Monitoring the Reproductive Success of Naturally Spawning Hatchery and Natural Spring Chinook Salmon in the Wenatchee River, 2008-2009 Progress Report.

Abstract

Executive SummaryWe investigated differences in the statistical power to assign parentage between an artificially propagated and wild salmon population. The propagated fish were derived from the wild population, and are used to supplement its abundance. Levels of genetic variation were similar between the propagated and wild groups at 11 microsatellite loci, and exclusion probabilities were >0.999999 for both groups. The ability to unambiguously identify a pair of parents for each sampled progeny was much lower than expected, however. Simulations demonstrated that the proportion of cases the most likely pair of parents were the true parents was lower for propagated parents than for wild parents. There was a clear relationship between parentage assignment ability and the degree of linkage disequilibrium, the estimated effective number of breeders that produced the parents, and the size of the largest family within the potential parents. If a stringent threshold for parentage assignment was used, estimates of relative fitness were biased downward for the propagated fish. The bias appeared to be largely eliminated by either fractionally assigning progeny among parents in proportion to their likelihood of parentage, or by assigning progeny to the most likely set of parents without using a statistical threshold.We used a DNA-based parentage analysis to measure the relative reproductive success of hatchery-and natural-origin spring Chinook salmon in the natural environment. Both male and female hatchery-origin fish produced far fewer juvenile progeny per parent when spawning naturally than did natural origin fish. Differences in age structure, spawning location, weight and run timing were responsible for some of the difference in fitness. Male size and age had a large influence on fitness, with larger and older males producing more offspring than smaller or younger individuals. Female size had a significant effect on fitness, but the effect was much smaller than the effect of size on male fitness. For both sexes, run time had a smaller but still significant effect on fitness, with earlier returning fish favored. Spawning location within the river had a significant effect on fitness for both males and females, and for females explained most of the reduced fitness observed for hatchery fish in this population.While differences have been reported in the relative reproductive success of hatchery and naturally produced salmonids Oncorhynchus spp., factors explaining the differences are often confounded. We examined the spawning site habitat and redd structure variables of hatchery and naturally produced spring Chinook salmon O. tshawytscha of known size that spawned in two tributaries of the Wenatchee River. We controlled for variability in spawning habitat by limiting our analysis to redds found within four selected reaches. No difference in the instantaneous spawner density or location of the redd in the stream channel was detected between reaches. Within each reach, no difference in the fork length or weight of hatchery...

Early male maturity explains a negative correlation in reproductive success between hatchery‐spawned salmon and their naturally spawning progeny

“…In contrast, and similar to the coho salmon study, we found little evidence that the use of wild origin fish as broodstock influenced the reproductive success of their progeny. This observation appears consistent with the observed high rates of exchange between the hatchery and natural environments in our study population (Ford et al 2011).…”

A mobile sex-determining region, male-specific haplotypes, and rearing environment influence age at maturity in Chinook salmon

“…A hatchery program was established on the Chiwawa River, a major spring-run Chinook spawning tributary of the Wenatchee River, in 1989 to supplement the wild population; this hatchery uses a mixture of natural and hatchery origin fish captured within the watershed each year for broodstock. Similarly, approximately 50%-80% of the natural spawners in a given year are hatchery-origin fish (Ford et al 2013). The high rates of exchange between the hatchery broodstock and the natural spawning population make this an ‘integrated’ hatchery program with the goal of minimizing genetic divergence between the hatchery and natural groups (Mobrand et al 2005).…”

Using parentage analysis to estimate rates of straying and homing in Chinook salmon (Oncorhynchus tshawytscha)

“…Since 1989, hatchery supplementation using broodstock captured within the watershed has been used to increase abundance, and the hatchery has produced 50-80% of the spawners in the river each year (Ford et al 2013). Here, a hatchery-origin fish refers to a fish whose parents were spawned in the hatchery, and a natural-origin fish refers to a fish whose parents spawned in the stream, regardless of their prior ancestry.…”