PROJECT COORDINATION AND PARTNERSHIPS
The genetics pedigree work will be carried out by Michael Blouin at Oregon State University.  This project is coordinated with the Hood River steelhead hatchery and research program, funded by Bonneville Power Administration and administered and implemented by the Oregon Department of Fish and Wildlife and the Warm Springs Tribes (project numbers 198805307, 198805308, 198805304 and 198805303).  These projects include operation and maintenance of the Oak Springs and Parkdale hatchery facilities, and operation and maintenance of the fish collection and handling facility at Powerdale Dam, as well as database management and data analysis on the part of ODFW.

LOCATION OF PROJECT
Steelhead samples were collected at Powerdale Dam, Hood River, under supervision of Rod French, ODFW, who will also coordinate aging of scale samples.  All laboratory work and genetics data analysis to be conducted in the laboratory of Michael Blouin at Oregon State University.

BACKGROUND AND RESULTS TO DATE FROM THE HOOD RIVER
The Hood River supports two populations of steelhead, a summer run and a winter run.  They spawn only above the Powerdale Dam, which is a complete barrier to all salmonids.  Since 1991 every adult passed above the dam has been measured, cataloged and sampled for scales or fin snip.  Therefore, we have a DNA sample from every adult steelhead that went over the dam to potentially spawn in the Hood River from 1991 to the present.  Similar numbers of hatchery and wild fish have been passed above the dam during the last decade.  During the 1990's "old" domesticated hatchery stocks of each run (multiple generations in the hatchery, out-of-basin origin; hereafter “Hold”) were phased out, and conservation hatchery programs were started for the purpose of supplementing the two wild populations (hereafter "new" hatchery stocks, “Hnew”).  The winter-run Hnew were started in 1991, and the summer-run Hnew were started in 1997.  In a supplementation program such as this, wild-born broodstock are used as parents in the hatchery in an attempt to circumvent the low fitness induced by multiple generations of selection in the hatchery.  These samples give us the unprecedented ability to estimate, via microsatellite-based pedigree analysis, the relative total reproductive success (adult to adult production) of hatchery (H) and wild (W) fish for two populations (summer and winter), over multiple brood years.  We now have a three-generation pedigree that is complete for all anadromous fish. Note, however, that we are missing samples from resident fish that apparently are the parents of many steelhead.  We compared the relative success of two "old" hatchery stocks vs. wild fish (the winter run “Big Creek” stock and the summer run “Skamania” stock), and showed they have much lower total fitness than wild fish when both breed in the wild (Araki et al., 2007a).  In that paper we also concluded that the winter-run Hnew were not significantly different from wild fish, based on 3 run years of data.  But in a subsequent analysis based on six run years of data the difference was significant, with the Hnew winter run fish averaging about 85% the fitness of wild fish (Araki et al., 2007d).  

One problem with interpreting an observed difference in fitness between fish raised in a hatchery and fish raised in the wild is that the difference can have a genetic and/or environmental basis (because the H fish experienced a very different environment during the juvenile phase).  Therefore, the question of whether the hatchery effect is genetic or environmental in origin is very important.  In Araki et al. (2007d) we were also able to compare the first generation, Hnew fish with second-generation hatchery fish raised in the same hatchery.  These data suggest that the second generation fish have ~55% the reproductive fitness of the first generation fish (Araki et al., 2007d).  Because both types of fish experienced identical environments, the difference between them must be genetically based.  This result also suggests that the decline in fitness that results from recycling “hatchery genes” back through the hatchery can occur very quickly.  

Thus, we have demonstrated a genetically-based effect of hatchery culture that reduces fitness in the wild and that accumulates with each generation of hatchery culture.  Nevertheless, even if captive-bred individuals are genetically different and produce fewer offspring than wild individuals, adding them to a wild population can still give a demographic boost without substantial harm to a wild population that is below carrying capacity if (1) the genetic effects do not persist into the next generation (i.e., natural selection purges the offspring generation of their deleterious alleles before they reproduce), and (2) enough captive-bred individuals are added each generation to make up for their lower productivity.   If the first condition is not true, however, genetic effects will accumulate over time, potentially leading to a downward spiral in the absolute fitness of the supplemented wild population.  Thus, the key question is whether the wild-born descendents of captive-bred fish are less reproductively successful than the descendents of wild fish.  With the completion of the third generation of the pedigree (i.e. figure 1 in Araki et al., 2009) we have now been able to analyze the fitness of wild-born fish as a function of their parentage.  We found that wild-born offspring of two first-generation hatchery fish averaged 37% the fitness of the offspring of wild fish, while offspring of hatchery-by-wild crosses averaged 87% (Araki et al., 2009).  These results suggest that the hatchery genetic load is not purged from the wild-born population after a full generation of natural selection in the wild.  

To summarize the work to date on the Hood River, we have shown: (1) the older, multi-generation, summer and winter hatchery stocks from the Hood River had very low fitness relative to wild fish (10-30%).  This result is consistent with results of many other studies on old stocks (Berejikian and Ford, 2004; Araki et al., 2008). (2) first generation winter run fish have significantly lower fitness than wild fish (about 85%), second generation fish do even worse, and the effect is genetically based. (3) The genetic effects of hatchery culture identified for the winter-run stock persist into the first wild-born generation, with the fitness of wild-born fish depending on whether their parents were both wild, both hatchery or one of each.  Again, the common environment experienced by these three types of wild fish suggests a genetic effect.

In addition to completing our main mission of analyzing the fitness of hatchery and wild fish and their descendents, we have also addressed several other applied and basic questions.  These topics include the effects of hatchery stock and resident fish on the effective size of the Hood River population (Araki et al., 2007b) and methodological work on methods for fitness estimation (Araki and Blouin, 2005) and estimation of effective size (Araki et al., 2007c).  We just finished testing what fraction of missing parents were hatchery residualized fish, and found that only a very few could have been.  Therefore, residualized hatchery fish are not a significant route of gene flow from the hatchery into the wild steelhead population (Christie et al., 2010).  

CONTINUING AND FUTURE WORK

We will focus on the following three questions (see the Narrative of Work Element C (162) ‘Analyze/Interpret data’ for additional background and references):

(1) How general are the results that we found for winter-run steelhead in the Hood River?  
It was no surprise that older stocks had extremely low fitness, but the low fitness of the first and second generation winter-run hatchery fish was unexpected.  Because of the management implications of our results, it is important to assess their generality. We can now estimate the relative fitness of the first-generation hatchery summer-run steelhead in the Hood River.  Because the winter and summer run are reproductively independent and breed in different forks of the Hood River, these summer-run data will represent an independent test of the hypothesis that first-generation hatchery steelhead have lower fitness than wild fish.

(2) What are the mechanisms that cause the rapid decline?
This is probably the most important question that needs to be answered.  It appears that strong selection in some part of the life cycle is causing hatchery fish to quickly evolve to be different than wild fish.  But we do not know which traits are involved.  The answer to this question would help identify ways to modify the hatchery experience in order to lessen those selection pressures.  Here we will attempt to identify any genes that are differentially expressed between fry raised in identical environments, but that differ in parentage (parents we either wild or hatchery fish).  Any genes that are differentially expressed between the two types of fish may point us to the physiological pathways that responded to selection, thus potentially identifying the selective pressure.

REFERENCES CITED
Araki, H. and M.S. Blouin. 2005. Unbiased estimation of relative reproductive success of different groups: evaluation and correction of bias caused by parentage assignment errors. Molecular Ecology, 13:4907-4110.

Araki, H., W.R. Ardren, E. Olsen, B. Cooper and M.S. Blouin. 2007a. Reproductive success of captive-bred steelhead trout in the wild: evaluation of three hatchery programs in the Hood River. Conservation Biology 21:181-190.

Araki, H., R.S. Waples, W.R. Ardren, B. Cooper and M.S. Blouin. 2007b. Effective population size of steelhead trout: influence of variance in reproductive success, hatchery programs, and genetic compensation between life-history forms. Molecular Ecology 16:953-966

Araki, H., R.S. Waples and M.S. Blouin. 2007c. A potential bias in the temporal method for estimating Ne in admixed populations under natural selection. Molecular Ecology 16: 2261–2271

Araki, H., B. Cooper and M.S. Blouin. 2007d. Genetic effects of captive breeding cause a rapid, cumulative fitness decline in the wild. Science 318: 100-103.

Araki, H., B. Berejikian, M. Ford, and M.S. Blouin. 2008 Fitness of hatchery-reared salmonids in the wild. Evolutionary Applications 1:342-355.

Araki, H., B. Cooper and M.S. Blouin. 2009. Carry-over effect of captive breeding reduces reproductive fitness of wild-born descendents n the wild. Biology Letters doi: 10.1098/rsbl.2009.0315

Berejikian, B. A., and M. J. Ford. 2004. Review of the Relative Fitness of Hatchery and Natural Salmon. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-61. 28 p. Northwest Fisheries Science Center, Seattle, WA.

Blouin, M.S. V. Thuillier, B. Cooper, V. Amarasinghe, L. Cluzel, H. Araki and C. Grunau. 2010. No evidence for large differences in genomic methylation between wild and hatchery steelhead trout (Oncorhynchus mykiss). Canadian Journal of Fisheries and Aquatic Sciences. 67: 217-224.

Christie, M.R., M.L. Marine and M.S. Blouin. 2011. Who are the missing parents? Grandparentage analysis identifies multiple sources of gene flow into a wild population. Molecular Ecology, 20, 1263–1276