We used parentage analysis based on microsatellite genotypes to measure rates of homing and straying of Chinook salmon (Oncorhynchus tshawytscha) among five major spawning tributaries within the Wenatchee River, Washington. On the basis of analysis of 2248 natural-origin and 11594 hatchery-origin fish, we estimated that the rate of homing to natal tributaries by natural-origin fish ranged from 0% to 99% depending on the tributary. Hatchery-origin fish released in one of the five tributaries homed to that tributary at a far lower rate than the natural-origin fish (71% compared to 96%). For hatchery-released fish, stray rates based on parentage analysis were consistent with rates estimated using physical tag recoveries. Stray rates among major spawning tributaries were generally higher than stray rates of tagged fish to areas outside of the Wenatchee River watershed. Within the Wenatchee watershed, rates of straying by natural-origin fish were significantly affected by spawning tributary and by parental origin: progeny of naturally spawning hatchery-produced fish strayed at significantly higher rates than progeny whose parents were themselves of natural origin. Notably, none of the 170 offspring that were products of mating by two natural-origin fish strayed from their natal tributary. Indirect estimates of gene flow based on FST statistics were correlated with but higher than the estimates from the parentage data. Tributary-specific estimates of effective population size were also correlated with the number of spawners in each tributary.

We used genetic parentage analysis of 6200 potential parents and 5497 juvenile offspring to evaluate the relative reproductive success of hatchery and natural steelhead (Onchorhynchus mykiss) when spawning in the wild between 2008 and 2011 in the Wenatchee River, Washington. Hatchery fish originating from two prior generation hatchery parents had <20% of the reproductive success of natural origin spawners. In contrast, hatchery females originating from a cross between two natural origin parents of the prior generation had equivalent or better reproductive success than natural origin females. Males originating from such a cross had reproductive success of 26–93% that of natural males. The reproductive success of hatchery females and males from crosses consisting of one natural origin fish and one hatchery origin fish was 24–54% that of natural fish. The strong influence of hatchery broodstock origin on reproductive success confirms similar results from a previous study of a different population of the same species and suggests a genetic basis for the low reproductive success of hatchery steelhead, although environmental factors cannot be entirely ruled out. In addition to broodstock origin, fish size, return time, age, and spawning location were significant predictors of reproductive success. Our results indicate that incorporating natural fish into hatchery broodstock is clearly beneficial for improving subsequent natural spawning success, even in a population that has a decades-long history of hatchery releases, as is the case in the Wenatchee River.

We applied acoustic telemetry methods to characterize migration pathways and estimate associated travel times and survival probabilities for juvenile Chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss migrating downstream through the Columbia River estuary (from river kilometer [rkm] 86 to rkm 8). Acoustic‐tagged fish were detected as migrating in the navigation channel and in off‐channel areas at each of the estuarine reaches we examined during May–August 2010. However, the majority of fish traveled in the main navigation channel from rkm 86 to rkm 37, at which point most fish left the river‐influenced navigation channel; crossed a broad, shallow tidal flat; and migrated the final 37 km in a secondary channel, which was characterized as having greater tidal transport than the navigation channel. The pathway used by acoustic‐tagged smolts to migrate through the estuary affected their rate of travel. In most reaches, navigation channel migrants traveled significantly faster than fish that migrated through off‐channel areas. Contrary to observations from previous studies, smolts that migrated through off‐channel areas at a slower rate did not experience lower survival than their cohorts that used the navigation channel. Although no significant differences in survival probability were observed between navigation channel migrants and off‐channel migrants, areas of high mortality were identified between rkm 37 and rkm 8. Dispersion of juvenile salmonids into multiple pathways during downstream migration can be beneficial in terms of increased expression of life history diversity and resiliency to environmental perturbations. Our results, which document juvenile salmon migration pathways and associated travel time and survival through a large estuary, can be used to focus future research and management activities in areas identified as having high mortality and therefore can be used to aid in the recovery of Endangered Species Act‐listed salmon populations.

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Spawning is a critical stage in the life history of salmonids. Spawning location has been reported to be a significant factor in the fitness differences between natural‐ and hatchery‐origin (natural and hatchery, respectively) female spring Chinook Salmon Oncorhynchus tshawytscha, although the mechanisms responsible remain uncertain. The objectives of this study were to compare the spawning distributions of hatchery and natural female spring Chinook salmon within the Chiwawa River, Washington, and determine whether spawning characteristics differ between hatchery and natural female Chinook Salmon or between channel types within the Chiwawa River. Over a 10‐year period, locations of female carcasses were examined to assess differences in the spawning distribution of hatchery and natural females. Additionally, a suite of metrics was measured from redds of known origin females to characterize the spawning location and redd characteristics. A greater proportion of hatchery females spawned in the lower watershed within plane‐bed channels than spawned upstream. Conversely, the majority of natural females spawned farther upstream in pool‐riffle channels. The distribution of hatchery fish was presumably strongly influenced by the hatchery acclimation–release location in the lower river. Given the geomorphic characteristics of plane‐bed channels, salmon were unable to build redds there similar to those in more typical pool‐riffle channels. Redds constructed in plane‐bed channels were smaller, shallower, and closer to stream banks than redds in pool‐riffle channels. Limited differences were detected in redd characteristics between natural and hatchery females in pool‐riffle channels. Smaller hatchery females constructed smaller redds with lower tailspill relief than did larger natural fish. As the results of differences in spawning distribution and fish size, redds constructed by hatchery females were more susceptible to environmental sources of mortality than were redds constructed by natural females. This study provides insight into the possible mechanisms responsible for the reported lower reproductive success among hatchery females spawning in the natural environment. Received December 14, 2016; accepted May 24, 2017 Published online July 31, 2017