Richard W. Zabel

The road to extinction is paved with good intentions: negative association of fish hatcheries with threatened salmon

Hatchery programmes for supplementing depleted populations of fish are undergoing a worldwide expansion and have provoked concern about their ramifications for populations of wild fish. In particular, Pacific salmon are artificially propagated in enormous numbers in order to compensate for numerous human insults to their populations, yet the ecological impacts of this massive hatchery effort are poorly understood. Here we test the hypothesis that massive numbers of hatchery–raised chinook salmon reduce the marine survival of wild Snake River spring chinook, a threatened species in the USA. Based on a unique 25–year time–series, we demonstrated a strong, negative relationship between the survival of chinook salmon and the number of hatchery fish released, particularly during years of poor ocean conditions. Our results suggest that hatchery programmes that produce increasingly higher numbers of fish may hinder the recovery of depleted wild populations.

Evolutionary responses by native species to major anthropogenic changes to their ecosystems: Pacific salmon in the Columbia River hydropower system

The human footprint is now large in all the Earths ecosystems, and construction of large dams in major river basins is among the anthropogenic changes that have had the most profound ecological consequences, particularly for migratory fishes. In the Columbia River basin of the western USA, considerable effort has been directed toward evaluating demographic effects of dams, yet little attention has been paid to evolutionary responses of migratory salmon to altered selective regimes. Here we make a first attempt to address this information gap. Transformation of the free‐flowing Columbia River into a series of slack‐water reservoirs has relaxed selection for adults capable of migrating long distances upstream against strong flows; conditions now favour fish capable of migrating through lakes and finding and navigating fish ladders. Juveniles must now be capable of surviving passage through multiple dams or collection and transportation around the dams. River flow patterns deliver some groups of juvenile salmon to the estuary later than is optimal for ocean survival, but countervailing selective pressures might constrain an evolutionary response toward earlier migration timing. Dams have increased the cost of migration, which reduces energy available for sexual selection and favours a nonmigratory life history. Reservoirs are a benign environment for many non‐native species that are competitors with or predators on salmon, and evolutionary responses are likely (but undocumented). More research is needed to tease apart the relative importance of evolutionary vs. plastic responses of salmon to these environmental changes; this research is logistically challenging for species with life histories like Pacific salmon, but results should substantially improve our understanding of key processes. If the Columbia River is ever returned to a quasinatural, free‐flowing state, remaining populations might face a Darwinian debt (and temporarily reduced fitness) as they struggle to re‐evolve historical adaptations.

Using Time Series Analysis to Characterize Evolutionary and Plastic Responses to Environmental Change: A Case Study of a Shift toward Earlier Migration Date in Sockeye Salmon

Environmental change can shift the phenotype of an organism through either evolutionary or nongenetic processes. Despite abundant evidence of phenotypic change in response to recent climate change, we typically lack sufficient genetic data to identify the role of evolution. We present a method of using phenotypic data to characterize the hypothesized role of natural selection and environmentally driven phenotypic shifts (plasticity). We modeled historical selection and environmental predictors of interannual variation in mean population phenotype using a multivariate state-space model framework. Through model comparisons, we assessed the extent to which an estimated selection differential explained observed variation better than environmental factors alone. We applied the method to a 60-year trend toward earlier migration in Columbia River sockeye salmon Oncorhynchus nerka, producing estimates of annual selection differentials, average realized heritability, and relative cumulative effects of selection and plasticity. We found that an evolutionary response to thermal selection was capable of explaining up to two-thirds of the phenotypic trend. Adaptive plastic responses to June river flow explain most of the remainder. This method is applicable to other populations with time series data if selection differentials are available or can be reconstructed. This method thus augments our toolbox for predicting responses to environmental change.

Influence of River Conditions on Survival and Travel Time of Snake River Subyearling Fall Chinook Salmon

Abstract From 1995 to 2000, subyearling fall chinook salmon Oncorhynchus tshawytscha reared at Lyons Ferry Hatchery were PIT-tagged at the hatchery, trucked upstream, acclimated, and released into free-flowing sections of the Snake River weekly from early June to mid-July. We estimated survival probabilities and travel time through the lower Snake River and detection probabilities at dams for each weekly release group. The average median time between release and arrival at Lower Granite Dam was 43.5 d. For each group, we split this time into two nearly equal (on average) periods: one when most fish in the group were rearing and one when most fish had apparently begun active seaward migration. The estimated survival for hatchery fish from release to the tailrace of Lower Granite Dam decreased with release date each year. The estimated survival through this reach was significantly correlated with three environmental variables: survival decreased as discharge (“flow”) decreased, as water transparency increas...

Migration Timing, Growth, and Estimated Parr-to-Smolt Survival Rates of Wild Snake River Spring–Summer Chinook Salmon from the Salmon River Basin, Idaho, to the Lower Snake River

Abstract Survival, growth, and juvenile migration timing are key life history traits for at-risk salmon populations. To estimate these traits in threatened wild Snake River spring–summer Chinook salmon Oncorhynchus tshawytscha, we tagged fish as parr in 3–17 natal streams per year from 1991 to 2003. We injected passive integrated transponder tags into parr collected from streams within the Salmon River basin in Idaho. Each spring, after the previous summers tagging, fish were detected as smolts in the juvenile fish bypass systems of lower Snake River dams. Estimated parr-to-smolt survival to Lower Granite Dam (excluding migration year 1992) ranged from 3% to 48% for individual populations and from 8% to 25% (yearly average = 16%) for all streams combined. From 1998 to 2004, estimated parr-to-smolt survival declined from 25% to 8%, in part because of parr density-dependent effects. Overall annual average growth rates from tagging to detection at Little Goose Dam ranged from 39.7 to 43.3 mm during 2001–200...

SELECTIVE MORTALITY IN CHINOOK SALMON: WHAT IS THE ROLE OF HUMAN DISTURBANCE?

While many recovery programs for threatened species focus on acute sources of mortality, understanding some of the evolutionary processes of these species may lead to more effective recovery efforts, especially in cases where human-induced disturbances have resulted in artificial selection pressures. We developed a Monte Carlo test to determine whether Snake River spring/summer chinook salmon (Oncorhynchus tshawytscha) experienced selective mortality as a function of their juvenile length and timing of downstream migration. Actively migrating juvenile fish (smolts) were captured, tagged, and released in 1995 and 1996 approximately 700 km upstream from the Pacific Ocean, and returning adults were detected at the same location. We analyzed data from two groups of fish: those that migrated downstream in-river and those that were barged downstream as part of the juvenile-salmon transportation program. These groups were further separated into wild and hatchery fish. Length at release was significantly greater in returning adults than in the general population for fish that migrated downstream in-river (both wild and hatchery) or were transported (hatchery only). From the 1995 seaward migration, adult returns of both wild and hatchery fish that migrated in-river were composed of fish released significantly earlier than the general population. In contrast, the opposite trend existed for wild and hatchery transported fish. From the 1996 seaward migration, no significant difference in release date was found between returning adults and the original population for any of the groups analyzed. Fish length at migration is a result of factors encountered in early life stages but selectively determines mortality in the smolt-to-adult stage. Thus freshwater habitat improvements, such as salmon carcass supplementation, directed at increasing nutrient levels and thus fish length may result in an increase in overall survival. The development of hydroelectric dams in the migratory corridors of these fish has disrupted their arrival timing to the estuary. Mitigation efforts designed to shift arrival timing toward that experienced prior to impoundment may confer considerable survival benefits.

Interacting effects of density and temperature on body size in multiple populations of Chinook salmon

1. The size individuals attain reflects complex interactions between food availability and quality, environmental conditions and ecological interactions. A statistical interaction between temperature and the density of conspecifics is expected to arise from various ecological dynamics, including bioenergetic constraints, if population density affects mean consumption rate or activity level. Density effects on behaviour or size-selective predation could also generate this pattern. This interaction plays an important role in bioenergetic models, in particular, and yet has not been documented in natural populations. 2. The lengths of 131 286 juvenile wild Chinook salmon (Oncorhynchus tshawytscha) across 13 populations spread throughout the Salmon River Basin, Idaho, USA over 15 years were compared to test whether juvenile density alters the relationship between body size and temperature. 3. Strong evidence for a negative interaction between mean summer temperature and density emerged, despite the relatively cool temperatures in this high elevation habitat. Growth correlated positively with temperature at lower densities, but the correlation was negative at the highest densities. 4. This is the first study to document this interaction at such a large spatial and temporal scale, and suggests that warmer temperatures might intensify some density-dependent processes. How climate change will affect individual growth rates in these populations will depend intimately on ecological conditions, particularly food availability and population dynamics. More broadly, the conditions that led to the interactions observed in our study - limited food availability and temperatures that ranged above those optimal for growth - likely exist for many other natural populations, and warrant broader exploration.

Potential for anthropogenic disturbances to influence evolutionary change in the life history of a threatened salmonid

Although evolutionary change within most species is thought to occur slowly, recent studies have identified cases where evolutionary change has apparently occurred over a few generations. Anthropogenically altered environments appear particularly open to rapid evolutionary change over comparatively short time scales. Here, we consider a Pacific salmon population that may have experienced life‐history evolution, in response to habitat alteration, within a few generations. Historically, juvenile fall Chinook salmon (Oncorhynchus tshawytscha) from the Snake River migrated as subyearlings to the ocean. With changed riverine conditions that resulted from hydropower dam construction, some juveniles now migrate as yearlings, but more interestingly, the yearling migration tactic has made a large contribution to adult returns over the last decade. Optimal life‐history models suggest that yearling juvenile migrants currently have a higher fitness than subyearling migrants. Although phenotypic plasticity likely accounts for some of the change in migration tactics, we suggest that evolution also plays a significant role. Evolutionary change prompted by anthropogenic alterations to the environment has general implications for the recovery of endangered species. The case study we present herein illustrates the importance of integrating evolutionary considerations into conservation planning for species at risk.

Non-indigenous brook trout and the demise of Pacific salmon: a forgotten threat?

Non–indigenous species may be the most severe environmental threat the world now faces. Fishes, in particular, have been intentionally introduced worldwide and have commonly caused the local extinction of native fish. Despite their importance, the impact of introduced fishes on threatened populations of Pacific salmon has never been systemically examined. Here, we take advantage of several unique datasets from the Columbia River Basin to address the impact of non–indigenous brook trout, Salvelinus fontinalis, on threatened spring/summer–run chinook salmon, Oncorhynchus tshawytscha. More than 41 000 juvenile chinook were individually marked, and their survival in streams without brook trout was nearly double the survival in streams with brook trout. Furthermore, when brook trout were absent, habitat quality was positively associated with chinook survival, but when brook trout were present no relationship between chinook survival and habitat quality was evident. The difference in juvenile chinook survival between sites with, and without, brook trout would increase population growth rate (λ) by ca. 2.5%. This increase in λ would be sufficient to reverse the negative population growth observed in many chinook populations. Because many of the populations we investigated occur in wilderness areas, their habitat has been considered pristine; however, our results emphasize that non–indigenous species are present and may have a dramatic impact, even in remote regions that otherwise appear pristine.

SURVIVAL AND SELECTION OF MIGRATING SALMON FROM CAPTURE-RECAPTURE MODELS WITH INDIVIDUAL TRAITS

Capture-recapture studies are powerful tools for studying animal population dynamics, providing information on population abundance, survival rates, population growth rates, and selection for phenotypic traits. In these studies, the probability of ob- serving a tagged individual reflects both the probability of the individual surviving to the time of recapture and the probability of recapturing an animal, given that it is alive. If both of these probabilities are related to the same phenotypic trait, it can be difficult to distinguish effects on survival probabilities from effects on recapture probabilities. However, when animals are individually tagged and have multiple opportunities for recapture, we can properly partition observed trait-related variability into survival and recapture components. We present an overview of capture-recapture models that incorporate individual variability and develop methods to incorporate results from these models into estimates of population survival and selection for phenotypic traits. We conducted a series of simulations to un- derstand the performance of these estimators and to assess the consequences of ignoring individual variability when it exists. In addition, we analyzed a large data set of > 153 000 juvenile chinook salmon (Oncorhynchus tshawytscha) and steelhead (0. mykiss) of known length that were PIT-tagged during their seaward migration. Both our simulations and the case study indicated that the ability to precisely estimate selection for phenotypic traits was greatly compromised when differential recapture probabilities were ignored. Estimates of population survival, however, were far more robust. In the chinook salmon and steelhead study, we consistently found that smaller fish had a greater probability of recapture. We also uncovered length-related survival relationships in over half of the release group/river segment combinations that we observed, but we found both positive and negative rela- tionships between length and survival probability. These results have important implications for the management of salmonid populations.