Category: Southeast Alaska

Coho and Chinook Early Saltwater Introduction Rearing

The Port Armstrong Hatchery (PAH), which is owned and operated by Armstrong-Keta, Inc. (AKI), has been producing cohos annually since 1988 and Chinooks since 2001. The expansion of facilities at PAH for the production of both species has been supported by a series of Chinook Mitigation grants, including the US/Canada Mitigation Fund, the Southeast Sustainable Salmon Fund and the Chinook Mitigation Fund and these projects have had full support of the Alaska Trollers Association (ATA) and various Southeast Alaska communities. The ATA has encouraged AKI to submit this current application for boosting coho and Chinook production by acquiring additional net pens and making use of our new early introduction saltwater techniques, thereby avoiding the burdensome costs of developing increased freshwater delivery to the hatchery and installing on-land rearing raceways. The management and staff of the Little Port Walter Research Station have been similarly encouraging of this plan, as they have decades of expertise in the propagation of various Chinook stocks for dissemination to production hatcheries throughout Southeast Alaska and are interested in increasing their contributions to the Alaska salmon industry via collaboration with the salmon enhancement hatcheries.

AKI’s goal is to maximize the return of adult coho and Chinook salmon to lower Chatham Strait in order to benefit the troll and sport fisheries. Common property contributions of Port Armstrong cohos have ranged from 42% to 67%, with averages over 50%, as measured by ADF&G coded-wire tag recoveries. PAH has experienced higher contribution rates in recent years and also in years when buyers have been stationed locally, which in turn increases the number of trollers in the area. There is currently a processor stationing a buying barge at Port Armstrong each summer to take advantage our PAH production as well as the wild salmon in the area.

Relaxed selection in salmon hatcheries

Hatchery fish are a significant component of fisheries subject to management under the Pacific Salmon Treaty (PST), and research on the costs and benefits of additional enhancement opportunities is a priority of the Northern Fund. The genetic risks of hatcheries, including potential loss of fitness to wild stocks, have been a long-standing concern (Waples and Do 1994, Naish et al. 2008, Grant et al. 2017). This study will investigate domestication in hatchery populations arising from relaxation of natural selection, a little-studied pathway for hatchery-induced changes. The results could have implications for the design of additional enhancement efforts as well as for practices at current enhancement facilities.

Chinook salmon genetic baseline update for Southeast Alaska and Canadian AABM fisheries

Southeast Alaska (SEAK) and Canadian aggregate abundance-based management (AABM) fisheries harvest Chinook salmon originating from throughout Southeast Alaska, Canada, and the southern U.S.  This diverse mixture of migrating stocks requires a comprehensive coastwide genetic baseline to accurately estimate the stock composition of harvests. The overall goal of this project is to use a phased approach to develop a coastwide Chinook salmon single nucleotide polymorphisms (SNPs) baseline to estimate the stock composition of harvests in SEAK and Canadian AABM fisheries.

The two biggest hurdles to assembling a coastwide Chinook salmon SNP baseline are: 1) no single agency has all of the baseline tissue or DNA samples necessary to adequately represent coastwide Chinook salmon production, and 2) different agencies do not all necessarily use the same SNP panels. To address these hurdles, we have worked with collaborators at the University of Washington (UW) to compile lists of SNP markers and populations screened by agency and university labs from Canada and the U.S.

Origins of Chinook Salmon Harvested in Southeast Alaska Fisheries

U.S. fisheries in Southeast Alaska (SEAK) harvest stocks of Chinook salmon bound for river systems in Alaska, Canada, and the continental U.S. Thus, fisheries in SEAK are managed under the purview of the Pacific Salmon Treaty (PST), in which an abundance-based management framework is used for Chinook fisheries. This requires management to have access to reliable information on stock-specific catch, escapement, and recruitment to forecast indices of abundance in PST fisheries.

This project aims to improve fishery management and provide independent estimates of stock composition in commercial troll and sport Chinook salmon fisheries in Southeast Alaska. Further, the project will take the analysis beyond basic estimation of stock composition by combining genetic assignment of individuals from selected stocks and fisheries with their associated age and mark information to provide additional information about Chinook salmon in SEAK fisheries for Chinook Technical Committee needs. This type of information has been used to measure the effectiveness of management actions in SEAK as well as to contribute to applications outside of SEAK (e.g. estimating age-specific terminal returns of stock groups and forecasting returning run sizes). This project is an integral part of a larger SEAK genetic stock identification program for Chinook salmon, which includes comprehensive coverage of major gillnet, troll, and sport fisheries.


Southeast Alaska Coastal Monitoring

Alaska stocks of pink (Oncorhynchus gorbuscha) and Chinook salmon (O. tshawytscha) spend large portions of their life histories in marine waters within the U.S. Exclusive Economic Zone (EEZ) and beyond the 200-mile EEZ of the coastal States. However, the strength of salmon year-classes is often set during the early overwintering phases of immatures or during the nearshore seaward migration phase of juveniles. Thus, the Alaska Fisheries Science Center (AFSC), Auke Bay Laboratories (ABL) initiated the Southeast Alaska Coastal Monitoring (SECM) project in 1997 to better understand the effects of climate and near-shore Ocean conditions on year-class strength of salmon and ecologically-related species. This research in turn provides improved information for resource management of salmon in the Pacific Salmon Treaty (PST) northern boundary. In particular SECM data provides a forecast index for northern southeast Alaska (SEAK) Transboundary River Chinook salmon returns, an annual pink salmon abundance forecast, and long term environmental and population data that are used by harvest managers in the PST northern boundary, which includes PST Chapter 2 pink salmon treaty issues in districts 101, 102, 103, and 104.


Chum Salmon Hatchery-Wild Interactions

The Alaska Department of Fish and Game in concert with Alaska Salmon Hatchery Operators and financial support from the salmon processing community has undertaken a long-term study concerning interactions of hatchery and natural origin salmon in natural systems. Samples have been collected from 4 chum salmon streams in Southeast Alaska (SEAK) for studies of potential relative difference in survival of offspring between hatchery and wild fish spawning in wild stock streams. This information will allow us to assess the ecological and genetic consequences of hatchery strays on fitness of wild spawners at the drainage scale. Evaluation of this scale is important because it will provide insight into how much these consequences can vary locally (and, potentially, why). Adult chum were sampled in 2013 and 2014 to establish genetic markers for identification of progeny in subsequent years. Otolith analysis reveals if a spawner is of hatchery or natural origin and tissue samples will be used to identify parentage of progeny beginning in 2017 and continuing in 2018 – 2023. Fish spawning in the 4 study streams will be similarly sampled for two complete generations; for chum salmon, sampling in each stream will occur over 11 years with the goal to sample F1 and F2 progeny from the first years of the project.


SEAK Commercial Chinook Port Sampling

Chinook salmon are harvested in commercial fisheries in Southeast Alaska (SEAK) waters east of Cape Suckling and north of Dixon Entrance. These fisheries harvest mixed stocks of Chinook salmon, including those originating from Alaska, British Columbia, and the Pacific Northwest. Significant numbers of both hatchery and wild stock Chinook salmon have coded-wire-tags (CWTs) inserted into their heads before they are released from hatcheries or as they migrate to sea. These fish are marked externally by removal of the adipose fin. CWTs are recovered by sampling programs intended to sample a minimum proportion of fishery catches and escapements. Analyses of CWT data provide estimates of fishery exploitation rates and other statistics employed for stock/fishery assessments and planning.

The Pacific Salmon Commission (PSC) technical committees rely upon selected groups of CWT hatchery and wild Chinook and coho as surrogates to estimate impacts on natural stocks. Recent trends in Pacific Northwest towards mass-marking of Chinook salmon smolts released from hatcheries in conjunction with increased hatchery production up to 150 million smolts annually have resulted in a large volume of adipose fin clipped Chinook salmon in SEAK fisheries that do not contain a CWT (No Tags).

The presence of No Tags exceeded 70% of the adipose-clipped fish sampled during the SEAK summer troll fishery in 2015. Alaska Department of Fish and Game (ADF&G) commercial fisheries port samplers have utilized visual sampling of these adipose clipped fish to recover CWTs for over three decades. The escalating presence of No Tags in SEAK fisheries has impacted CWT sample rates by statistical week and area. Although most SEAK Commercial Fisheries port samplers are using electronic tag detection wands to determine if a tag is actually present in the head of adipose fin clipped fish; the No Tag rate is so high that it requires two samplers per sampling event to be efficient at examining adipose clipped Chinook salmon harvested in the SEAK troll fisheries to determine if valid CWTs are present before CWT processing protocols are invoked.

In an effort to increase or maintain CWT sample rates and decrease shipping costs we propose to continue funding port sampling staff in the ports of Craig, Juneau, Pelican, Wrangell, Petersburg, Ketchikan, and Sitka. Southeast Alaska port samplers will use electronic tag detection wands to examine adipose clipped Chinook salmon harvested in the summer Southeast Alaska troll fisheries to determine if valid CWTs are present before CWT processing protocols are invoked. The heads of any positively identified tagged fish will be collected and the tags decoded by ADF&G staff. This will increase sampling rates by decreasing the amount of fish heads to be organised and shipped.

Genetic changes associated with in-basin supplementation of a population of Sockeye salmon

This joint project by NOAA and the University of Alaska Fairbanks evaluates the long term fitness of hatchery and wild sockeye salmon within a small watershed in Southeast Alaska. Concern over preserving wild stock fitness in enhancement project watersheds has been expressed in the case of both the Pacific Salmon Commission (PSC) Transboundary River Plans on the Taku and Stikine Rivers, and the PSC Northern Boundary Treaty Area of Southern Southeast Alaska (Hugh Smith and MacDonald Lakes). Measurement of the fitness effects and potential impact of such enhancement projects is needed to avoid long term undesirable effects on wild stocks. Initial genetic sampling and trial fish culture work in 2008, 2009, and 2010 showed potential for utilizing microsatellite and single nucleotide polymorphism (SNP) markers to assess the parentage of Auke Lake sockeye and to identify the progeny of wild and enhanced fish, and this allows the evaluation of the survival and introgression, if any, of the enhanced fish into the wild population. Furthermore, we have demonstrated the ability to sample very close to 100% of the adult sockeye entering the system and provided a low impact design for sampling, capturing, maturing and spawning small numbers for use as brood stock in this study. During the summers of 2011, 2012 and 2013, we captured and held adult sockeye in the Auke Creek Research hatchery, and conducted experimental matings in all three years. We have incubated, cultured and released approximately 50,000 juvenile sockeye into Auke Lake in the springs of 2012, 2013, and 2014. Complete sampling of upstream migrating adult sockeye has occurred from 2008 thru 2015 and smolt sub-sampling has occurred in May and June of those years as well.

Beginning in 2016, additional objectives were added to cover the sampling, marking and recovery of coho salmon at Auke Creek. Because of the operational efficiencies and base support this was accomplished with a small budget increment. Auke Creek is the longest and most complete coho salmon time series in Southeast Alaska, and is used as an indicator of marine survival, harvest and productivity for coho in the region.


Northern and Transboundary Sockeye Matched Scale-Tissue Sampling

Provisions of the 1999 Pacific Salmon Treaty (PST) specify abundance-based harvest sharing arrangements of Nass and Skeena River sockeye salmon returns for the U.S. and Canada. The United States is allowed to harvest a fixed percentage of the annual allowable harvest of Nass and Skeena sockeye stocks in Alaska’s District 101 gillnet and District 104 purse seine fisheries. Accurate estimates of the stock-specific catch in commercial fisheries of each nation are required to estimate the total return of these stocks and the percentage of each stock caught in treaty-limited fisheries.
Since 1982, scale pattern analysis (SPA), sometimes in conjunction with other biological markers, has been used to survey the weekly catch of Northern Boundary and Transboundary sockeye salmon stocks in Southeast Alaska fisheries. However, problems in accurately estimating stock-specific catches and total returns of sockeye salmon in the early years of the Pacific Salmon Treaty resulted in an extensive investigation, and it was concluded that improved stock identification techniques, such as genetic stock analysis, were needed to accurately evaluate effectiveness and improve, if possible, existing run reconstruction methods. Two blind tests of scale analysis vs. genetic analysis demonstrated that, while both techniques were accurate, the genetic analysis had higher precision and could also often identify many specific stocks, while scale analysis is limited to identifying a few stock-groups. Neither technique can identify enhanced fish where the brood stock came from wild stocks that are also present in the mixed stock fisheries; thus, otoliths are used in annual stock composition estimates and run reconstructions.
ADF&G proposes to continue collecting weekly otolith, tissue, and scale samples of sockeye from the Southeast Alaska commercial harvest in the District 101 gillnet and District 104 purse seine fisheries, among other districts and fisheries for projects that complement this program. Stock identification analysis using age composition, thermal mark presence, and new, more stock-discrete DNA techniques will be conducted at NOAA’s Auke Bay Laboratory. This project also complements the continuing work by DFO in Areas 3, 4 and 5.


Mixed Stock Analysis of Districts 106, 108 and 111 Sockeye

Sockeye runs from the Stikine and Taku rivers in Southeast Alaska are harvested in Canadian aboriginal, recreational, and commercial gillnet fisheries, and in US subsistence, personal use, and commercial gillnet fisheries. In the US, commercial gillnet fisheries in Districts 106 and 108 harvest wild stocks of sockeye salmon bound for Southeast Alaska island and mainland lakes, and for lakes and tributaries in the Stikine, Nass, and Skeena River drainages, while fisheries in District 111 harvest wild stocks of sockeye primarily bound for systems in the Taku River or to Crescent and Speel lakes in Alaska. Significant numbers of enhanced sockeye salmon bound for release sites in the Stikine and Taku rivers or to Snettisham Hatchery are also caught in these fisheries. Catches of Stikine and Taku river sockeye salmon stocks in Districts 106, 108 and 111 gillnet fisheries and the U.S. Stikine subsistence fishery are subject to a harvest sharing agreement outlined in Annex IV of the Pacific Salmon Treaty, in which the US is allowed 50% of the Total Allowable Catch of Stikine River and a variable proportion of Taku River sockeye salmon depending on the return of enhanced fish. Stock contribution estimates are critical to document compliance with the harvest sharing agreements, reconstruct runs of wild stocks, estimate the return of enhanced fish, forecast upcoming returns, and support sustainable management.
Genetic stock identification (GSI) is the preferred method for estimating stock contributions in fisheries in and near the Stikine and Taku rivers, and has been in use for transboundary management since 2011. GSI has improved estimates compared to past methods (scale pattern analysis), and is less logistically complex, less labor intensive, less expensive, more accurate, and delivers more timely results at a finer resolution.
This project has been conducting GSI analysis on sockeye salmon tissue samples collected from commercial gillnet fisheries in areas in and near the Stikine and Taku rivers in Southeast Alaska since 2012. The analysis will be focused on tissue samples collected in Districts 106, 108, and 111.