Abstract.-Life history traits in hatchery and wild spring Chinook salmon Oncorhynchus tshawytscha from the upper Yakima River were compared to determine whether locally adapted traits had diverged after one generation of state-of-the-art artificial propagation. Sex composition in wild-and hatchery-origin fish differed in three of four brood years (P 0.01). The proportion of hatchery males, primarily age 3, increased from 38% to 49% over time. Conversely, the sex composition of wild fish did not exhibit a similar linear trend. Most hatchery-and wild-origin fish reached maturity at age 4 (!76%), followed in magnitude by ages 3 and 5. Wild mean age at maturation demonstrated no significant trend over time, while hatchery mean age at maturation declined (P ¼ 0.05). Mean lengths of 3-5-year-old hatchery fish were shorter than those of wild fish of the same age (differences of 2.7 cm for age 3, 1.7 cm for age 4, and 1.9 cm for age 5). Likewise, body weights of hatchery fish were lower than those of wild fish (differences of 0.3 kg for age 3, 0.3 kg for age 4, and 0.6 kg for age 5), representing a change in body size of between 0.5 and 1.0 standard deviation (SD). Median arrival timing of hatchery and wild fish at a broodstock collection site just downstream of ancestral spawning grounds showed no consistent difference. However, the median arrival date of age-3 fish was 19-20 d later than that for fish of ages 4 and 5 (P , 0.01). Mean spawn timing of hatchery fish was significantly earlier (5.1 d) than that of wild fish in a ''common-garden'' experiment (P , 0.05). We estimate that fitness could be reduced by as much as 1-5% for traits diverging from their optima by 0.5-1.0 SD. The degree of genetic determination of the divergence is unknown, but future monitoring will help clarify this. Perhaps the most important conclusion of our study is that even a hatchery program designed to minimize differences between hatchery and wild fish did not produce fish that were identical to wild fish.

The Cle Elum Supplementation and Research Facility in the Yakima River basin, Washington, is an integrated spring Chinook Salmon Oncorhynchus tshawytscha hatchery program designed to test whether artificial propagation can increase natural production and harvest opportunities while keeping ecological and genetic impacts within acceptable limits. Only natural‐origin (naturally spawned) fish are used for hatchery broodstock. Spawning, incubation, and early rearing occur at a central facility; presmolts are transferred for final rearing, acclimation, and volitional release at sites adjacent to natural spawning areas, where returning adults can spawn with natural‐origin fish. The first wild broodstock were collected in 1997, and age‐4 adults have returned to the Yakima River since 2001. An unsupplemented population in the adjacent Naches River watershed provides a reference for evaluating environmental influences. The program has been comprehensively monitored from its inception. A synthesis of findings, many already published, is as follows: supplementation increased the harvest, redd counts, and spatial distribution of spawners; natural‐origin returns were maintained; straying to nontarget systems was negligible; natural‐origin females had slightly higher breeding success (production of surviving fry) in an artificial spawning channel, while the behavior and breeding success of natural‐ and hatchery‐origin males were similar; hatchery‐origin fish showed differences in morphometric and life history traits; high rates of hatchery age‐2 (minijack) production were reported, but the observed proportions of out‐migrating juvenile and adult (ages 4 and 5) returning males were comparable for hatchery‐ and natural‐origin fish; hatchery smolts did not affect the levels of pathogens in natural smolts; and the ecological interactions attributed to the program were within adopted guidelines. Continued study is required to assess the long‐term impacts on natural production and productivity.

Captive breeding has the potential to rebuild depressed populations. However, associated genetic changes may decrease restoration success and negatively affect the adaptive potential of the entire population. Thus, approaches that minimize genetic risks should be tested in a comparative framework over multiple generations. Genetic diversity in two captive-reared lines of a species of conservation interest, Chinook salmon (Oncorhynchus tshawytscha), was surveyed across three generations using genome-wide approaches. Genetic divergence from the source population was minimal in an integrated line, which implemented managed gene flow by using only naturally-born adults as captive broodstock, but significant in a segregated line, which bred only captive-origin individuals. Estimates of effective number of breeders revealed that the rapid divergence observed in the latter was largely attributable to genetic drift. Three independent tests for signatures of adaptive divergence also identified temporal change within the segregated line, possibly indicating domestication selection. The results empirically demonstrate that using managed gene flow for propagating a captive-reared population reduces genetic divergence over the short term compared to one that relies solely on captive-origin parents. These findings complement existing studies of captive breeding, which typically focus on a single management strategy and examine the fitness of one or two generations.

Abstract.-We tagged juvenile upper Yakima River hatchery spring Chinook salmon Oncorhynchus tshawytscha with passive integrated transponder (PIT) and coded wire snout tags in a double-tag study to test the assumptions that tags are not lost and do not affect postrelease survival, behavior, or growth. The average loss of PIT tags was 2.0% (95% confidence interval [CI] ¼ 0.7-3.2%) in juveniles before release and 18.4% in recaptures returning 6 months to 4 years after release (95% CI ¼ 17.2-19.5%). Adult tag losses were not significantly correlated with age of return (analysis of covariance, P ¼ 0.40), indicating that the majority of PIT tag loss had occurred within the first 6 months after release. Smolt-to-adult recruit survival (SARS) of PIT-tagged fish was significantly lower (P , 0.05) than that of non-PIT-tagged (NPT) fish because of tag loss and reduced survival, resulting in an average underestimate of SARS of 25.0%. After correcting for tag loss, we estimated PIT tag-induced mortality to be as great as 33.3% with a mean of 10.3% over all brood years (P , 0.05). Mean lengths and weights of PIT-tagged adults were less than those of NPT adults in all age comparisons. However, only age-4 PIT-tagged adults were significantly smaller than NPT fish of the same age (mean length difference ¼ 1.1 cm; mean body weight difference ¼ 0.1 kg; analysis of variance, P , 0.05). There was no significant difference between migration timing of PIT-tagged and NPT adults within the upper Yakima River (MannWhitney test, P . 0.09). Given the widespread and increasing use of PIT tags, and their use in calculating critical estimators related to salmonid life history of Endangered Species Act populations, the effects of using PIT tags must be quantitatively considered under actual study conditions and, if necessary, be accounted for.

A novel application of genomewide association analyses is to use trait‐associated loci to monitor the effects of conservation strategies on potentially adaptive genetic variation. Comparisons of fitness between captive‐ and wild‐origin individuals, for example, do not reveal how captive rearing affects genetic variation underlying fitness traits or which traits are most susceptible to domestication selection. Here, we used data collected across four generations to identify loci associated with six traits in adult Chinook salmon (Oncorhynchus tshawytscha) and then determined how two alternative management approaches for captive rearing affected variation at these loci. Loci associated with date of return to freshwater spawning grounds (return timing), length and weight at return, age at maturity, spawn timing, and daily growth coefficient were identified using 9108 restriction site‐associated markers and random forest, an approach suitable for polygenic traits. Mapping of trait‐associated loci, gene annotations, and integration of results across multiple studies revealed candidate regions involved in several fitness‐related traits. Genotypes at trait‐associated loci were then compared between two hatchery populations that were derived from the same source but are now managed as separate lines, one integrated with and one segregated from the wild population. While no broad‐scale change was detected across four generations, there were numerous regions where trait‐associated loci overlapped with signatures of adaptive divergence previously identified in the two lines. Many regions, primarily with loci linked to return and spawn timing, were either unique to or more divergent in the segregated line, suggesting that these traits may be responding to domestication selection. This study is one of the first to utilize genomic approaches to demonstrate the effectiveness of a conservation strategy, managed gene flow, on trait‐associated—and potentially adaptive—loci. The results will promote the development of trait‐specific tools to better monitor genetic change in captive and wild populations.