Genetic mixed-stock analysis reveals evidence of adverse effects on fall Chum Salmon tagged in the Yukon River

Objective In 1999, radiotelemetry data suggested that 25% of the fall Chum Salmon Oncorhynchus keta migration in the Yukon River above the confluence with the Tanana River remained in the Yukon Flats, an extensive, highly braided main-stem area of the Yukon River. Our objective was to determine whether this represents Chum Salmon spawning within main-stem reaches of the Yukon Flats or a handling effect impacting fish from stocks destined for spawning areas farther upstream. Methods To assess the validity of the radiotelemetry-based stock composition estimates, we conducted genetic mixed-stock analysis on tissue samples collected from radio-tagged fish. Results Nonoverlapping CIs provided evidence that radiotelemetry and genetic stock composition estimates were different for upper Yukon River stocks. The genetic-based composition estimate (42%) for upper Yukon River stocks was greater than the radiotelemetry estimate (18%). Overlapping CIs provided no evidence that the estimates from the two methods were different for the U.S. border and upper Porcupine River. For fish last located by radiotelemetry in the Yukon Flats, genetic stock composition estimates classified most (86%) as upper Yukon River stocks. The likelihood ratio test revealed strong evidence that genetic stock composition estimates were different between fish tracked to terminal locations and those not tracked to terminal locations. A greater proportion of fish from the upper Yukon River was present in the mixture of fish that did not reach terminal locations, whereas a greater proportion of fish from the U.S. border was present in the terminal mixture. The assignment test revealed strong evidence that radiotelemetry samples had a higher proportion of misassignments than known-origin samples. Most (64%) misassignments involved fish that were genetically assigned to the upper Yukon River. Conclusions These results indicate that upper Yukon River fish in the radiotelemetry study suffered from residual handling effects and were less likely to reach their natal spawning grounds.