Richard W. Carmichael

Evolutionary effects of alternative artificial propagation programs: implications for viability of endangered anadromous salmonids

Most hatchery programs for anadromous salmonids have been initiated to increase the numbers of fish for harvest, to mitigate for habitat losses, or to increase abundance in populations at low abundance. However, the manner in which these programs are implemented can have significant impacts on the evolutionary trajectory and long‐term viability of populations. In this paper, we review the potential benefits and risks of hatchery programs relative to the conservation of species listed under the US Endangered Species Act. To illustrate, we present the range of potential effects within a population as well as among populations of Chinook salmon (Oncorhynchus tshawytscha) where changes to major hatchery programs are being considered. We apply evolutionary considerations emerging from these examples to suggest broader principles for hatchery uses that are consistent with conservation goals. We conclude that because of the evolutionary risks posed by artificial propagation programs, they should not be viewed as a substitute for addressing other limiting factors that prevent achieving viability. At the population level, artificial propagation programs that are implemented as a short‐term approach to avoid imminent extinction are more likely to achieve long‐term population viability than approaches that rely on long‐term supplementation. In addition, artificial propagation programs can have out‐of‐population impacts that should be considered in conservation planning.

Evolutionary consequences of habitat loss for Pacific anadromous salmonids

Large portions of anadromous salmonid habitat in the western United States has been lost because of dams and other blockages. This loss has the potential to affect salmonid evolution through natural selection if the loss is biased, affecting certain types of habitat differentially, and if phenotypic traits correlated with those habitat types are heritable. Habitat loss can also affect salmonid evolution indirectly, by reducing genetic variation and changing its distribution within and among populations. In this paper, we compare the characteristics of lost habitats with currently accessible habitats and review the heritability of traits which show correlations with habitat/environmental gradients. We find that although there is some regional variation, inaccessible habitats tend to be higher in elevation, wetter and both warmer in the summer and colder in the winter than habitats currently available to anadromous salmonids. We present several case studies that demonstrate either a change in phenotypic or life history expression or an apparent reduction in genetic variation associated with habitat blockages. These results suggest that loss of habitat will alter evolutionary trajectories in salmonid populations and Evolutionarily Significant Units. Changes in both selective regime and standing genetic diversity might affect the ability of these taxa to respond to subsequent environmental perturbations. Both natural and anthropogenic and should be considered seriously in developing management and conservation strategies.

Diminished Reproductive Success of Steelhead from a Hatchery Supplementation Program (Little Sheep Creek, Imnaha Basin, Oregon)

Abstract Hatchery supplementation programs are designed to enhance natural production and maintain the fitness of the target population; however, it can be difficult to evaluate the success of these programs. Key to the success of such programs is a relatively high reproductive success of hatchery fish. This study investigated the relative reproductive success (RRS) of steelhead Oncorhynchus mykiss (anadromous rainbow trout) by creating pedigrees for hatchery and natural spawning steelhead. We genotyped adult steelhead that returned to a weir and were released upstream to spawn in Little Sheep Creek, a tributary to the Imnaha River in eastern Oregon. The broodstock for this supplementation program were originally chosen from natural-origin steelhead returning to the weir and in subsequent years consisted of both natural- and hatchery-origin individuals. Microsatellite analyses showed the broodstock to be genetically similar to the natural population across years. We also genotyped adult resident rainbow t...

Run Timing, Spawn Timing, and Spawning Distribution of Hatchery- and Natural-Origin Spring Chinook Salmon in the Imnaha River, Oregon

Abstract We evaluated 16 years (1990–2005) of weir collection and spawning ground survey data to examine differences in run timing, spawn timing, and spawning distribution between naturally and hatchery-reared Chinook salmon Oncorhynchus tshawytscha in the Imnaha River, Oregon, and to look for changes in these variables over time. We compared run timing based on arrival time at the weir and found that naturally reared Chinook salmon arrived earlier than hatchery-reared fish in all 16 years. Carcasses of naturally reared fish of either or both sexes were recovered on the spawning grounds earlier than carcasses of hatchery-reared fish for all years combined and during 5 of 16 years, indicating earlier spawning by naturally reared fish. We compared spawning distribution using the percent of female carcasses recovered in each spawning ground survey reach. The percent recovery of the carcasses of naturally reared females was greater in reaches above the weir than below the weir and these carcasses were farther...

Salmon Restoration in the Umatilla River: A Study of Straying and Risk Containment

Abstract The use of artificial propagation may produce unexpected results and the need for risk containment. Stray chinook salmon (Oncorhynchus tshawytscha) from Umatilla River releases put the threatened Snake River stock at risk, caused conflict between two plans, altered management, and greatly increased the costs for hatchery-based restoration. Stray Umatilla returns captured or observed in the Snake River averaged more than 200 fish annually and comprised up to 26% of the escapement. The risk to the threatened population stimulated a series of containment actions, including wire tagging 2–3 million fish annually, use of acclimation ponds, altering release locations, flow enhancement, and broodstock management changes. Actions for the use of artificial propagation where straying or unexpected results are a concern include marking or tagging most or all fish, limiting the number of fish initially released, recognizing environmental variables that influence straying, ensuring that funding for risk conta...

Postrelease Performance of Acclimated and Directly Released Hatchery Summer Steelhead into Oregon Tributaries of the Snake River

Abstract In a study using 14 paired-release groups over 10 release years, we compared the performance of hatchery summer steelhead Oncorhynchus mykiss that were acclimated as smolts (AC) for 16–57 d before release into ponds supplied with ambient stream water with that of fish trucked from the hatchery and directly released (DR) into Spring, Deer, and Little Sheep creeks in northeastern Oregon. After releasing the fish into streams, we monitored out-migration travel times and survival to Lower Granite Dam (LGD) on the Snake River using freeze brand marks or implanted passive integrated transponder tags in a subsample of each release group. Across all release groups, travel time was significantly slower for AC fish (34.7 d) than for DR fish (31.8 d), though there was no significant difference in survival probability to LGD. We used recoveries of coded wire tags to estimate smolt-to-adult survival (SAS) and a stray rate index (SRI) for the AC and DR strategies. Across all release groups, SAS was 33% higher ...

Migration Characteristics of Hatchery and Natural Spring Chinook Salmon Smolts from the Grande Ronde River Basin, Oregon, to Lower Granite Dam on the Snake River

Abstract Smolts of spring Chinook salmon Oncorhynchus tshawytscha experience substantial mortality while migrating through free-flowing reaches of the Snake River basin before reaching Lower Granite Dam, the first dam encountered in the Columbia-Snake river hydrosystem. We investigated the patterns of travel time and survival of hatchery and natural smolts fitted with passive integrated transponder (PIT) tags through specific reaches of the migration corridor during the 2000-2006 migration years for two populations originating in the Grande Ronde River basin (Lostine River and Catherine Creek). For both populations, median travel times for natural smolts were significantly longer in the upper reaches of the migration corridor but shorter in the lower reaches than for their hatchery counterparts. Also, among both hatchery and natural smolts, smaller individuals spent more time in the upper reaches, presumably feeding to attain a larger size before continuing their migration. Within populations, both hatche...

The Effect of Moderately Increased and Variable Raceway Flow Rates on Juvenile Physiology, Survival, and Adult Return of Hatchery-Reared Chinook Salmon

Abstract Increasing hatchery raceway flow to a rate similar to that seen in nature exercises salmon in the expectation that improving swimming ability will result in better survival. However, insufficient water prevents most hatcheries from fully simulating natural stream currents. We examined the effect of moderate and seasonally variable flow rates (0.25–0.75 body lengths/s) on growth and physiology of juvenile Chinook salmon Oncorhynchus tshawytscha and their ability to withstand acute stress, survive downstream migration, and return as adults. Changes in salmon growth, condition, and hematocrit followed similar patterns and did not substantially vary between treatments or cohorts. Patterns of change in plasma glucose levels were also similar for each treatment. Hepatosomatic index was higher in the 1994 cohort than in the 1995 cohort and in the exercised salmon. Liver glycogen levels were higher in the 1995 cohort. Plasma glucose and cortisol levels increased after stress and were greater in the contr...

Analyzing large‐scale conservation interventions with Bayesian hierarchical models: a case study of supplementing threatened Pacific salmon

Myriad human activities increasingly threaten the existence of many species. A variety of conservation interventions such as habitat restoration, protected areas, and captive breeding have been used to prevent extinctions. Evaluating the effectiveness of these interventions requires appropriate statistical methods, given the quantity and quality of available data. Historically, analysis of variance has been used with some form of predetermined before-after control-impact design to estimate the effects of large-scale experiments or conservation interventions. However, ad hoc retrospective study designs or the presence of random effects at multiple scales may preclude the use of these tools. We evaluated the effects of a large-scale supplementation program on the density of adult Chinook salmon Oncorhynchus tshawytscha from the Snake River basin in the northwestern United States currently listed under the U.S. Endangered Species Act. We analyzed 43 years of data from 22 populations, accounting for random effects across time and space using a form of Bayesian hierarchical time-series model common in analyses of financial markets. We found that varying degrees of supplementation over a period of 25 years increased the density of natural-origin adults, on average, by 0–8% relative to nonsupplementation years. Thirty-nine of the 43 year effects were at least two times larger in magnitude than the mean supplementation effect, suggesting common environmental variables play a more important role in driving interannual variability in adult density. Additional residual variation in density varied considerably across the region, but there was no systematic difference between supplemented and reference populations. Our results demonstrate the power of hierarchical Bayesian models to detect the diffuse effects of management interventions and to quantitatively describe the variability of intervention success. Nevertheless, our study could not address whether ecological factors (e.g., competition) were more important than genetic considerations (e.g., inbreeding depression) in determining the response to supplementation.

Survival and Straying of Hatchery Steelhead following Forced or Volitional Release

Abstract In this study, conducted over four release years, we compare the performance of hatchery steelhead Oncorhynchus mykiss that were force-released (FR) from acclimation ponds with that of fish given a 2-week volitional release (VR). After fish were released into streams, we monitored smolt out-migration travel times and survival to Lower Granite Dam on the Snake River using passive integrated transponder (PIT) tags in a subsample of each release group. To better understand the out-migration characteristics of volitionally departing fish, we also captured and PIT-tagged fish as they exited ponds in the first and last 24 h of VR. Across all release groups, travel time was 3% faster for fish that were forced from acclimation ponds than for VR groups; however, the average survival of VR groups (65.0%) was significantly higher than that of FR groups (58.6%). On average, fish that departed acclimation ponds in the first 24 h of VR took 6 d longer to reach Lower Granite Dam and had lower survival (50.3%) t...