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 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
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.  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”).  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 and wild (W) fish for two populations, over multiple brood years, and for multiple generations through F2's.  We are comparing the relative success of two "old" hatchery stocks vs. wild fish (the winter run “Big Creek” stock and the summer run “Skamania” stock), and two "new", supplementation hatchery stocks vs. wild (one created in the early 1990’s for winter run, and one created in the late 1990’s for summer run).  Our previous analyses of samples from the 1990's show that "old" hatchery stocks have much lower total fitness than wild fish when both breed in the wild, but that the first three years of comparison between Hnew and wild showed no statistically significant difference (Araki et al., 2007a).  We have now analyzed an additional three years of data comparing Hnew to wild, and over the total of  six years we see a significant difference, with Hnew averaging 85% the production of surviving adult offspring as 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 showed evidence for a genetic effect of recycling hatchery fish back through the hatchery.  This was a common garden experiment in which we compared the fitness of hatchery fish created using either two wild parents or a wild and a hatchery parent.  In 1995 the Hood River program changed their spawning protocols and started incorporating first-generation, returning Hnew adults into their broodstock.  They used a returning first-generation Hnew fish as one parent and a wild fish as the second parent (H x W) in about 2/3 of the crosses each year.  The other 1/3 of crosses were W x W as before.  Thus, they created two types of Hnew fish.  I will refer to these two different types of Hnew fish as Hnew-hxw and Hnew-wxw.  This mixing of Hnew and wild fish in the broodstock of the supplementation program was done five years in a row (1995-1999).  We have analyzed the fitness of the Hnew that were created in 1995-1997, which returned to spawn in the wild mostly in 1998-2000, and whose offspring returned through 2006.  These data suggest that the Hnew-hxw have ~55% the reproductive fitness of Hnew-wxw (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 cumulative, genetically-based effect of hatchery culture that reduces fitness in the wild.  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 former 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 organisms are less reproductively successful than the descendents of wild organisms.  We will soon be able to test that hypothesis by comparing the reproductive fitness of adult, wild-born steelhead trout (Oncorhynchus mykiss) that descended from captive-bred or from wild-born parents that spawned side-by-side in the Hood River.  We now have the returned grand-offspring in hand to do that analysis for three run years of wild-born F1 fish that had either two wild parents, two hatchery parents, or one of each.

Overall project goals:
Estimate the reproductive success (total fitness defined as adult-to-adult production) of hatchery-origin steelhead relative to that of wild-origin steelhead that have been spawning in the Hood River.  Estimate this difference using "old" hatchery stock vs. wild, and "new" hatchery stock vs. wild.  Do the comparison for multiple brood years, in both the summer and winter runs, in order to estimate the year-to-year variance in the parameters.  To date we have compared the fitness of wild and hatchery winter run from the 1991 (Hold), and 1995 to2000 (Hnew) run years, and for Hold summer run from the 1994 through 1997 run years.  We propose continuing sampling and genotyping through the rest of this decade, and finishing the back log of samples back to 1991, in order to generate an almost 20 year pedigree for the two runs.  From this pedigree we will obtain estimates of the mean and year-to-year variance in the relative reproductive success of hatchery vs. wild fish, parameter estimates that are critical for predicting the effects of hatchery supplementation on wild steelhead populations.  We will, in particular, focus on the long-term effects of cycling hatchery genes back through the hatchery, and on the persistence of hatchery effects into the next wild generation (as outlined above).  These data will be very relevant to the question of whether or not successful reproduction by supplementation hatchery fish in the wild has negative genetic effects on the wild population.  Finally, we will also use the pedigree to ask a number of other applied and basic questions on topics including the fitness of repeat spawners and the genetic interactions between resident and anadromous O. mykiss.  Other applied questions we have successfully addressed using this dataset include analysis of 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).

Specific objectives for fiscal year 2009 (Oct 2009 through Sept 2010)

(1) Manage and supervise one year of work.
Work element E (119). Involves supervision of project personnel, interviewing and hiring, budgeting, coordination with collaborators and university personnel, and making decisions on project design and prioritization of effort, such as which samples to run and which analyses to focus on each year.

(2) Genotype 3000 fish.
Work element C (157).  Involves obtaining, for each fish, a genotype at the eight microsatellite loci that we use for this project (Araki et al., 2007a).  Includes initial runs, re-running samples as needed, inputting each genotype into the master database of all fish sampled from the Hood River, and error checking.  We will focus on last year’s returns and on the backlog of summer-run samples from the early 1990’s.

(3) Analyze the data in terms of relative fitness of hatchery and wild fish
Work element B (162).  We will work on two main sets of analyses.  (a) Winter-run: relative fitness of wild-born fish that had different types of parents (b) Analyze the fitness of repeat spawners.  

(4) Produce quarterly and annual reports describing progress and results
Work elements F (132) and G (185).  Reports detailing progress towards completion of each work element, and final report summarizing accomplishments for the year.

(5) Communicate results via scientific meetings and publications
Work element D (161).  Post doc or principle investigator to attend at least one professional meeting to present current year’s results.  


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.