U.S. Fish & Wildlife Service Yukon River Chum Salmon Genetic Analysis of an Interjurisdictional Fishery Introduction The Yukon River flows more than 2000 miles through Canada and Alaska. Chum salmon spawn throughout the drainage in both countries, and are known in general to exhibit fidelity to natal spawning grounds. There are two runs of chum salmon: summer and fall. Summer chum salmon, which enter the river between early June and early July, spawn primarily in tributaries of the lower 500 miles of the Yukon. Fall chum enter the river from mid-July to late August and spawn from the Tanana River confluence to the headwaters of the Yukon River. Both summer and fall run chum salmon are an extremely Figure 1. Baseline stocks and reporting groups. Summer stocks are important resource for subsistence 1-14, and fall stocks are 15-29 and shaded grey. fisheries in the U.S. and Canada. Yukon River chum salmon are managed Methods analyzed in order to estimate the stock under Pacific Salmon Treaty mandates compositions for each major “pulse” of to conserve and equitably share the Tissue samples were collected from chum salmon; estimates are reported resource between the U.S. and Canada. over 5000 fish representing 15 summer to state and federal managers within Of primary concern is the distinction and 14 fall stocks (Figure 1). Genetic 24-48 hours of receiving the samples at between harvested chum salmon relationships were determined the CGL. originating in the U.S. and Canada. through analysis of allelic variation Determining the relative contributions at 22 microsatellite loci. This allowed Results and Discussion of stocks caught in the harvest is us to estimate stock structure and essential for effective management. develop a genetic baseline for MSA in Temporal and spatial structuring are This task is difficult because the collaboration with the Department of observed among Yukon River chum harvest takes place before the stocks Fisheries and Oceans Canada (DFOC). salmon. Analysis reveals gradient like segregate into spawning aggregates. Tests with samples of known origin transitioning from lower river summer Genetic mixed-stock analysis (MSA) were conducted to evaluate the power stocks to upper river fall stocks (Figure is a method for estimating the relative of the genetic baseline to apportion 2). Eight reporting groups are defined: proportion of specific Yukon River chum mixtures to reporting groups defined Lower River Summer, Middle River salmon stocks in harvest mixtures. The by the genetic, geographic, and political Summer, Tanana River Fall, Border Alaska Region Conservation Genetics relationships among the stocks. U.S. Fall, Porcupine Canada Fall, Laboratory (CGL) has successfully Mainstem Canada Fall, White River applied this analysis to assist in the Every summer since 2004, samples Fall, and Teslin River Fall. Mixed-stock management of Yukon River chum collected from Pilot Station sonar test analysis for samples of known origin, salmon since 2004. fisheries (near #2 in Figure 1) are using Bayesian mixture modeling, is Conservation Genetics Laboratory - Alaska Region Figure 3. Comparison of USFWS (blue) and DFOC (red) stock specific estimates for Pulse 3 of the 2004 chum salmon run. Figure 2. Neighbor-joining dendrogram showing the relative genetic relationships among baseline collections. within approximately two percent of the actual proportions (Table 1), indicating Figure 4. Comparison of regional abundance that our baseline accurately apportions for the genetic/sonar and upriver escapement mixture samples to stock of origin. project estimates. The USFWS and DFOC derived method. Furthermore, stock specific baseline provides data to reconstruct concordant stock composition estimates abundance estimates (the product of the total stock-specific returns, allowing for for the 2004 Pilot Station samples; genetic composition estimates and the improved escapement goals based upon a most estimates are within one standard Pilot Station sonar passage estimates), thorough analysis of the stock dynamics. deviation of each other (Figure 3), are highly correlated with data from demonstrating the robustness of the other escapement projects (Figure 4). Each summer we continue to estimate Table 1. Analysis of known origin the composition of Yukon River chum samples. salmon sampled from Pilot Station sonar test fisheries using our highly effective Reporting Group Expected Estimated (S.D.) genetic baseline. Our data provide Lower Summer 25.0 22.9 (5.3) Middle Summer 25.0 27.2 (5.9) managers the ability to more effectively Tanana Fall 25.0 24.1 (4.3) regulate fisheries in order to meet Upper Fall 25.0 25.3 (3.2) escapement goals, prevent differential Summer 50.0 50.1 (4.6) harvest rates, and conserve genetic Fall 50.0 49.9 (4.6) diversity, all of which are essential for Fish wheels, used for subsistence U.S. 75.0 74.4 (3.3) sustained salmon productivity. Moreover, fishing, are a common sight along Canada 25.0 25.6 (3.3) MSA with our Yukon chum salmon the Yukon River. For additional details, see: For more information contact: Flannery BG, Beacham TD, Candy JR, Blair Flannery Holder RR, Maschmann GF, Kretschmer EJ, U.S. Fish and Wildlife Service Wenburg JK (2010) Mixed-Stock Analysis Conservation Genetics Laboratory of Yukon River chum salmon: application 1011 E. Tudor Road and validation in a complex fishery. North Anchorage, Alaska 99503 American Journal of Fisheries Management 907/786 3355 30, 1324-1338. [email protected] alaska.fws.gov/fisheries/genetics November 2010.