Charles M. Guthrie

A comparison of genetic variation between an anadromous steelhead, Oncorhynchus mykiss, population and seven derived populations sequestered in freshwater for 70 years

In 1926 cannery workers from the Wakefield Fisheries Plant at Little Port Walter in Southeast Alaska captured small trout, Oncorhynchus mykiss, from a portion of Sashin Creek populated with a wild steelhead (anadromous O. mykiss) run. They planted them into Sashin Lake which had been fishless to that time and separated from the lower stream by two large waterfalls that prevented upstream migration of any fish. In 1996 we sampled adult steelhead from the lower creek and juvenile O. mykiss from an intermediate portion of the creek, Sashin Lake, and five lakes that had been stocked with fish from Sashin Lake in 1938. Tissue samples from these eight populations were compared for variation in: microsatellite DNA at 10 loci; D-loop sequences in mitochondrial DNA; and allozymes at 73 loci known to be variable in steelhead. Genetic variability was consistently less in the Sashin Lake population and all derived populations than in the source anadromous population. The cause of this reduction is unknown but it is likely that very few fish survived to reproduce from the initial transplant in 1926. Stockings of 50–85 fish into five other fishless lakes in 1938 from Sashin Lake did not result in a similar dramatic reduction in variability. We discuss potential explanations for the observed patterns of genetic diversity in relation to the maintenance of endangered anadromous O. mykiss populations in freshwater refugia.

Atlantic Salmon in Marine Waters of Southeastern Alaska

Abstract An immature female Atlantic salmon Salmo salar, caught by a commercial salmon troller off southeastern Alaska on 20 July 1990, is the first documented representative of this species in the marine waters of Alaska. Identification was based on morphology, meristic characters, and protein electrophoresis. Scale growth patterns, an eroded or clipped dorsal fin, and a high proportion of regenerated scales indicate that the fish escaped from an aquaculture pen during spring 1990. Five additional Atlantic salmon were subsequently caught by commercial fishermen in southeastern Alaska during August 1991; identification was based on morphology and color patterns, Escaped Atlantic salmon are unlikely to have a genetic impact on native Pacific salmonids, but the possibility exists that they will disseminate nonendemic pathogens or parasites.

Genetic structure of wild chinook salmon populations of Southeast Alaska and northern British Columbia

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. A neighbor-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 — a period of sufficient time to allow for isolation by distance to occur.

Genetic stock composition analysis of the chinook salmon (Oncorhynchus tshawytscha) bycatch from the 2016 Bering Sea walleye pollock (Gadus chalcogrammus) trawl fishery

A genetic analysis of samples from the Chinook salmon (Oncorhynchus tshawytscha) bycatch of the 2016 Bering Sea-Aleutian Island (BSAI) trawl fishery for walleye pollock (Gadus chalcogrammus) was 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. In 2016, genetic samples from the Bering Sea were collected using a systematic random sampling protocol where one out of every 10 Chinook salmon encountered was sampled. Based on the analysis of 1,910 Chinook salmon bycatch samples collected throughout the 2016 BSAI walleye pollock trawl fishery, Coastal Western Alaska and British Columbia regions (34% and 29% respectively) dominated the sample set with smaller contributions from West Coast US (14%), and North Alaska Peninsula (13%) regions. Analysis of temporal groupings within the pollock “A” and “B” seasons revealed changes in stock composition during the course of the year with lower contributions of Coastal Western Alaska and North Alaska Peninsula regions and higher contributions of West Coast US, British Columbia, and NW Gulf of Alaska, regions during the “B” season when compared to the “A” season.

Genetic stock composition analysis of the Chinook salmon bycatch samples from the 2014 Gulf of Alaska trawl fishery

A genetic analysis of samples from the Chinook salmon (Oncorhynchus tshawytscha) bycatch of the 2014 Gulf of Alaska (GOA) trawl fisheries for walleye pollock (Gadus chalcogrammus), rockfish (Sebastes spp.), and arrowtooth flounder (Atheresthes stomias) was undertaken to determine the stock composition of the sample sets. 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. In 2014, genetic samples were collected from Chinook salmon taken in the bycatch of the Gulf of Alaska (GOA) pollock trawl fisheries using a simple random sample protocol with trip being the primary unit. This is the first year for this sampling protocol and resulted in the largest available genetic sample set to date with 10.7% of the salmon bycatch successfully genotyped. Based on the analysis of 1,163 Chinook salmon bycatch samples, British Columbia (43%), West Coast U.S. (35%), Coastal Southeast Alaska (16%), and Northwest Gulf of Alaska stocks (5%) comprised the largest stock groups. Weighting the available sample sets to the total bycatch by season and statistical area did not appreciably change the overall stock composition. In 2014, genetic samples from the bycatch of the rockfish catcher vessel (CV) fishery in the central GOA were collected by the fishing industry using a census sampling protocol where every Chinook salmon encountered was sampled. Based on the genotyping of 398 Chinook salmon bycatch samples collected from the 2014 GOA rockfish CV trawl fishery in NMFS Statistical Areas 620 and 630, West Coast U.S. stocks (WA/OR/CA) represented the largest stock grouping (72%) with smaller contributions from British Columbia (17%), Coastal Southeast Alaska (7%), and Northwest GOA (3%) stocks. Based on the genotyping of 404 Chinook salmon bycatch samples collected throughout the 2014 GOA arrowtooth flounder trawl fishery from the catcher-processors (CP) FV Vaerdal and FV US C4 GOA Chinook Genetics Rpt APRIL 2016

Genetic stock composition analysis of the Chinook salmon bycatch from the 2014 Bering Sea walleye pollock (Gadus chalcogrammus) trawl fishery

A genetic analysis of samples from the Chinook salmon (Oncorhynchus tshawytscha) bycatch of the 2015 Bering Sea-Aleutian Island (BSAI) trawl fishery for walleye pollock (Gadus chalcogrammus) was 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. In 2015, genetic samples from the Bering Sea were collected using a systematic random sampling protocol where one out of every 10 Chinook salmon encountered was sampled. Based on the analysis of 1,757 Chinook salmon bycatch samples collected throughout the 2015 BSAI walleye pollock trawl fishery, Coastal Western Alaska stocks dominated the sample set (40%) with smaller contributions from British Columbia (22%), West Coast U.S. (WA/OR/CA) (15%), and North Alaska Peninsula (11%) stocks. Analysis of temporal groupings within the pollock “A” and “B” seasons revealed changes in stock composition during the course of the year with lower contributions of Coastal Western Alaska, North Alaska Peninsula, and Upper Yukon stocks and higher contributions of West Coast U.S. (WA/OR/CA), British Columbia, NW Gulf of Alaska, and Coastal Southeast Alaska stocks during the “B” season.

Genetic stock composition analysis of Chinook salmon bycatch samples from the rockfish and arrowtooth flounder 2013 Gulf of Alaska trawl fisheries and the Gulf of Alaska salmon excluder device test

A genetic analysis of samples from the Chinook salmon (Oncorhynchus tshawytscha) bycatch of the 2013 Gulf of Alaska (GOA) trawl fisheries for Pacific rockfish (Sebastes spp.) and arrowtooth (Atheresthes stomias) flounder was undertaken to determine the stock composition of the sample sets. 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. In 2013, genetic samples from the bycatch of the GOA rockfish fishery were collected by the fishing industry using a census sampling protocol where every Chinook salmon encountered was sampled. Based on the analysis of 2,029 Chinook salmon bycatch samples collected throughout the 2013 GOA rockfish trawl fishery, West Coast U.S. stocks (WA/OR/CA) represented the largest stock grouping (60%) with smaller contributions from British Columbia (31%), Coastal Southeast Alaska (6%), and Northwest GOA (2%) stocks. Genetic samples were also collected from Chinook salmon taken in the bycatch of the 2013 GOA arrowtooth flounder trawl fisheries. Those samples were collected opportunistically from a single vessel; consequently, the resulting stock composition estimates should be considered as stock compositions of the sample set rather than a representative composition of the overall bycatch. Based on the analysis of 279 Chinook salmon bycatch samples, West Coast U.S. (43%), British Columbia (39%), Coastal Southeast Alaska (14%), and Northwest GOA (3%) stocks comprised the largest stock groups. We also produced a stock composition estimate of Chinook salmon from a single test haul of the salmon excluder device performed in April 2013 in an area near Kodiak Island in Shelikof Strait. Stock composition results showed that the majority of those 95 Chinook salmon originated from West Coast U.S. (79%), British Columbia (17%), and Coastal Southeast Alaska (3%) stocks.