Project summary

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 winter run "new" stocks have fitness that is about equal to that of wild, winter-run fish (Araki et al., 2007a).  We also showed that the winter-run supplementation program should achieve the short term goal of boosting population size for a single generation.  

Although our data to date suggest that supplementation can be used successfully for a short-term demographic boost, an unanswered question is the long-term effects of supplementation beyond a single generation.  Even if one always uses unmarked, wild-born fish as broodstock each year, the problem with supplementation programs that extend beyond one generation is that one normally does not know the pedigree of those unmarked fish.  Thus, one inevitably starts cycling “hatchery genes” back through the hatchery.  Although a large amount of data (including our results on Hold vs. wild) show that multiple generations through the hatchery causes substantial fitness declines, how fast such an effect will occur in a supplementation program remains an open empirical question.  We will address this question in two ways.  First, beginning in 1999 appreciable numbers of wild-born (unmarked) fish that had Hnew parents began returning as adults.  Because they were unmarked, some of these fish were taken into the hatchery and used as broodstock.  We will eventually be able to test whether Hnew fish that had hatchery grandparents, are less fit than Hnew fish that had wild grandparents.  This will be a direct test of the predicted long-term, cumulative fitness effects of supplementation beyond a single generation.  Note that we require several more years of returns before we can conduct these analyses, so these are not proposed for the current fiscal year.  The second way we will examine the effects of cycling hatchery genes back through the hatchery (and which can be done now) involves an experiment that was set up in the mid-1990’s.  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 now 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 initial results suggest that the Hnew-hxw are substantially less fit than the Hnew-wxw.  Because both types of fish experienced identical environments, the difference between them must be genetically based.  This result suggests that the decline in fitness that results from recycling “hatchery genes” back through the hatchery can occur very quickly.  For FY08 we will do the same analysis for the next run year, and so on in each coming year until we have analyzed all five cohorts.  

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, 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 2008 (Oct 2007 through Sept 2008)

(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 3600 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 three main sets of analyses.  (a) Winter-run: relative fitness of the three types of fish that spawned in 1998-2001 (wild, Hnew-hxw and Hnew-wxw.  (b) Summer run: relative fitness of wild vs. Hold fish that spawned in 1993 - 1997.  (c) 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