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.
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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
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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
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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 Canyon yielded samples. The three sites included the Scud River slough, the Porcupine River slough, and Fowler’s slough. Finally, Christina Lake sockeye were collected and sampled over a two day period commencing on 20 September.
Sites within the Iskut sub-drainage were accessed via a Bell 206 Long Ranger helicopter, as were three sites within the Stikine River drainage. Christina Lake was accessed via a Beaver fixed wing aircraft. Gillnets were deployed to catch Christina Lake sockeye, while fishing poles (snagging) and some gaffing was deployed for all the other sites.
As in 2011, no Chinook samples were obtained from the Taku River. Attempts were made at Yeth Creek and the Sutlahine River (see Appendix 3 for details). No fish were available at Yeth Creek and the Sutlahine River excursion had to be aborted due to navigational challenges. As can be seen in Figure 3, the (preliminary) estimate of escapement is the lowest on record.
Taku sockeye samples from the Tatsatua River just upstream from Little Tatsamenie Lake were collected on September 11 and 12 using rod and reel. Samples from the Nahlin River were collected on August 30 and 31 using a beach seine; those from the Nakina River were collected opportunistically at a Chinook carcass weir in August. The Tatsatua River was accessed by float plane and boat; the Nahlin River by floatplane and helicopter, and the Nakina River by helicopter. Mainstem stocks appear to be genetically similar; hence it was recommended that sample
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collection take place on an opportunistic basis only - excursions to these locations were not undertaken.
Alsek Chinook samples were obtained from Goat (August 15 th ), Village (July 28 th ), and Stanley (August 16 th ) creeks and were accessed by road/foot. On August 8 th , a helicopter was used to survey the Kudwat and Tweedsmuir sites but high water and a low abundance of Chinook in the Alsek precluded the collection of samples. Angling was used to capture Alsek Chinook.
Alsek sockeye samples were obtained from Tweedsmuir (August 8 th ), Border Slough (September 18 th ), Kudwat Creek (September 18 th ), and the Tatshenshini River in the Bridge/Silver rivers area (September 18 th ). These sites were accessed by helicopter, and the capture method was angling. Additional samples were collected (angled) in the Goat and Datlasaka creek areas beginning in late August through to early October, which were accessed by road/foot.
4.0 Results and Discussion
A total of 26 Chinook salmon samples from four spawning locations, and 763 sockeye salmon samples from 14 spawning locations, were collected from all three drainages. Collections by species and drainage are presented in Tables 1-6.
Generally speaking, high water (with the exception of the Alsek River) did not affect sample collection, unlike in some previous years (most notably 2007). However, as noted Chinook sample collection on the Taku was hampered by poor escapements (Figure 3). Escapement of Taku River sockeye was very similar to the 2011 escapement, which was the highest in the previous five years (Figure 4). Escapements of Stikine River Chinook were below average (Figure 1), while those of Stikine River sockeye were near average (Figure 2). Escapement levels of Alsek sockeye, as indexed by the Klukshu River, favoured sample collection but was not the case for Chinook (Figures 5 and 6).
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A total of 7 samples were collected from one Stikine River Chinook salmon spawning location (Table 1).
Table 1. Chinook salmon samples collected in the Stikine River drainage 2007-2012.
Drainage: Stikine 2007-2012 Chinook Stock 2007 2008 2009 2010 2011 2012 Total Johnny Tashoots Creek 37 33 4 74 Shakes Creek 75 75 Tahltan River 83 89 172 Tuya River 6 4 9 19 Verrett Creek 90 150 240 Total 165 120 128 154 4 9 580
A total of 145 samples were collected from six Stikine River sockeye salmon spawning locations (Table 2).
Table 2. Sockeye salmon samples collected in the Stikine River drainage 2007-2012.
Drainage: Stikine 2007-2012 Sockeye Stock 2007 2008 2009 2010 2011 2012 Total Iskut mainstem at Bronson Slough 16 16 Iskut mainstem at Craig 22 11 33 Iskut mainstem at Hoodoo 11 11 Iskut mainstem at Verrett 63 16 19 9 21 128 Stikine mainstem at Porcupine 12 12 Stikine mainstem at Fowler 11 12 8 4 36 18 89 Stikine mainstem at Andy Smith 10 4 11 11 36 Stikine mainstem at Devil's Elbow 50 150 50 250 Chutine River 154 190 344 Chutine Lake 67 33 163 263 Christina Lake 14 36 34 84 Porcupine River 36 3 3 23 43 12 120 Scud River 90 48 61 23 60 23 305 Shakes Creek 30 30 Tuya River 208 208 Verrett River 41 36 37 114 Zappa 7 7 Total 197 701 433 180 394 145 2050
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No samples were collected from Taku River Chinook salmon spawning locations in 2012. Table 3 presents sample collections from 2007 - 2010.
Table 3. Chinook salmon samples collected in the Taku River drainage 2007-2010.
Drainage: Taku 2007-2010 Chinook Stock 2007 2008 2009 2010 Total Hackett River 35 168 203 Tatsatua River 273 273 Nakina River 18 36 54 Nahlin River 34 34 King Salmon River 2 13 2 17 Tseta Creek 80 172 252 Yeth Creek 41 6 9 56 Sutlahine River 4* 4 Total 362 338 6 187 893 * Juvenile samples.
A total of 321 samples were collected from three Taku River sockeye salmon spawning locations (Table 4).
Table 4. Sockeye salmon samples collected in the Taku River drainage 2007-2012.
Drainage: Taku 2007-2012 Sockeye Stock 2007 2008 2009 2010 2011 2012 Total Hackett River 16 64 133 213 Nahlin River 76 179 255 Little Tatsamenie Lake 60 140 200 Tulsequah River 18 53 199 270 Yellow Bluff 34 31 17 82 Tuskwa Creek 19 19 Tuskwa Slough 34 100 134 Tuskwa to Chunk 171 138 309 Shustahine Creek 95 112 207 Takwahoni / Sinwa 69 64 41 174 Yonakina 7 7 Nakina River 4 2 6 King Salmon Lake 144 65 209 Total 110 470 755 239 190 321 2085
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A total of 17 samples were collected from three Alsek River Chinook salmon spawning locations (Table 5).
Table 5. Chinook salmon samples collected in the Alsek River drainage 2007-2012.
Drainage: Alsek 2007-2012 Chinook Stock 2007 2008 2009 2010 2011 2012 Total Goat Creek 54 15 25 20 10 6 130 Takhanne 15 5 20 Low Fog 2 2 Stanley 17 12 3 32 Kudwat Creek 3 46 24 73 Village Creek 8 8 Tweedsmuir 5 1 6 Total 54 18 30 100 52 17 271
A total of 297 samples were collected from five Alsek River sockeye salmon spawning locations (Table 6).
Table 6. Sockeye salmon samples collected in the Alsek River drainage 2007-2012.
Drainage: Alsek 2007-2012 Sockeye Stock 2007 2008 2009 2010 2011 2012 Total Klukshu (early) 215 215 Blanchard 111 9 63 183 Border Slough 50 22 30 40 40 182 Detour Creek 4 4 Goat Creek 13 1 14 Kudwat Creek 45 0 20 50 30 25 170 Nesketahin 199 199 Tatshenshini at Stinky 40 40 Tatshenshini at Bridge/Silver 30 75 105 Tatshenshini at Kwatini 65 65 Tatshenshini at Datlasaka Creek 150 150 Tweedsmuir 51 0 66 12 20 7 156 Tats Lake 13 13 Tatshenshini at Sediment Creek 12 12 Vern Richie 64 38 95 22 219 Total 533 69 274 324 230 297 1727
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Figures 1-6 present escapement data for the Stikine, Taku and Alsek river systems. Note that all 2012 escapement figures are preliminary. The Klukshu River serves as an index for the Alsek River drainage.
70,000
60,000
50,000
40,000
30,000
Escapement 20,000
10,000
0 1996 1998 2000 2002 2004 2006 2008 2010 2012
Figure 1. Escapements of Chinook salmon to the Stikine River 1996-2012.
80000
70000
60000
50000
40000
30000 Escapement 20000
10000
0 1991 1993 1995 1997 1999 2001 2003 2005 2007 2009 2011
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.)
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120,000
100,000
80,000
60,000
40,000
20,000
0 1991 1993 1995 1997 1999 2001 2003 2005 2007 2009 2011
Figure 3. Escapements of Chinook salmon in the Taku River 1991-2012.
180,000
160,000
140,000
120,000
100,000
80,000
60,000
40,000
20,000
0 1991 1993 1995 1997 1999 2001 2003 2005 2007 2009 2011 Figure 4. Escapements of sockeye salmon in the Taku River 1991-2012.
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6,000
5,000
4,000
3,000
2,000
1,000
0 1991 1993 1995 1997 1999 2001 2003 2005 2007 2009 2011 Figure 5. Escapements of Chinook salmon to the Klukshu River 1991-2012.
35,000
30,000
25,000
20,000
15,000
10,000
5,000
0 1991 1993 1995 1997 1999 2001 2003 2005 2007 2009 2011
Figure 6. Escapements of sockeye salmon to the Klukshu River 1991-2012.
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4.1 Budget and Project Operations
As presented in Appendix 2, the expenditures of Northern Funds amounted to $56,369. The largest expenditure was in the travel category, and was primarily for helicopter/fixed wing charters. A summary of Fund expenditures in relation to budgeted amounts is as follows: a) Labour: $21,370 (proposed $19,600) b) Travel: $30,720 (proposed $42,000) c) Supplies: $4,168 (proposed $2,700) d) Shipping: $111 (proposed $300) e) Total Expenditures: $56,369 (proposed $64,600)
5.0 Conclusion
More progress was made towards achieving the 200 sample target for a number of baseline stocks in 2012. As of 2010, collections for the easily accessible and abundant stocks were complete. However, as noted in previous reports, due to limited accessibility and abundance sample collection for other stocks is extremely challenging and could take several years. Radio or acoustic tagging, if undertaken in the future, could assist in this endeavour (collection of tissue samples at time of application from fish subsequently tracked to spawning areas eliminates the need to sample there). However, radio and acoustic tagging programs are costly, and there are currently no plans or funding to undertake them.
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6.0 Acknowledgements
Individuals who assisted with sample collection include Sean Stark, Shawn McFarland, Mark McFarland, Andy Carlick, Johnny Sembsmoen, Jodie Mackenzie-Grieve, Michael Lake, Jassin Godard, Marty Mossop, and Clodie-Pascale Brasset-Villeneuve of DFO; Alex Joseph, Kyle Inkster, and Clayton Tashoots of the Tahltan First Nations; Mark Connor, Richard Erhardt and Angela Milani through the Taku River Tlingit First Nation; and Jeff Williams of ADF&G. Colleen Claggett, Annie Martin and Marnie Barteaux of DFO assisted with administration and accounting.
7.0 Literature Cited
Pacific Salmon Commission 2007. Joint Transboundary Technical Committee Report. TCTR 07- 02: Summary of the Transboundary Genetic Stock ID Workshop: January 18-19, 2007 .
Pacific Salmon Commission 2012. Joint Transboundary Technical Committee Report. TCTR (12)-1. Salmon management and enhancement plans for the Stikine, Taku and Alsek rivers, 2012.
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Appendix 1. Transboundary Technical Committee Sample Targets
Excerpt from: Pacific Salmon Commission 2012. Joint Transboundary Technical Committee Report. TCTR (12)-1. Salmon management and enhancement plans for the Stikine, Taku and Alsek rivers, 2012.
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Appendix Table 1. Proposed Genetic stock ID field projects, 2012. Project/Dates Function Priority Agency Stikine Chinook baseline samples (sample goal 200 per population) Farragut– need 65 M ADF&G/NMFS East or North Bradfield – need 164 H ADF&G/NMFS Harding – need 155 M ADF&G/NMFS Tahltan R. – need 0 DFO/ADF&G Chutine – need 200 M DFO Tuya – need 176 M DFO Beatty – need 200 M DFO/ADF&G Bear – need 200 H DFO Johnny Tashoots Creek – need 120 H DFO Craig - need 87 M DFO Katete - need 200 L DFO Stikine (above Chutine) - need 200 L DFO Stikine (below Chutine) - need 200 M DFO N. Arm (US section) - need 182 L ADF&G Goat (US section) - need 177 L ADF&G Alpine/Clear (US section) - need 100 L ADF&G Kikahe (US section) - need 177 L ADF&G
Stikine Chinook fishery samples Lower Stikine commercial fishery – target is 120 per week DFO Kakwan Pt tagging site – collect tissues from each fish ADF&G/DFO D-108 GN – 120/wk (directed); 80/wk (non-directed) ADF&G D-108 sport - Petersburg target sample is 450; Wrangell is 200 spread over season. ADG&G D-108 spring troll - Petersburg target sample is 100; Wrangell is 300 spread over season. ADF&G
Stikine sockeye baseline samples (sample goal 200 per population) Scud – need 0 DFO Porcupine – need 92 H DFO Tahltan R – need 200 L DFO Stikine mainstem – Andy Smith – need 164 H DFO Stikine mainstem – Fowler – need 129 H DFO Verrett River – need 123 H DFO Iskut – Verrett Slough – need 93 H DFO Iskut – Inhini Slough– need 200 H DFO Iskut - Bronson Slough/Bugleg– need 184 L DFO Iskut - Twin – need 200 L DFO Iskut – Craigson Slough - 157 H DFO Iskut – Craig – need 151 H DFO Chutine Lake – need 0 DFO Chutine R. – need 0 DFO Christina Lake (lake spawners) – need 137 H DFO Christina Lake (inlet spawners) – need 200 H DFO Katete – need 200 M DFO 13 | P a g e
Project/Dates Function Agency Stikine steelhead baseline samples Collect bulk samples opportunistically from inriver fisheries.
Shakes Sl (US section) – need 146 L ADF&G Andrew Cr (US section) – need 197 L ADF&G
Stikine sockeye fishery samples Lower Stikine commercial fishery – target is 120 per week DFO Lower Stikine test fishery – target is 120 per week DFO Upper Stikine test fishery – sample goal is 200. D-108 – sample goal for Petersburg and Wrangell ADF&G 520/wk/combined D-106 – sample goal for Sumner and Clarence is 520/wk/ea – ADF&G 106-30, 106-41
Taku Chinook baseline samples Yeth- need 144 H DFO King Salmon- need 183 H DFO Sloko- need 200 M DFO mainstem Taku- need 200 L DFO Sutlahine- need 196 L DFO Tseta- need 0
Taku Chinook fishery samples Taku assessment fishery – sample target is 120/wk DFO Taku commercial fishery – target is 120/wk DFO D-111 – sample target is 120/wk (directed); incidental non- ADF&G directed, n=80/wk Juneau area sport – sample target is 600 ADF&G
Taku sockeye baseline samples King Salmon - need 0 DFO/TRT Taku Mainstem (look alike) – Yellow Bluff – need 118 L DFO/ADF&G Tuskwa Creek- need 75 L DFO/ADF&G Takwahoni – need 26 L DFO/ADF&G Yonakina – need 193 L DFO/ADF&G Other Taku mainstem – opportunistic L DFO/ADF&G Hackett- need 6 L DFO Nahlin – 116 M DFO Nakina– need 193 M TRT Fish Cr (US section) – need 0 H ADF&G Yehring (US section) – need 19 H ADF&G Johnson (US section) – need 200 L ADF&G Samotua - need 200 L DFO
Taku steelhead baseline samples Collect bulk samples opportunistically from the fish wheels and
inriver fisheries.
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Appendix Table 1. (continued) Project/Dates Function Agency Taku sockeye fishery samples Taku Inriver commercial fishery – target is 125 per week DFO D-111 – sample target is up to 800 weekly ADF&G
Alsek Chinook baseline samples Goat Cr. – need 89 H DFO Lofog – need 198 L DFO mainstem Tatshenshini (middle, i.e. Kudwat) – need 127 H DFO mainstem Tatshenshini (lower) – need 200 H DFO mainstem Tatshenshini (upper) – need 200 H DFO mainstem Alsek – need 200 L DFO Tweedsmuir – need 195 DFO Situk (adjacent) – need 200 H ADF&G
Alsek sockeye baseline samples Klukshu River early – need 0 DFO Blanchard Lake- need 21 H DFO Takhanne R. – need 200 H DFO Goat Cr – need 188 M Mainstem Tatshenshini (upper) – need 22 H DFO Mainstem.Tatshenshini (lower) – DFO Tats Lake- need 187 M DFO Detour- need 196 L DFO Kudwat- need 58 M DFO Stinky- need 160 M DFO Alsek mainstem (Can) – need 15 H DFO Vern Ritchie – need 0 Tweedsmuir – need 51 M Alsek mainstem (US) - need 163 L ADF&G Border Slough – need 57 M Tanis (US section) - need 200 L ADF&G Basin (US section) - need 200 H ADF&G Ahrnklin R- need 10 L ADF&G Akwe- need 7 L ADF&G Italio- need 200 L ADF&G Lost- need 13 M ADF&G Dangerous- need 0 ADF&G
Alsek fishery samples Chinook test fishery – all fish ADF&G Dry Bay commercial – Chinook and sockeye – target is 800 ADF&G sockeye and 600 Chinook spread over run. ______
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Appendix Table 1. (continued)
GSI sampling protocol: 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 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 labeled vials. o Axillary appendages and opercular punches will be stored in ethanol (full strength) and each sample appropriately labeled (date, location ( GPS ), species, number of samples, fixative and volume thereof, collector, contact name, agency, phone number). o although it is recognized 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 last resort.
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Appendix 2. Financial Summary
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Project Budget Form
Name of Project: Transboundary Chinook and Sockeye Salmon DNA Stock ID Baseline Sample Collection 2012 - 2014.
PSC ELIGIBLE COSTS TOTAL OTHER N. FUND PROJECT FUNDING GRANT Labour BUDGET AMOUNT Wages & Salaries # of # of work hrs per rate per Total (In-kind & In-Kind PSC Actual Position crew days day hour cash + PSC Amount ) & Cash Amount Expenditures Variance project manager (DFO Bi-4) 1 2 7.5 42 632 632 biologist (DFO Bi-3) 1 7 7.5 39 2,048 2,048 Stikine technician (DFO Eg-5) 1 9 7.5 35 2,356 2,356 Alsek technician (DFO Eg-5) 1 9 7.5 35 2,356 2,356 Taku technician (DFO Eg-5) Financial officer (DFO As-2) 1 9 7.5 30 2,025 2,025 Sampling Technicans 2 15 7.5 32 7,200 7,200 Person Days (# of crew x work days) 51 sub total 16,617 16,617 - - -
Labour - Employer Costs ( percent of wages subtotal amount ) rate 12% sub total 1,994 1,994 -
# of # of work hrs per rate per Subcontractors & Consultants crew days day hour Stikine (rate includes boat) 2 14 10 40 11,200 11,200 4,941 6,259 Taku 2 14 10 30 8,400 8,400 16,429 (8,029)
Insurance if applicable rate 0% sub total 19,600 - 19,600 21,370 (1,770)
# of # of work hrs per Volunteer Labour crew days day Skilled Un-skilled Insurance if applicable rate 0% sub total
Total Labour Costs 38,211 18,611 19,600 21,370 (1,770)
Provide details in the space below Site / Project Costs (use an additional page if needed ) Travel (do not include to & fromaircraft work) charters, per diems, lodging 42,000 42,000 30,720 11,280 Small Tools & Equipment Site Supplies & Materials groceries, field supplies 2,700 2,700 4,168 (1,468) Equipment Rental Work & Safety Gear Repairs & Maintenace Permits Technical Monitoring Other site costs Total Site / Project Costs 44,700 - 44,700 34,887 9,813
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Project Budget Form (continued) Page 2 of 2
ELIGIBLE COSTS BUDGET OTHER CONTRIBUTION FUNDING FUNDING
Total (PSC + In- In-Kind PSC Actual Training (e.g Swiftwater, bear aware, electrofishing, etc). kind + cash) & Cash Amount Expenditures Variance # of Name of course crew # of days
Total Training Costs - - - - -
Overhead / Indirect Costs Office space; including utilities, etc. 800 800 Insurance Office supplies 100 100 Telephone & long Distance 500 500 Photocopies & printing Indirect/overhead costs (If the PSC contribution to Indirect costs exceeds 20% of the total PSC grant you will be required to submit back-up documentation justifying the expense). Other overhead costs Shipping 300 300 111 189 Total Overhead Costs 1,700 1,400 300 111 189
Provide details in the space below Capital Costs / Assets (use an additional page if needed ) Assets are things of value that have an initial cost of $250 or more and which can be readily misappropriated for personal use or gain or which are not, or will not be, fully consumed during the term of the project.
Total Capital Costs
Project Total Costs 84,611 20,011 64,600 56,369 8,231
Project Balance 8,231.08 Budget Summary Hold Back (not deposited) 6,460.00 (PSC + in-kind + cash) Refunded to PSC 1,771.08
Total Labour Costs 38,211 Total Site / Project Costs 44,700 Total Training Costs - Total Overhead Costs 1,700 Total Capital Costs - Project Total 84,611
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Appendix 3. Yeth Creek and Sutlahine River Report
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Yeth Creek and Sutlahine River Chinook Genetic Sampling Projects - 2012
- Final Report -
January, 2013
Prepared by: Richard Erhardt
For: Fisheries and Oceans Canada – Whitehorse and The Northern Fund of the Pacific Salmon Commission
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TABLE OF CONTENTS
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
LIST OF FIGURES:
Figure 1: General location of survey areas ...... 25 Figure 2: Total seining catch for Sutlahine River ...... 27 Figure 3: Average seine CPUE for Sutlahine River ...... 27 Figure 4: Specific sites of the Yeth Creek ground survey ...... 28 Figure 5: Sutlahine River aerial survey points of interest ...... 29 Figure 6: Sutlahine River seining sites ...... 30
LIST OF TABLES:
Table 1: Summary of Chinook genetic samples ...... 31 Table 2: GPS coordinates for observations – 2012 ...... 33 Table 3: Sutlahine River seine data - 2012 ...... 34
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LIST OF PHOTOS:
Photo 1: Upper Yeth Creek - 2012 ...... 35 Photo 2: Sutlahine River – landing/launch site ...... 35 Photo 3: Sutlahine R. – Site #1 ...... 36 Photo 4: Sutlahine R. – Site #2 ...... 36 Photo 5: Sutlahine R. – Site #3 and camp ...... 37 Photo 6: Sutlahine R. – Site #4 ...... 37 Photo 7: Sutlahine R. – Site #5 ...... 38 Photo 8: Sutlahine R. – Site #6 ...... 38 Photo 9: Sutlahine R. – Site #7 ...... 39 Photo 10: Sutlahine R. – Site #8 ...... 39
ACKNOWLEDGEMENTS
These projects were administered through DFO - Whitehorse as a Northern Fund program under the Pacific Salmon Commission. The projects included cooperation and participation from Taku River Tlingit Fisheries. In this regard it is appropriate to acknowledge the following individuals for their role in the projects:
Ian Boyce (from DFO) for assisting with project planning and providing overall administration and support; Mark Connor and Eric Telford (TRTFN) for providing in- kind field assistance during the projects; Angus Mackay and Victor Keong (NF/PSC) for coordination under the Northern Fund; Nicole Gordon (TRTFN) for assisting with project logistics and equipment; and Discovery Helicopters in Atlin for providing rotor wing air services.
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INTRODUCTION Rationale: The main goal of these projects was to collect Chinook salmon genetic samples within the Taku drainage from Yeth Creek and the Sutlahine River. This was part of a larger, ongoing initiative to continue the development of DNA baselines for Transboundary Chinook, sockeye and coho salmon in the Taku, Stikine and Alsek drainages.
Previously, there was little information upon which to determine specific stock compositions for Taku Chinook salmon. The development of genetic baselines will help to improve in-season stock specific management related to certain spawning targets and/or harvest shares. By improving data related to run timing, catches and relative abundance of specific stocks, this information can be utilized in the refinement of in- season management and the monitoring of specific stocks.
Project locations: General locations of the two survey areas are portrayed in Figure 1 below. Yeth Creek is approximately 100km SSW of the community of Atlin and flows into the Inklin River. It is influenced by several landslide sites, one of which has resulted in an area of steep rapids. Yeth Creek is known to be utilized by Chinook and coho salmon as well as Dolly Varden and steelhead.
The Sutlahine River drainage originates from the glaciated mountains of the Boundary Ranges and is therefore heavily influenced by glaciers and has no lake modification. It has quite extensive channel complexity and is known to be utilized by coho salmon and Dolly Varden. Anecdotal and distribution information indicates the Sutlahine River likely supports Chinook salmon but specific locations are not well documented. A telemetry study in 1991 identified the Inklin main-stem downstream of the Sutlahine confluence as a possible spawning area for Chinook.
Objectives: The objectives for Yeth Creek were to capture up to 200 adult post-spawn Chinook salmon. Sampling was to include: collection and preservation of duplicate axillary appendages for genetic analysis; taking scales for age; determining length/sex/spawning condition; and assessing for tags/clips/or secondary marks.
The objectives for Sutlahine River were to capture up to 200 Chinook salmon fry. Fish were to be sacrificed, divided into two equal parts and placed in separate containers for subsequent genetic analysis. Fork lengths would be recorded to the nearest millimeter on every second fish.
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Figure 1: General location of survey areas
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METHODS Yeth Creek: On August 1 st a crew of two field staff flew by rotor wing from Atlin to Yeth Creek and remained there until August 3rd . Selection of the landing site was based upon where most Chinook have been observed in previous years of field work. A temporary satellite camp was set up and subsequent ground surveys were conducted upstream and downstream from this location. The crew searched for post-spawn adult Chinook salmon to sample for ASL and genetics.
Sutlahine River: On September 1 st a crew of two field staff flew by rotor wing from Atlin to the Sutlahine River and remained there until September 3rd . An aerial survey was conducted to identify potential sampling sites (or others of interest) along with potential water hazards. Seining was conducted on the ground at various sites during the survey. Initially, access to seining sites was by floating the river with inflatable kayaks. However, due to safety considerations a helicopter was used during the latter part of the survey. A 5m long, small-mesh seine was utilized to try and capture Chinook fry. All juvenile fish obtained were counted, identified by species and then released.
RESULTS Yeth Creek: During the project the crew walked approximately 1km upstream and 2.5km downstream from the camp location. (Specific sites are portrayed on a map in Figure 4 and associated GPS coordinates are listed within Table 2 of Appendix 1.) Water clarity was considered good, however, only one adult Chinook was observed. No Chinook were captured or sampled.
Sutlahine River: Some sites of interest were observed during the initial aerial survey. The Sutlahine River contains some off-channel clear water wetland areas. In the central section of the river there is a canyon area where the river becomes a single / confined channel with steep banks and class 3 rapids with boulder gardens. The upper river area is highly braided with multiple channels and a wide floodplain. (These sites are portrayed on a map in Figure 5 and associated GPS coordinates are listed within Table 2 in Appendix 1.)
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A total of 32 seines were pulled at 3 sites above the canyon and 5 sites below. To note, negotiating the canyon area with kayaks was not considered to be safe at the time. Therefore, the remaining sites were accessed during the rotor wing flight out.
Seining efforts resulted in the capture of 36 dolly varden / bull trout (of which 1 was adult and the rest fry) and 19 coho fry. No Chinook fry were captured. See Figure 2 below. (Specific seining sites are portrayed on a map in Figure 6 and associated GPS coordinates are listed within Table 2 in Appendix 1.) The resulting average CPUE is shown in Figure 3 below with 1.1 fish/seine for dv/bt and 0.6 fish/seine for coho.
Figure 2: Total seining catch for Sutlahine River
0, 0%
19, 35% DV / BT
Coho
Chinook
36, 65%
Figure 3: Average seine CPUE for Sutlahine River
1.2 1.1
1.0
DV / BT 0.8
0.6 Coho 0.6 Chinook
0.4
0.2 Averageseine) CPUEfish (#/ 0.0 0.0 Fish Species
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Figure 4: Specific sites of the Yeth Creek ground survey
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Figure 5: Sutlahine River aerial survey points of interest
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Figure 6: Sutlahine River seining sites (Site #7 not shown / no GPS point taken)
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Discussion
A summary of the total genetic samples collected thus far for these 2 sites is depicted below in Table 1. (A total of 200 samples are recommended to complete the baseline for each location.)
Table 1: Summary of Chinook genetic samples
CH CH Total Total # of samples samples samples Remaining project collected collected collected to samples Site years previously in 2012 date needed Yeth Creek 5 56 0 56 144 Sutlahine River 2 4 0 4 196
Yeth Creek: The number of adult Taku Chinook available to sample in 2012 may have been somewhat affected by a relatively low return of total Taku Chinook salmon. The only year that sampling at Yeth Creek produced what could be considered an adequate result was in 2008 with 41 samples being collected. Spawning habitats in Yeth Creek are generally considered to be of good value and are probably being underutilized.
Prior to the field project, some consideration was given to potentially conducting the field survey from the lower Yeth Creek area near the confluence with Inklin River. ADF&G was asked to fly the lower portion of Yeth Creek during their Chinook aerial surveys. It was reported that in flying the bottom 4km of the creek only 6 Chinook were observed in one group about 0.5km above the mouth.
In 2010 attempts were made to capture Chinook fry during the surveys at either Yeth Creek. None were obtained, which could be attributed to a number of potential factors including: a low brood year return in 2009; very low in-stream Chinook fry densities; and possible early fry migration to downstream creek or main-stem Taku areas.
Sutlahine River: During Sutlahine River reconnaissance surveys in 2010, a total of 4 Chinook fry were captured during 10 seine sets at 3 different sites. Such was the impetus for the project in 2012. Unfortunately, no Chinook fry were captured this year despite a greater degree of effort. This could be attributed to a number of potential factors including: a low adult brood year return; very low in-stream Chinook fry densities; and possible early fry migration to downstream creek or main-stem Taku areas.
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Some coho fry were captured above the canyon area in 2012 (along with 1 Chinook in 2010). The canyon area is considered likely to be a velocity barrier for fry, however, not for adult salmon. It is possible that fry in the immediate lower reaches of the Sutlahine River could have moved up from elsewhere in the Taku system.
Recommendations
Yeth Creek: Some results from earlier project years (i.e. in 2008) indicated that adult Chinook genetic sampling in upper Yeth Creek was feasible but very dependent upon yearly instream abundance. However, overall the cost-effectiveness of this project is now considered very low. Conducting this project and only obtaining a few samples (or none at all) makes for a skewed cost/benefit ratio. From this perspective, it is recommended that the project not be continued in future years. As a potential alternative, opportunistic capture of adult Chinook at the lower end of Yeth Creek (just above the mouth where there is boat access) could be considered.
Sutlahine River: Given that no Chinook fry were captured in 2012 (and only 4 in 2010), the cost-effectiveness of this project is considered very low. Conducting this project and only obtaining a few samples (or none at all) makes for a skewed cost/benefit ratio. From this perspective, it is recommended that the project not be continued in future years.
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APPENDIX 1 – Tables
Table 2: GPS coordinates for observations – 2012
Survey Location Reference / Comments UTM type Yeth Creek Ground Camp location 08 640964E / 6533595N Yeth Creek Ground Upper extent of ground survey 08 641606E / 6533585N Yeth Creek Ground Lower extent of ground survey 08 639208E / 6533738N Location Reference / Comments UTM Sutlahine River Aerial Wetlands on both sides 08 627144E / 6499330N Sutlahine River Aerial Wetland on left bank side 08 624574E / 6497473N Sutlahine River Aerial Clear Tributary - left bank side 08 621344E / 6494577N Sutlahine River Aerial Confined rapids / rock gardens 08 619554E / 6491708N Sutlahine River Aerial Wetlands on both sides 08 618718E / 6490742N Sutlahine River Aerial Wetland on left bank side 08 616680E / 6488976N Sutlahine River Aerial Upstream extent of aerial flight 08 610546E / 6476595N Sutlahine River Ground Landing / Launch site 08 613753E / 6481564N Sutlahine River Ground Site #1 - seines 1-3 08 614077E / 6481959N Sutlahine River Ground Site #2 - seines 4-5 08 615182E / 6485523N Sutlahine River Ground Site #3 - seines 6-16 (Camp) 08 616849E / 6488861N Sutlahine River Ground Site #4 - seines 17-19 08 621024E / 6494131N Sutlahine River Ground Stie #5 - seines 20-22 08 621200E / 6494197N Sutlahine River Ground Site #6 - seines 23-25 08 626626E / 6497920N Sutlahine River Ground Site #7 -seines 26-27 not recorded Sutlahine River Ground Site #8 -seines 28-32 08 629954E / 6512310N
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Table 3: Sutlahine River seine data - 2012
General Date Habitat Site Seine Catch & CPUE (# fish/seine) Location (m/d/y) Type # # DV / BT Coho Chinook Upper Sutl. R. 09/01/2012 Side channel - turbid 1 1 0 0 0 Upper Sutl. R. 09/01/2012 Side channel - turbid 1 2 0 0 0 Upper Sutl. R. 09/01/2012 Side channel - turbid 1 3 0 0 0 Upper Sutl. R. 09/01/2012 Side channel - turbid 2 4 0 0 0 Upper Sutl. R. 09/01/2012 Side channel - turbid 2 5 0 0 0 Upper Sutl. R. 09/02/2012 Backwater - turbid 3 6 0 0 0 Upper Sutl. R. 09/02/2012 Backwater - clear 3 7 6 0 0 Upper Sutl. R. 09/02/2012 Side channel - turbid 3 8 0 0 0 Upper Sutl. R. 09/02/2012 Side channel - turbid 3 9 0 0 0 Upper Sutl. R. 09/02/2012 Side channel - turbid 3 10 0 0 0 Upper Sutl. R. 09/02/2012 Side channel - turbid 3 11 0 0 0 Upper Sutl. R. 09/02/2012 Entrapped pool - clear 3 12 21 3 0 Upper Sutl. R. 09/02/2012 Side channel - turbid 3 13 0 0 0 Upper Sutl. R. 09/02/2012 Side channel - turbid 3 14 0 0 0 Upper Sutl. R. 09/02/2012 Side channel - turbid 3 15 0 0 0 Upper Sutl. R. 09/02/2012 Side channel - turbid 3 16 0 0 0 Lower Sutl. R. 09/03/2012 Tributary - clear 4 17 0 0 0 Lower Sutl. R. 09/03/2012 Tributary - clear 4 18 0 0 0 Lower Sutl. R. 09/03/2012 Tributary - clear 4 19 0 2 0 Lower Sutl. R. 09/03/2012 Mainstem - mixed 5 20 0 0 0 Lower Sutl. R. 09/03/2012 Mainstem - mixed 5 21 0 0 0 Lower Sutl. R. 09/03/2012 Mainstem - mixed 5 22 0 0 0 Lower Sutl. R. 09/03/2012 Entrapped channel- clear 6 23 0 0 0 Lower Sutl. R. 09/03/2012 Entrapped channel- clear 6 24 0 0 0 Lower Sutl. R. 09/03/2012 Entrapped channel- clear 6 25 7 14 0 Lower Sutl. R. 09/03/2012 Side channel - turbid 7 26 0 0 0 Lower Sutl. R. 09/03/2012 Side channel - turbid 7 27 1 0 0 Lower Sutl. R. 09/03/2012 Side channel - turbid 8 28 1 0 0 Lower Sutl. R. 09/03/2012 Side channel - turbid 8 29 0 0 0 Lower Sutl. R. 09/03/2012 Side channel - turbid 8 30 0 0 0 Lower Sutl. R. 09/03/2012 Mainstem - turbid 8 31 0 0 0 Lower Sutl. R. 09/03/2012 Side channel - turbid 8 32 0 0 0 totals 36 19 0 ave. 1.1 0.6 0.0
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APPENDIX 2 - Photos
Photo 1: Upper Yeth Creek - 2012
Photo 2: Sutlahine River – landing/launch site
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Photo 3: Sutlahine R. – Site #1
Photo 4: Sutlahine R. – Site #2
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Photo 5: Sutlahine R. – Site #3 and camp
Photo 6: Sutlahine R. – Site #4
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Photo 7: Sutlahine R. – Site #5
Photo 8: Sutlahine R. – Site #6
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Photo 9: Sutlahine R. – Site #7
Photo 10: Sutlahine R. – Site #8
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