Genetic and Coded Wire Tag Results Combine to Allow More-Precise Management of a Complex Chinook Salmon Aggregate

Abstract Conservation concerns for small, relatively unproductive populations of Chinook salmon Oncorhynchus tshawytscha limit the utility of fisheries in Canada's Fraser River. To identify population-specific migration time and to index abundance, we analyzed 4,822 fish sampled for genetic variation in 2000 and 2001 and 580 fish with coded wire tags (CWTs) caught from 1987 to 2004 in a test fishery near the river mouth. Population sizes estimated from microsatellite variation were within 3.4% of the known-origin population composition and were unbiased in comparison with known-origin population sizes. All but 1 of the 30 populations detected by both genetic methods and CWTs had overlapping migration times, but these times differed significantly for only 7 populations. Migration times were identified for another 23 untagged populations identified by using genetics, which resulted in the assignment of migration timing groups (peak passage) for 53 populations as spring (March–May), early summer (June), midsummer (July), late summer (August), and fall (September–October). Population abundance indices at the test fishery were significantly associated with run size at the river mouth. When populations were aggregated by geographic stock structure and migration time, the abundance indices for the test fishery explained 80% of the variation in run size. Incorporating genetic information can substantially improve the utility of test fishery data and thereby allow more-precise management of complex population aggregates such as those in the Fraser River.