are often unreliable and tend to differ significantly from post season estimates. There is also a need to truth the present stock identification techniques used in the management of some Transboundary sockeye salmon; some of the current post season estimates based on historical methods do not correlate well with observations. The techniques presently used include SPA, egg diameter measurement, and brain parasite prevalence. Presently there are only limited tools to assist managers in stock specific management of Chinook salmon. Renewed Transboundary Chinook arrangements of the PST for the 2009-2018 period require the implementation of a genetic stock ID program which was to have commenced in 2009. The primary objective of this project is to continue to develop the DNA baseline for Transboundary Chinook and sockeye salmon in years 2012 to 2014. Once baselines are established/refined, they will be used in the analyses of mixed stock fisheries located in Canada and the U.S. to determine run timing and catches of specific Transboundary river Chinook and sockeye stocks, and eventually provide managers with reliable inseason stock specific catch numbers and run reconstructions where required to improve management regimes. They will also be used to monitor the relative abundance of specific spawning stocks and improve stock assessment databases to enable development/improvement of biologically based escapement goals. This is a continuation of sample collections that occurred from 2007-2011 under previously accepted Northern Fund projects. 2.0 Objectives Collection of tissue samples from Transboundary salmon stocks in order to establish a DNA baseline for identification of stocks in Canadian and U.S. fisheries. Appendix 1 lists stock-specific sample requirements as identified by the Transboundary Technical Committee. 3.0 Methods Tissue samples consisting of individual axillary appendage clips were taken from Transboundary Chinook and sockeye salmon stocks, for inclusion in microsatellite and/or single nucleotide polymorphism (SNP) baselines. Sampling was conducted according to the following protocol developed by the Transboundary Technical Committee (Pacific Salmon Commission 2007 - TCTR (07)-02): o the target sample size is 200 adult samples per population; o the preferred tissue to sample is the axillary appendage. For baseline samples, each fish will be sampled for two appendages; one to be sent to the DFO lab and the other to the ADF&G lab. For fishery samples, each fish will be sampled for one axillary appendage which will be shared if requested; o if opercular punches are taken, two punches will be taken from each fish, again one for each of the respective labs. To eliminate problems associated with potential 1 | P a g e delamination of punches in composite samples i.e. where punches from one population and/or location are all stored in one vial as has been the practice, opercular punches will now be stored in individual labelled vials; o Axillary appendages and opercular punches will be stored in ethanol (full strength) and each sample appropriately labelled (date, location, species, number of samples, fixative and volume thereof, collector, contact name, agency, phone number); o although it is recognised that there are potential efficiencies in terms of effort, time, storage, shipping and archiving associated with using scale samples for GSI, this should not be a tissue of choice when obtaining fishery or other samples for GSI (e.g. out of a tote) but may be used as a last resort. The locations sampled were remote and generally not accessible by road except to limited departure points (Dease Lake, Telegraph Creek, Atlin, and Haines Junction). Access to most spawning populations was via helicopter or float-plane, with a few accessible by river boat. Sample collection took place from July through October 2012. Fish capture methods included weirs, angling, gaffing, gillnetting, and seine netting for post-spawn fish. Stikine Chinook samples were obtained from the Tuya River spawning site on 26-29 July. Johnny Tashoots Creek was surveyed but no fish were available to sample. Access to the Tuya River was via a helicopter charter. Access to Johnny Tashoots Creek was by foot from the DFO facility located at Tahltan Lake. Stikine River sockeye samples were collected from six sites located principally in the lower reaches of the river, including the Iskut River sub-drainage. Verrett River samples were collected on 22 September (attempts were made to collect Verrett River sockeye in early August; however, high water and the paucity of fish resulted in zero samples. Sockeye DNA samples were collected 22 September from a site near the Verrett River locally known as Verrett Sloughs (this site is not connected with the Verrett River, but is located only 4 km west of it.) Other potential spawning sites within the Iskut sub-drainage were explored for samples, but no fish was observed. Three sites within the Stikine River drainage above the Canada and US border and below Little
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