Clues to Chinook Salmon Nearshore Migration in Southeast Alaska from Estimates of Stock Composition in Troll Harvests William D

Clues to Chinook salmon nearshore migration in Southeast Alaska from estimates of stock composition in troll harvests William D. Templin and Lisa W. Seeb Gene Conservation Laboratory, Alaska Department of Fish and Game, 333 Raspberry Road, Anchorage, Alaska 99518, USA

Introduction Collections in the Coastwide Baseline The Southeast Alaska troll fishery harvests Chinook salmon originating from Alaska, British Columbia, and the Pacific Northwest. Management of the chinook salmon harvest in South- east Alaska depends, in part, on information from coded-wire tag recoveries, a marker applied only to a subset of populations (mainly hatcheries). Genetic stock identification can provide stock composition information unavailable from the tag data. This method has been used extensively to estimate the composition of mixed-stock fisheries for Chinook salmon in the Pacific Northwest and is possible because standardized baseline data for allozyme loci are available from throughout the species range. Since 1999, the Alaska Department of Fish and Game has used allozymes to provide independent estimates of the stock composition of the harvest throughout the year in Southeast Alaska troll fisheries. Legal-sized (longer than 71 cm) Chinook salmon were sampled from landings during the summer (July to September), winter (October to April) and spring (May to June) troll fisheries and from sublegal-sized Chinook incidentally caught during the summer fishery. Estimates indicate that the abun- dance of many stocks of Chinook salmon varies seasonally and by age class.

Southeast Alaska Troll Fishery The troll fishery in Southeast Alaska occurs in State and Federal Exclusive Economic Zone waters east of Cape Alaska NPAFC Document 440 Yakutat 20 km Suckling and north of Dixon Entrance. Comprehensive Allozyme Database Discriminates Chinook Salmon Around the Pacific Rim. The fishery is in part managed by a D. Teel, P. Crane, C. Guthrie, A. Marshall, D. Van Doornik, W. Templin, N. Varnavskaya, and L. quota established by the Pacific Salmon Seeb. October 1999 Commission (PSC). The quota is Elfin Cove Northern dependent on the projected abundance Pelican Inside of Chinook salmon forecasted by the Chinook Technical Committee (CTC) of Northern Outside the PSC using the Chinook salmon Temporal Changes in Abundance Sitka Southern model which integrates data on catch, The contribution of major stock groups Petersburg Outside escapement, coded-wire tag recovery, to the troll fishery changes through Annual Variation in Contribution of Selected Stocks Port Alexander Number of Relative and recruitment information. Genetic time, an indication of the migration data are now being used to estimate the timing of these stocks through the salmon contribution Ketchikan 0.6 origin of Chinook salmon harvested in Craig nearshore waters of Southeast Alaska. Mid and North Oregon Mid and North Oregon Mid and North Oregon these troll fisheries to provide indepen- Southern 0.4 Inside dent estimates to compare to those - Chinook salmon from the 2000 2001 2002 0.2 derived from the CTC model. Oregon and Washington 0.0 40,000 * coasts were major contributors Upper Columbia Summer Upper Columbia Summer Upper Columbia Summer to the summer troll fisheries, Fishery Sampling 20,000 but were absent during the During the years from 1999 to 2002, Chinook salmon were collected winter and spring. from landings at processors at ports in Southeast Alaska during 0 * 0.6 Washington Coastal Washington Coastal Washington Coastal Chinook salmon retention periods in the early winter troll fishery Chinook salmon from the 0.4 (October 11-December 31), the late winter troll fishery (January 1-April - 0.2 14), the summer fishery ( July and August-September). Samples Upper Columbia River summer were stratified by management quadrant (Northern Outside, Northern and fall stocks were major 0.0 40,000 * Inside, Southern Outside, Southern Inside) and were subsampled contributors to the fishery Thompson River Thompson River Thompson River proportional to the catch in each quadrant so that estimates would not except for during the spring. be biased by location of catch. Muscle, eye, and fin tissues were 20,000 assayed for genetic variation at 26 allozyme loci. Stock composition - Chinook salmon from the 0 * 0.6 estimates for 28 stock groups were made using SPAM 3.6 (http:// Thompson River were usually Southern SE Alaska Southern SE Alaska Southern SE Alaska www.cf.adfg.state.ak.us/geninfo/research/genetics/software/ present in large numbers only 0.4 spampage.htm). during the month of July. 0.2 * 0.0 Oc Jan Jul Au Oc Jan Ma Jul Au Oc Jan Ma Jul Au - Chinook salmon from Southern t-De -Ap y 00 g-Se t-De -Ap y-Ju y 01 g-Se t-De -Ap y-Ju y 02 g-Se c 99 r 00 pt 0 c 00 r 01 n 0 pt 0 c 01 r 02 n 0 pt 0 Southeast Alaska are mainly 0 1 1 2 2 harvested in the spring. * May – June 00 missing Coastwide Baseline A coastwide allozyme baseline for Chinook salmon has been developed that is composed of allele frequency estimates for 44 loci in 254 populations from around the Pacific Rim including Distribution of Age-classes Contribution of Selected Stocks to Summer Samples major populations potentially contributing to the Southeast Alaska troll fishery (See Map Differences in the stock composition of samples from legal- and Above Right). Populations were grouped into reporting regions based on genetic similarity sublegal-sized Chinook salmon during the summer fishery indi- Relative Relative Contribution Contribution and geographic proximity. The identifiability of these reporting regions was investigated by cates that different stocks of salmon use the nearshore waters of Sublegal Legal creating simulated mixtures composed entirely of salmon from a single region. When the Southeast Alaska at different lifestages. In the nearshore waters of 1999 0.3 composition of these mixtures is estimated, the percent correctly identified to the region-of- Southeast Alaska: origin indicates how well this region can be identified. Correct allocation greater than 90% 0.2 indicates a “highly identifiable” region. Simulations of the dataset verified that 44 fine scale 0.1 - Chinook salmon from the Oregon and Washington coasts and 29 broad scale genetic aggregates could be identified in mixtures (See Below). 0.0 and Thompson River are present as larger, more mature 2000 individuals. 0.3 0.2 Central Valley California/Southern Oregon Coastal 0.1 Klamath River Basin - Chinook salmon from the Upper Columbia summer and fall Mid and North Oregon Coastal stocks are present as both immature and maturing 0.0 Willamette River 2001 Lower Columbia River individuals. 0.3 Mid & Up. Columbia Sp., Snake Sp. & Su. 0.2 Up. Columbia Su. & F., Snake F. Washington Coastal - Chinook salmon from the Lower Columbia, Willamette 0.1 Puget Sound River, Puget Sound, coastal British Columbia and South- Lower Fraser River 0.0 ern Southeast Alaska are present as smaller, less mature Thompson River 0.3 2002 Mid and Upper Fraser River individuals. Strait of Georgia 0.2 West Coast Vancouver Island Central BC Coastal 0.1 Skeena River Nass River 0.0 Alaska/BC Transboundary a e t i tt st er ast e a nd Southern Southeast Alaska o o u orgia laska C am C So King Salmon River n ll n i et son Riv Chilkat River W g of Ge SE A ego mp t th Gulf of Alaska Or wer Columb per Columbia Pu ai o p hingto ho U T Str Susitna River /N. L Central BC SouCoas id Was Kodiak Island M Alaska Peninsula Western Alaska Canadian Yukon Russia 80% 85% 90% 95% 100% Conclusions Correct Allocation Estimates indicate that the primary populations of Chinook salmon present in Southeast Alaska during the summer are from the upper Columbia River, the Oregon and Washington coasts, Thompson River, West Coast Vancouver Island, Central British Columbia, and Southern Southeast Alaska. During the early winter a similar assemblage of populations is present except for a reduction in the Washington and Oregon coastal and Point estimates and 90% bootstrap confidence intervals are given. Thompson River populations. Southeast Alaska and northern British Columbia are increasingly prevalent toward the spring. In the spring fishery, the Upper Columbia River stocks, which are a major population component at all other times of the year, are almost absent.

Legal- and sublegal-sized Chinook salmon present in Southeast Alaska during the summer are from different stock groups; evidence that waters of Southeast Alaska are used by many populations of Chinook salmon during different parts of their life history.

Acknowledgements Funding for this study was received from the Southeast Sustainable Fisheries Fund, Chinook Technical Committee of the Pacific Salmon Commission, and NOAA Saltonstal-Kennedy Award No. NA46FD0356. Judy Berger, Andy Barclay and Eric Lardizabal were instrumental in collecting the data for this analysis.