Tanana Chiefs Conference, Fisheries Program Collection of Teedraanjik Chinook Salmon Tissue Samples for the Yukon River DNA Baseline, 2016. Funded by the Yukon River Chinook Salmon Federal Fishery Disaster of 2012 Administered by the Pacific States Marine Fisheries Commission Tanana Chiefs Conference, Fisheries Program Fairbanks, Alaska April, 2017
2 The Tanana Chiefs Conference s Fisheries Program strives to continually build educational capacity and expertise in fisheries science and management throughout the TCC region, including the Yukon and Kuskokwim River drainages. Our goals are to utilize western science and traditional knowledge to enable sustainable fisheries, and to advocate for cultural and traditional fishing and hunting rights. We endeavor to accomplish these goals by partnering with other Tribal organizations, NGO s, and State and Federal agencies to better manage, protect, and preserve our fisheries resources. http://www.tananachiefs.org/sustainability/fish-wildlife/ Cover Photo: Chinook salmon spawning in Tetthajik Creek, 2015 (B. McKenna). Author: Brian McKenna Tanana Chiefs Conference Wildlife & Parks Department 201 First Avenue, Suite 300 Fairbanks, Alaska 99701 Phone: 907-452-8251 ext. 3318 Brian.mckenna@tananachiefs.org
3 Contents Abstract...4 Introduction...4 Objectives...5 Study Area and Methods...5 Results and Discussions...6 Recommendations...7 Acknowledgements...7 References...8 List of Figures Figure 1. Map illustrating the general location of the Teedraanjik as a tranboundary river originating in Yukon Territory and flowing into Alaska... 9 Figure 2. Map illustrating the location of Chinook salmon tissue samples collected in the Teedraanjik in 2015 and 2016... 10 List of Tables Table 1. Number of adult Chinook salmon tissue samples collected from the Teedraanjik in 2015 and 2016... 11 Table 2. GPS coordinates and number of samples per location for Chinook salmon tissue samples collected from the Teedraanjik in 2015 and 2016... 11 List of Appendices Appendix 1. 2015 Yukon River Panel s R&E Priorities for Chinook and Chum Salmon Genetic Baseline Tissue Collections... 12 Appendix 2. Approximate Location of Chinook Salmon Pulses by Date of the Pulse Past Sonar near Pilot Station Continuing up the Yukon River, 2016 (ADF&G Yukon Daily Update, July 20, 2016)... 13 Appendix 3. Non-lethal Bulk Sampling Finfish Tissues for DNA Analysis (ADF&G Gene Conservation Laboratory, Anchorage, Alaska)... 14
4 Abstract The purpose of this project was to continue to develop and refine genetic baselines for Yukon River Chinook salmon stocks through the collection and genetic analyses of tissue samples from representative spawning populations within the Yukon River. Continued development of the genetic baselines are necessary to obtain the most accurate allocations in mixed stock analysis, a critical tool for both inseason management and postseason evaluation of Yukon River salmon runs. This project consisted of the collection of Chinook salmon tissue samples from the Teedraanjik (Salmon Fork River). A total of 51 tissue samples were collected between July, 2015 and August 2016. These samples will be analyzed by the Alaska Department of Fish and Game s Gene Conservation Laboratory, and will be added to the existing ADF&G and DFO baselines. Samples were collected from live fish and recently deceased fish with red gills, preserved in ethyl alcohol, and shared among the three genetics laboratories (ADF&G, DFO, & USFWS) which conduct mixed stock analyses of Yukon River salmon runs. Introduction Management of Chinook salmon in the Yukon River requires differentiation between stocks originating from the various tributaries in both the United States and Canada. Genetic stock identification (GSI) is effectively used to distinguish country of origin and broad and fine scale stock groupings of Chinook salmon caught in the commercial and subsistence fisheries on the Yukon River (e.g. Decovich and Howard 2011). Fundamental to accurate GSI is the development of a comprehensive baseline genetic database which represents all spawning stocks that potentially contribute to the mixed stock fishery. Genetic baselines for Yukon River salmon populations were originally constructed using allozyme markers starting in the late 1980 s (e.g. Beacham et al. 1989). Single nucleotide polymorphisms (SNP) have been preferentially used as markers in the Chinook salmon baseline since 2004 (Smith et al. 2005), replacing the older allozyme database. At the beginning of the 2016 season, the Chinook baseline was comprised of 36 separate populations, and given adequate sample sizes, stocks can be identified to one of nine reporting groups (DeCovich and Howard 2011). Sampling salmon populations within the Yukon River drainage for genetic baselines is logistically difficult due to the large number of genetically discrete spawning populations distributed over a vast and remote region. Timing of spawning periods can be variable and flooding and turbidity during the spawning period may preclude sampling from occurring. The genetics sub-committee of the Yukon River Panel s (YRP) Joint Technical Committee (JTC) developed a prioritized list for baseline collections which is used as a guideline to direct sampling efforts each season (Appendix 1). High priority areas for sampling are those which could serve to further differentiate between genetically distinct groups and which contribute substantial numbers of spawners to Yukon River Chinook salmon returns overall. This genetics baseline sampling project has been funded by the YRP s Restoration and Enhancement (R&E) fund between 2007 and 2015, and has fostered partnerships between governmental agencies such as the Alaska Department of Fish and Game (ADF&G), the United States Fish and Wildlife Service (USFWS), and the Department of Fisheries and Oceans Canada (DFO), Alaska Native organizations such as the Tanana Chiefs Conference (TCC), Native Alaskan Tribes, and local resource users. Funding for the 2016 season was provided by the 2012 Yukon River Chinook Salmon Federal Fishery Disaster, and administered by the Pacific States Marine Fishery Council (PSMFC). Genetic baseline tissue samples have also been contributed by other projects and funding sources and samples may be collected opportunistically when another project is operating in an area from which samples are needed. Sampling may extend over a number of years to achieve sample sizes needed to distinguish among stock groups within an acceptable level of precision. Adding to and improving the Yukon River Chinook salmon
5 baseline is an ongoing process which will ultimately result in more accurate and timely management decisions. Objectives 1. Collect axillary process tissue samples appropriate for genetic (DNA) analyses from Chinook salmon spawning in the Teedraanjik (Salmon Fork River), and 2. Incorporate the sample genotypes into the existing genetic baselines. Study Area: The Teedraanjik, also known as the Salmon Fork of the Black River, is a tributary of the Draanjik (Black River) and Porcupine Rivers. The Teedraanjik is a trans-boundary river originating in the North Ogilvie Mountains of Yukon Territory, Canada (Yukon Ecoregions Working Group, 2004, Figure 1). It flows southwesterly crossing the international border just south of the Arctic Circle. West of the international boundary, the Teedraanjik crosses the Porcupine Plateau and flows westerly for roughly 74 river miles to the confluence with the Draanjik. Within Alaska, the Teedraanjik drains large portions of the Bureau of Land Management s (BLM) Eastern Interior Region, as well as the Yukon Flats National Wildlife Refuge (YFNWR). Methods: Location: The Teedraanjik was identified by the YRP s JTC as a high priority need for inclusion into the Chinook salmon genetic baseline. Prior to 2015 no samples had been collected in this system. In 2015, 50 samples were collected and spawning aggregation locations were identified and recorded (McKenna 2015). No samples were collected downstream of the Kevinjik confluence, and no surveys were conducted upriver of the international border. Therefore, in 2016 aerial surveys and sampling were scheduled to occur upriver of the Kevinjik confluence, and also to include the Canadian portion of the drainage. Timing: The Yukon River Daily Update distributed by the ADF&G provided the approximate location of Chinook salmon pulses by date based on run timing at the Pilot Station Sonar project operated by the ADF&G (Appendix 2). Chinook salmon in the Yukon River are estimated to travel approximately 40 river miles per day (mpd) while migrating to their spawning grounds. Chinook salmon spawning in the Teedraanjik depart the Yukon River and enter the Porcupine River near Fort Yukon, Alaska. From there they migrate 20 river miles up the Porcupine River before entering the Draanjik, another 138 river miles upriver on the Draanjik prior to entering the Teedraanjik, and finally another 74 river miles upriver on the Teedraanjik before reaching the international border. The Teedraanjik continues into the Yukon, Canada with its headwaters located in the Ogilvie Mountains. The last Chinook salmon pulse of the 2016 run was estimated to pass by Fort Yukon on July 19. Therefore, the majority of Chinook salmon were estimated to be present in the Teedraanjik approximately 6 days after passing Fort Yukon based on the distance to travel between Fort Yukon and the international border (n = 232 river miles) and the estimated travel time (n = 40 mpd).
6 Surveys were scheduled to occur between July 30 and August 3, 2016. To survey and sample the Teedraanjik, a Robinson R44 II helicopter was chartered through InFlight Helicopters. The survey crew based operations out of Circle, Alaska to save on flight time and fuel costs. Live fish, or recently deceased fish with red gills, were sampled on the spawning grounds. Collections were accomplished using rod and reel. Tissue samples were collected by clipping approximately a ½ - 1 portion of the pelvic axillary process of each individual fish according to the ADF&G Gene Conservation Laboratory s (GCL) protocol (Appendix 3). The sample size goal for Chinook salmon tissue samples in 2016 was to provide for a minimum of 50 samples, despite the need for 200 samples per tributary location to provide for optimal accuracy in identification of the baseline. Due to the sparseness of spawning salmon in these priority locations, samplers were instructed to collect as many samples as possible up to a maximum of 200 samples per location. Tissue samples were stored in bulk vials partially filled with anhydrous ethyl alcohol. The bulk vials were shipped to the ADF&G GCL. Samples were shared with the USFWS and with the DFO-Canada. The samples will be genotyped by the ADF&G GCL, and will be used to improve the existing genetic baseline. Results and Discussion The 2016 Chinook salmon escapement into the Teedraanjik occurred between late July and early August. Persistent high water during the peak and post peak of the Chinook salmon escapement into the Teedraanjik impeded sampling efforts in 2016. As such, a total of 1 Chinook salmon axillary process tissue sample was collected (Table 1). On July 29, the TCC field crew drove a TCC pick-up truck with the gear and supplies to Circle where they met with the InFlight Helicopter pilot. The field crew and the pilot based operations out of Circle for each day of surveying and sampling. July 30 was the first day of aerial surveys and sampling. On July 30, the survey crew flew from Circle to the confluence of the Kevinjik Creek and the Teedraanjik. The confluence was chosen as the starting point for surveys based on observations of spawning aggregations during the 2015 season (Figure 1). Aerial surveys occurred on the main stem of the Teedraanjik upriver of the Kevinjik confluence. The water level was at or above bank full, and no gravel bars were exposed. The high water limited our ability to visually observe Chinook salmon. Additionally, when salmon were observed, the high water level impeded our access and ability to catch the salmon for sampling. We also surveyed portions of the Kevinjik Creek, but high water levels continued to be problematic, so we returned to Circle. In consideration of the high water, and the costs associated with flight time and fuel consumption, we decided to cancel the next several days of scheduled surveys. We monitored the local weather and the NOAA river gauges in nearby systems. On August 2, an additional survey was completed of the headwaters within the Yukon Territory. The aerial survey began at the international border, and culminated in the headwaters. Again, the water levels were too high to visually observe or sample Chinook salmon. On August 3 the field crew departed Circle and returned to Fairbanks. While 200 samples are needed for optimal accuracy, the 50 samples collected in 2015, and the 1 sample collected in 2016 (Table 2), will be genotyped and added to the genetic baseline database. Additional samples are needed from this system to increase the accuracy and precision for this stock.
7 Recommendations: Additional Chinook salmon tissue samples are needed from numerous spawning tributaries throughout the Yukon River drainage in order to complete and further refine the Yukon River Chinook salmon genetic baseline. Several spawning tributaries in need of additional samples have already been identified by the Yukon River s Joint Technical Committee (Appendix 1). Several of these unique spawning populations are currently unrepresented, while other populations require additional samples to refine the accuracy and precision of mixed stock analysis and their associated genetic reporting groups. It is recommended that additional tissue samples be collected from each of the spawning populations identified by the JTC. Furthermore, each spawning population should continue to be sampled until 200 tissue samples have been collected per spawning population. It is recommended that future sampling crews incorporate dry suits, weight belts, and beach seines into their sampling toolbox. Spawning Chinook salmon are commonly found in deeper, swifter water making them inaccessible while wearing traditional chest waders. Additionally, Chinook salmon are often too far from shore to locate visually, thus not allowing for effective targeting while sampling with rod and reel. Lastly, utilizing a ladder or tower would increase the ability of visually locating spawning Chinook salmon by reducing surface glare that is increased at lower angles. Acknowledgements We would like to express our gratitude to the Pacific States Marine Fisheries Commission for administering the funding for this project through the 2012 Yukon River Chinook Salmon Federal Fishery Disaster Fund. We would like to acknowledge the Chalkyitsik Village Council and the Circle Tribal Council for their support for this project. We would also like to thank Dr. Brandon Hassett and Quintin Slade for their sampling and logistical support. We would like to thank the Canada Border Services Agency for authorizing this project to perform aerial surveys in the Yukon Territory. Finally, we also would like to thank the ADF&G GCL staff for their time in organizing sampling materials, intaking, processing, and analyzing samples.
8 References Beacham, T.D., C.N. Murray, and R.E. Withler. 1989. Age, morphology, and biochemical genetic variation of Yukon River Chinook salmon. Transactions of the American Fisheries Society, 118:1, 46-63. DeCovich, N.A., and K.G. Howard. 2011. Genetic stock identification of Chinook salmon harvest on the Yukon River 2010. Alaska Department of Fish and Game, Fishery Data Series No. 11-65, Anchroage. DeCovich, N., T. Dann, S. Rogers, H. Liller, L. Fox, J. Jasper, C. Habicht, and W. Templin. 2013. Chum salmon baseline based upon 96 SNPs. Alaska Department of Fish and Game, Regional Information Report series. Flannery, B.G., T.D. Beacham, R.R. Holder, E.J. Kretschmer, and J.K Wenburg. 2007. Stock structure and mixed stock analysis of Yukon River chum salmon. U.S. Fish and Wildlife Service, Alaska Fisheries Technical Report 97. McKenna, B., and DeCovich, N. 2015. Chinook Salmon Tissue Sample Collections for the Analysis of Yukon River DNA Baseline Samples in Alaska, 2015. Tanana Chiefs Conference, Wildlife and Parks Program, Technical Report for the Yukon River Panel Restoration and Enhancement Fund, Project Number CRE-78-14B, Fairbanks, Alaska. Smith, C.T, W.D. Templin, J.E. Seeb, and L.W. Seeb. 2005. Single nucleotide polymorphisms provide rapid and accurate estimates of the proportions of U.S. and Canadian Chinook salmon caught in Yukon River fisheries. North American Journal of Fisheries Management, 25:3, 944-953. Yukon Ecoregions Working Group, 2004. Yukon Coastal Plain. In: Ecoregions of the Yukon Territory: Biophysical properties of Yukon landscapes, C.A.S. Smith, J.C. Meikle and C.F. Roots (eds.), Agriculture and Agri-Food Canada, PARC Technical Bulletin No. 04-01, Summerland, British Columbia, p. 63-72. North Ogilvie Mountains, Taiga Cordillera Ecozone, Ecoregion 168, p. 123 130.
Figure 1 Map illustrating the general location of the Teedraanjik as a transboundary river originating in Yukon Territory and flowing into Alaska. 9
Figure 2 Map illustrating the location of Chinook salmon tissue samples collected in the Teedraanjik in 2015 and 2016. 10
11 Table 1 Chinook salmon tissue samples collected from the Teedraanjik in 2015 and 2016. Number of Samples Tributary (main) Branch Tributary 2015 2016 All years Porcupine River Teedraanjik (Salmon Fork) 50 1 51 Totals 50 1 51 Table 2 GPS coordinates (WGS84) and number of samples per location for Chinook salmon tissue samples collected from the Teedraanjik in 2015 and 2016. Totals Tributary Location No. Samples Latitude Longitude Method Year Teedraanjik 13 66.516660-141.966540 Aerial 2015 Teedraanjik 11, 1 66.469830-141.387540 Aerial 2015, 2016 Teedraanjik 4 66.513970-141.165130 Aerial 2015 Teedraanjik 1 66.517560-141.125320 Aerial 2015 Teedraanjik 3 66.527130-141.020980 Aerial 2015 Teedraanjik 6 66.516660-141.966540 Float 2015 Teedraanjik 1 66.474924-141.698844 Float 2015 Teedraanjik 1 66.470120-141.421110 Float 2015 Teedraanjik 4 66.470920-141.352250 Float 2015 Sub-Total Teedraanjik N = 45 Tetthajik Creek 6 66.509640-141.809621 Float 2015 Sub-Total Tetthajik Creek N = 6 Total Teedraanjik & Tetthajik Creek N = 51
12 Appendix 1 2015 R&E Priorities for Chinook and Chum Salmon Genetic Baseline Tissue Collections. 2015 R&E Priorities for adult Chinook genetic baseline tissue collections Country Main tributary Branch tributary US Kandik River Porcupine River Coleen River Black River Tanana River Chatanika River Canada Porcupine River Miner River Fishing Branch Pelly River Mainstem Population Ross River Stewart McQuesten River Janet River Teslin River Nisutlin River Morely River Jennings River White River Nisling River Tincup River Yukon Nordenskiold River North Big Salmon River 2015 R&E Priorities for adult Chum genetic baseline tissue collections Country Main tributary Branch tributary Comments US Porcupine River Big Salt River Tanana River Chena/Salcha Rivers Distinguish between summer and fall runs Canada Pelly River Stewart River White River Kluane Lake Yukon Klondike River Chandindu River Minto Tatchun Creek
Appendix 2 Approximate Location of Chinook Salmon Pulses by Date of the Pulse Past Sonar near Pilot Station Continuing up the Yukon River, 2016 (ADF&G Yukon Daily Update, July 20, 2016). 13
Appendix 3 Non-lethal Bulk Sampling Finfish Tissues for DNA Analysis (ADF&G Gene Conservation Laboratory, Anchorage, Alaska). 14