Allozyme variation was used to examine population genetic structure of adult chinook salmon, Oncorhynchus tshawytscha, collected between 1988 and 1993 from 22 spawning locations in Southeast Alaska and northern British Columbia. Thirty-five loci and two pairs of isoloci were variable, and of these, 25 loci and one pair of isoloci expressed the most abundant allele with a frequency of less than or equal to 0.95 in at least one collection. Aneighbor-joining (NJ) tree of genetic distances defined five regional groups: (1) King Salmon River (the only island collection), which has large allelic frequency differences from other populations in this study; (2) heterogeneous coastal populations from southern southeast Alaska; (3) transmountain collections from the Taku and Stikine Rivers on the eastern side of the coastal mountain range; (4) Chilkat River in northern Southeast Alaska; and (5) northern coastal Southeast Alaska, which consists of the Situk River and the Klukshu River, a tributary of the Alsek River. A second NJ tree that included collections from the Yukon River and British Columbia did not reveal any strong genetic similarity between Southeast Alaska and the Yukon River. The data suggest that Southeast Alaska may have been colonized from both northern and southern refugia following the last glaciation b?? a period of sufficient time to allow for isolation by distance to occur.

Genetic stock identification techniques were used to identify the origin and provide stock-specific migration and distribution patterns of juvenile chum (Oncorhynchus keta) salmon caught during annual fall surveys (2002) along the eastern Bering Sea (Fig. 1). Preliminary results indicate that: 1) Yukon River Fall chum salmon are widely distributed from offshore of the Yukon River, eastward to 62B0N, 172B0W, and as far south as Nunivak Island (60B0N), suggesting a southwesterly migration pathway along the Bering Sea shelf; 2) juvenile chum salmon from the Kuskokwim River are narrowly distributed south of Nunivak Island from the mouth of the Kuskokwim River, south to 58B0N, and as far west as 168B0W, suggesting a westerly migration pathway along the Bering Sea shelf; and 3) northern Russia juvenile chum salmon stocks (mainly stocks from rivers draining into the Gulf of Anadyr) are distributed as far east as 62B0N, 171B0W (Fig. 2). These results are unique in that they represent the first attempt to identify early marine distribution and migration of juvenile chum salmon stocks on the eastern Bering Sea shelf.

Allozymes from 46 loci were analyzed from chum salmon (Oncorhynchus keta) collected at 61 locations in southeast Alaska and northern British Columbia. Of the 42 variable loci, 21 had a common allele frequency <0.95. We observed significant heterogeneity within and among six regional groups: central southeast Alaska, Prince of Wales Island area, southern southeast Alaska b?? northern British Columbia, north-central British Columbia, and two groups in the Queen Charlotte Islands. Genetic variation among regions was significantly greater than within regions. The three island groups were distinct from each other and from the mainland populations. Allele frequencies were stable over time in 14 of 15 locations sampled for more than 1 yr. The geographic basis for heterogeneity among regions is confounded in part by spawning-time differences. The Prince of Wales and Queen Charlotte populations spawn in the fall; the mainland populations spawn mainly in the summer, although some overlap exists. Overall, most genetic diversity (97%) occurred within sampling locations; the remaining diversity was distributed almost equally within and among regions. Our genetic data may provide fishery managers a means to estimate stock composition in the mixed-stock fisheries near this boundary between the United States and Canada.

Summer surveys (Julyb??August) of juvenile salmon ecology along the continental shelf of the Gulf of Alaska are conducted annually by scientists from the Ocean Carrying Capacity program of the National Marine Fisheries Serviceb??s Auke Bay Laboratory. These surveys are an effort to link changes in salmon production to biological and physical factors in the ocean environment. An improved understanding of salmon distribution is one objective of this research. We identified the origin of juvenile chum salmon collected in transects from around the Gulf of Alaska in 2000 and 2001, using the presence of thermal marks in hatchery fish and the divergence of genetic characteristics among regional groups of populations.

Immature chum salmon were collected by the F/V Northwest Explorer between September 5 and October 8, during the 2002 BASIS survey across the eastern Bering Sea shelf and Aleutian Islands (for details, see Murphy et al. 2003). Approximately 1,600 fish were aged, checked for the presence of hatchery thermal marks, and genotyped for allozyme loci. Scale aging and otolith mark identification were done by the Alaska Department of Fish and Gameb??s Mark, Tag, and Age Laboratory in Juneau, Alaska. Otoliths with thermal marks were compared with voucher specimens to verify hatchery of origin. Heart, liver, and muscle tissues were extracted and then analyzed with protein electrophoresis to identify genotypes for the 20 allozyme loci in the chum salmon coastwide genetic baseline (Kondzela et al. 2002). Genetic data were pooled into one of four geographic areasb??western Aleutian Islands, eastern Aleutian Islands, southeastern Bering Sea shelf, and northeastern Bering Sea shelf. In the eastern and western Aleutian Islands, the catches were large enough to further stratify the data by ocean age. Regional origin estimates were made for each mixture collection using a conditional maximum likelihood method (Pella and Masuda model in SPAM v. 3.7, ADF&G 2001) and the full 356-population genetic baseline. The 95% nonsymmetric confidence intervals were determined from 1000 bootstrap estimates in which the baseline and mixture were re-sampled.

Genetic data of salmon bycatch samples collected by fisheries observers are used for mixed-stock analyses to determine geographic region of origin. This work is done at the Auk Bay Lab in Juneau Alaska. The data are loaded to the the North Pacific Halibut and Groundfish database maintained by FMA Division at the Alaska Fisheries Science Center in Seattle Washington

The purpose of this study was to genetically analyze axillary process samples from ~6,000 sockeye salmon harvested in the 2006 and 2007 Districts 101 gillnet and 104 purse seine sockeye fisheries to determine proportions of Canadian and U.S. fish. A SNP genetic baseline of 45 SNPs (41 markers as 3 groups of SNPs are linked) assayed in 84 sockeye populations from southeast Alaska and British Columbia was developed by the ADF&G. The 84 populations were grouped into 14 regions. With the exception of locus One_Serpin, which failed during genotyping, the same markers were evaluated in the baseline and mixtures. Stock proportions were estimated using a Bayesian mixture analysis. In addition to performing mixture analysis for the 2006 and 2007 fisheries, the sockeye baseline was also expanded as part of the 2007 project. Approximately 1700 fish from 21 locations were genotyped, which will be included in a future updated baseline.

This study is part of the Auke Bay Laboratoryb??s Ocean Carrying Capacity (OCC) which has extensively sampled salmon in the North Pacific since 1996 to obtain information on marine life history and migration patterns. Genetic stock identification techniques (protein electrophoresis) indicated that Bristol Bay stocks of immature sockeye salmon (Oncorhynchus nerka) made up the largest percentage in two samples taken near Unalaska Island in 1998. The substantial numbers of immature sockeye salmon captured at Cape Cheerful during May 1998 were unexpected, based on current migration models of western Alaska sockeye salmon. Immature sockeye constituted the largest percentage of our immature salmon catch captured at Cape Prominence during August 1998. This was also unexpected since immature chum salmon (O. keta) were the predominant catch during August 1996 and 1997 at the same location. These unexpected events may be due to changes in distribution resulting from the strong El NiC1o event during 1997-1998.

A genetic analyses of samples from the Chinook salmon (Oncorhynchus tshawytscha) bycatch from the 2007-2013 Bering Sea-Aleutian Island and Gulf of Alaska trawl fisheries for walleye pollock (Gadus chalcogrammus) were undertaken to determine the overall stock composition of the bycatch. Samples were genotyped for 43 single nucleotide polymorphism (SNP) DNA markers and results were estimated using the Alaska Department of Fish and Game (ADF&G) SNP baseline.

A genetic analysis of samples from the chum salmon (Oncorhynchus keta) bycatch of the 2010 Bering Sea groundfish trawl fishery was undertaken to determine the overall stock composition of the sample set. Samples were genotyped for 11 microsatellite markers and results were estimated using the current chum salmon microsatellite baseline. In 2010, genetic samples were collected as part of the species composition analysis of the Alaska Fisheries Science Centers North Pacific Observer Program. This sampling change for 2010 was an interim measure implemented until the systematic sampling protocols are finalized. Consequently, stock composition estimates apply to the sample set and may not represent the entire chum salmon bycatch. Based on the analysis of 1,048 chum salmon bycatch samples collected throughout the 2010 Bering Sea trawl fishery, East Asian (38%), North Asian (26%), Western Alaska (14%), and Eastern Gulf of Alaska/Pacific Northwest (13%) stocks dominated the sample set, with smaller contributions from Upper/Middle Yukon River (7%) stocks. The estimates for the 2010 chum salmon bycatch sample set were similar to the 20052009 chum salmon bycatch estimates, suggesting consistency of the regional stock contributions across years. Analysis of temporal groupings within the groundfish B season revealed changes in stock composition during the course of the season with decreasing contribution of Western Alaska and Eastern Gulf of Alaska/Pacific Northwest stocks and increasing contribution of North Asian stocks over time, but leaves unanswered whether these changes are due to temporal or spatial differences in the sample set.