Search

Fish in all the world's oceans exhibit variable body size and growth over time, with some populations exhibiting long-term declines in size. These patterns can be caused by a range of biotic, abiotic, and anthropogenic factors and impact the productivity of harvested populations. Within a given species, individuals often exhibit a range of life history strategies that may cause some groups to be buffered against change. One of the most studied declines in size-at-age has been in populations of salmon; Chinook salmon in the Northeast Pacific Ocean are the largest-bodied salmon species and have experienced long-term declines in size. Using long-term monitoring data, we develop novel size and growth models to link observed changes in Chinook size to life history traits and environmental variability. Our results identify three distinct trends in size across the 48 stocks in our study. Differences among populations are correlated with ocean distribution, migration timing, and freshwater residence. We provide evidence that trends are driven by interannual variation in certain oceanographic processes and competition with pink salmon.

People seek reliable natural resources despite climate change. Diverse habitats and biologies stabilize productivity against disturbances like climate, prompting arguments to promote climate-resilient resources by prioritizing complex, less-modified ecosystems. These arguments hinge on the hypothesis that simplifying and degrading ecosystems will reduce resources' climate resilience, a process liable to be cryptically evolving across landscapes and human generations, but rarely documented. Here, we examined the industrial era (post 1848) of California's Central Valley, chronicling the decline of a diversified, functional portfolio of salmon habitats and life histories and investigating for empirical evidence of lost climate resilience in its fishery. Present perspectives indicate that California's dynamic, warming climate overlaid onto its truncated, degraded habitat mosaic severely constrains its salmon fishery. We indeed found substantial climate constraints on today's fishery, but this reflected a shifted ecological baseline. During the early stages of a stressor legacy that transformed the landscape and -- often consequently -- compressed salmon life history expression, the fishery diffused impacts of dry years across a greater number of fishing years and depended less on cool spring-summer transitions. The latter are important given today's salmon habitats, salmon life histories, and resource management practices, but are vanishing with climate change while year-to-year variation in fishery performance is rising. These findings give empirical weight to the idea that human legacies influence ecosystems' climate resilience across landscapes and boundaries (e.g., land/sea). They also raise the question of whether some contemporary climate effects are recent and attributable not only to increasing climate stress, but to past and present human actions that erode resilience. In general, it is thus worth considering that management approaches that prioritize complex, less-modified ecosystems may stabilize productivity despite increasing climate stress and such protective actions may be required for some ecological services to persist into uncertain climate futures.

The portfolio effect plays a critical role in population productivity and stability. Age structure of spawning salmon represents an example of portfolio effects such that the risks of experiencing unfavorable conditions are spread across time. However, the distribution of maturation ages for Pacific salmon ( Oncorhynchus spp.) is increasingly concentrated into fewer and younger ages, which may impact population resilience to climate change. We explored the population dynamics of Sacramento River fall-run Chinook salmon ( O. tshawytscha) under different age structure scenarios using a life-cycle model and compared two mechanisms that can underlie these changes—mortality and maturation. In addition, we tested whether age structure promotes resilience to drought. We found that high age structure diversity increased the stability of population size and harvest compared with low diversity. However, mean population size responded differently depending on the underlying mechanism. Reduced mortality of adult fish ages 4–5 increased escapement, whereas delayed maturation decreased escapement. Overall, high age structure diversity was able to buffer against the adverse effects of droughts by reducing the variability of population size and harvest compared with low diversity. Our results suggest that age structure promotes stability of salmon in an increasingly variable climate.

Fish face many anthropogenic stressors. Authorities in marine, estuarine, and freshwater realms often share interdependent fisheries management goals, but address singular stressors independently. Here, we present a case study suggesting that coordinating stressor relief across management realms may synergize conservation efforts, especially to actualize restoration benefits. Major efforts are underway to restore juvenile salmon habitat across California’s Central Valley landscape, but it is unclear how fisheries and flow management will influence juvenile salmon occupancy of restored sites. Leveraging monitoring data, we find that for juvenile salmon (

Many ecological data sets are proportional, representing mixtures of constituent elements such as species, populations, or strains. Analyses of proportional data are challenged by categories with zero observations (zeros), all observations (ones), and overdispersion. In lieu of ad hoc data adjustments, we describe and evaluate a zero-and-one inflated Dirichlet regression model, with its corresponding R package (zoid), capable of handling observed data

Preseason abundance forecasts drive management of US West Coast salmon fisheries, yet little is known about how environmental variability influences forecast performance. We compared forecasts of Chinook salmon (Oncorhynchus tshawytscha) against returns for (i) key California-Oregon ocean fishery stocks and (ii) high priority prey stocks for endangered Southern Resident Killer Whales (Orcinus orca) in Puget Sound, Washington. We explored how well environmental indices (at multiple locations and time lags) explained performance of forecasts based on different methods (i.e. sibling-based, production-based, environment-based, or recent averages), testing for nonlinear threshold dynamics. For the California stocks, no index tested explained >50% of the variation in forecast performance, but spring Pacific Decadal Oscillation and winter North Pacific Index during the year of return explained >40% of the variation for the sibling-based Sacramento Fall Chinook forecast, with nonlinearity and apparent thresholds. This suggests that oceanic conditions experienced by adults (after younger siblings returned) have the most impact on sibling-based forecasts. For Puget Sound stocks, we detected nonlinear/threshold relationships explaining >50% of the variation with multiple indices and lags. Environmental influences on preseason forecasts may create biases that render salmon fisheries management more or less conservative, and therefore could motivate the development of ecosystem-based risk assessments.

Author(s): Cordoleani, Flora; Satterthwaite, William H.; Daniels, Miles E.; Johnson, Matthew R. | Abstract: Life cycle models (LCMs) provide a quantitative framework that allows evaluation of how management actions targeting specific life stages can have population-level impacts on a species. The LCM building process is also a powerful tool that can be used to identify data gaps existing in the knowledge of the target species, and that might strongly influence overall population dynamics. LCMs are particularly useful for species such as salmon that are highly migratory and use multiple aquatic ecosystems throughout their life. Furthermore, they are lacking for threatened Central Valley spring-run Chinook (Oncorhynchus tshawytscha; CVSC). Here, we developed a CVSC LCM to describe the dynamics of Mill, Deer and Butte Creek CVSC populations. We used model construction, calibration and a global sensitivity analysis to highlight important data gaps in the monitoring of those populations. In particular, we found strong model sensitivity and high uncertainty in various egg, juvenile and adult ocean life stages’ biological processes. We concluded that the current CVSC monitoring network is insufficient to support using a LCM to inform how future management actions (e.g., hydrology and habitat restoration) influence CVSC dynamics. We propose a series of monitoring recommendations, such as the development of an enhanced juvenile tracking monitoring program and the implementation of juvenile trapping efficiency methodology combined with genetic identification tools, to help fill highlighted data gaps. These additional data collection efforts will provide critical quantitative information about the status of this imperiled species at key life stages (e.g., CVSC juvenile abundance estimates), and create a more comprehensive monitoring framework fundamental for working on the recovery of the entire stock. Furthermore, additional data collection will strengthen the LCM parameterization and calibration process, and ultimately improve the model’s predictive performance.

Ocean fisheries often target and catch aggregations comprising multiple populations or groups of a given species. Chinook salmon (Oncorhynchus tshawytscha) originating from rivers throughout the west coast of North America support mixed-stock ocean fisheries and other ecosystem components, notably as prey for marine mammals. We construct the first coastwide state-space model for fall Chinook salmon tagged fish released from California to British Columbia between 1977 and 1990 to estimate seasonal ocean distribution along the west coast of North America. We incorporate recoveries from multiple ocean fisheries and allow for regional variation in fisheries vulnerability and maturation. We show that Chinook salmon ocean distribution depends strongly on region of origin and varies seasonally, while survival showed regionally varying temporal patterns. Simulations incorporating juvenile production data provide proportional stock composition in different ocean regions and the first coastwide projections of Chinook salmon aggregate abundance. Our model provides an extendable framework that can be applied to understand drivers of Chinook salmon biology (e.g., climate effects on ocean distribution) and management effects (e.g., consequences of juvenile production changes).

Klamath River Fall Chinook (KRFC) salmon from the Klamath-Trinity Basin are central to management of the ocean salmon fishery off the coasts of northern California and southern Oregon, with tagged KRFC serving as proxies for other stocks including spring run (KRSC). There has been no formal comparison of fall versus spring run ocean distributions, and published studies using genetic stock identification do not distinguish the runs. We modeled the spatial distribution of hatchery-origin fall versus spring run, inferred from coded-wire tag recoveries in the ocean commercial (troll) fishery while explicitly accounting for fishing effort, sampling rate, and release of sublegal-sized fish before sampling. Distributions for all stocks were confined to a similar core range, but varied seasonally, and with higher relative density of KRSC in the north. Only equivocal evidence was found for differences by age or within-basin source hatchery. The potential for such differences should be considered for analyses of coarser groupings in these and other stocks. Sensitivity analyses revealed differences in distributions inferred from recreational versus commercial fishery data, emphasizing the importance of recognizing the limitations of fishery-dependent data in representing the underlying spatial distribution of fish populations rather than spatial patterns in their interactions with specific fisheries.

Hatcheries can support salmon fisheries but also impact natural populations. We model the proportional hatchery contributions to ocean catch, natural-area spawning, and egg production based on hatchery production, maturation, fecundity, and straying. We develop indices of hatchery-origin catch per stray spawner measuring the trade-off between supplementing harvest and limiting natural-area impacts; higher values indicate success in increasing hatchery ocean harvest contributions relative to strays spawning in natural areas. Hatchery fish maturing early lowers catch per stray (and proportion hatchery-origin catch) by shifting the age distributions of both catch and spawners toward younger ages. Age-dependent fecundity may complicate predicted effects of changing maturation schedules. Increased straying does not affect catch but increases hatchery-origin spawning and decreases catch per stray. Differences in hatchery production affect hatchery contributions to both catch and spawning, exacerbating the trade-off between these conflicting goals but with no net effect on catch per stray. Fishery intensity magnifies the effects of accelerated hatchery fish maturation by reducing spawning contributions of older fish, with contrasting effects depending on whether hatchery fish mature early versus late.

Population diversity is a mechanism for resilience and has been identified as a critical issue for fisheries management, but restoration ecologists lack evidence for specific habitat features or processes that promote phenotypic diversity. Since habitat complexity may affect population diversity, it is important to understand how population diversity is partitioned across landscapes and among populations. In this study, we examined life history diversity based on size distributions of juvenile Central Valley Chinook salmon (Oncorhynchus tshawytscha) within the Yolo Bypass, a remnant transitional habitat from floodplain to tidal sloughs in the upper San Francisco Estuary (SFE). We used a generalized least squares model with an autoregressive (AR1) correlation structure to describe the distribution of variation in fish size from 1998 to 2014, and tested the effect of two possible drivers of the observed variation: (i) environmental/seasonal drivers within the Yolo Bypass, and (ii) the juvenile Chinook source population within the Sacramento River and northern SFE. We found that the duration of floodplain inundation, water temperature variation, season, and sampling effort influenced the observed time-specific size distribution of juvenile Chinook salmon in the Yolo Bypass. Given the lack of seasonally inundated habitat and low thermal heterogeneity in the adjacent Sacramento River, these drivers of juvenile size diversification are primarily available to salmon utilizing the Yolo Bypass. Therefore, enhancement of river floodplain-tidal slough complexes and inundation regimes may support the resilience of imperiled Central Valley Chinook salmon.

Invasive plants often occupy large ranges in the introduced region and consequently, local population dynamics vary in ways that affect the potential for biological control. We used matrix models to describe how density and population growth rate of Centaurea solstitialis varies in time and space. Matrix models were parameterized with data collected over 4 years from invasions at the coast, interior valleys and Sierra Nevada Mountains in California (USA). Asymptotic population growth rates (λ) varied dramatically across all populations and years (0.24–6.45), density varied by an order of magnitude and had a measurable effect on survival and λ in all populations. We used simulations to estimate the degree to which a biocontrol agent would need to reduce plant survival to control the weed. Because seedling survival was dependent on density, an agent that reduced seedling density had the effect of increasing the probability that the remaining plants survived to flowering. Interestingly, this meant that in the highest density populations the plant had the largest compensatory response to agent attack and experienced decline (λ ≤ 1.0) only after heavy losses (≥90%) to the agent. Conversely, in populations where density was so low that it had only a weak effect on survival, the agent was able to control the plant (λ ≤ 1.0) at much lower levels of attack (≤50%). In other words, the impact of a biocontrol agent is predicted to be lower where the plant reaches its highest densities because the surviving plants, now experiencing less intraspecific competition, are more likely to survive to flowering and produce more seeds. This may also be true for other invasive species in which strong density dependent processes are operating. For this reason, prospective agents ought to target density-independence vital rates.

We used coded wire tag data to compare spawner age structure and seasonal patterns of age-specific size at date among fish harvested in the ocean from the four seasonal run timings (fall, late-fall, winter, and spring) of Chinook Salmon Oncorhynchus tshawytscha from the Central Valley, California, and we examined differences between the fall-run fish (the most abundant run) from the Sacramento and San Joaquin River basins. The runs varied in their ocean size at a common age and date, and within each run, monthly mean ocean sizes appeared to stop increasing when spawners began to return to freshwater. Despite support for multiple hypotheses, no single factor explained all of the variation among and within runs. Ocean size at a common date was well explained by a “juvenile head-start” hypothesis, predicting larger sizes for the spring and fall runs due to earlier ocean entry. Month of spawner return was well explained by a “premature adult migration” hypothesis, predicting earlier returns (within ye...

We describe a new model developed for the purpose of projecting rebuilding periods for overfished Pacific salmon stocks as defined by the Pacific Fishery Management Council. The model has relatively low data requirements as it relies on past estimates of abundance to project future abundance, accounting for positive lag-1 autocorrelation if there is evidence of its existence. Replicate applications of the model allow for computation of the probability of achieving rebuilt status in future years. Application to simulated abundance and escapement data suggested that model-projected rebuilding times generally corresponded to simulated rebuilding times as raw errors were median unbiased. Simulations also suggested that results were generally robust to parameter misspecification and that increased levels of lag-1 autocorrelation in abundance were associated with longer rebuilding periods. The application of the model to five overfished stocks in 2018–2019 illustrated the differences in projected rebuilding times under alternative rebuilding management strategies. The model filled a need for relatively rapid assessment of alternative rebuilding strategies for Pacific salmon stocks, a need that will likely remain given current biological reference points and fluctuations in salmon abundance.

Many studies of semelparous salmon populations use Leslie matrices that classify individuals on the basis of age alone and do not explicitly impose death upon reproduction. Although these models may suffice for studying long-term population dynamics (like asymptotic growth rate), they do not accurately represent the diversity of individual life history outcomes in semelparous populations. Cohorts breeding at different ages have different life history traits (e.g., age at first reproduction and remaining life expectancy) that are obscured in Leslie models and this distorts our understanding of life history diversity and its importance for semelparous population dynamics. We present a simple transformation that uses age-specific breeding probabilities to reconfigure Leslie matrices as explicitly semelparous models. Explicitly semelparous models conserve asymptotic measures like population growth rate, vital rate elasticities, life expectancy at birth, and generation time but also better predict life history schedules and reproductive values. Strictly age-classified Leslie models underestimate ages at first reproduction and mean ages at death for older breeders but overestimate mean ages at death for early breeders. Leslie models also slightly overestimate variance in lifetime reproductive success, and underestimate entropy exhibited by life history outcomes.

Ecologists are pressed to understand how climate constrains the timings of annual biological events (phenology). Climate influences on phenology are likely significant in estuarine watersheds because many watersheds provide seasonal fish nurseries where juvenile presence is synched with favorable conditions. While ecologists have long recognized that estuaries are generally important to juvenile fish, we incompletely understand the specific ecosystem dynamics that contribute to their nursery habitat value, limiting our ability to identify and protect vital habitat components. Here we examined the annual timing of juvenile coldwater fish migrating through a seasonally warm, hydrologically managed watershed. Our goal was to (1) understand how climate constrained the seasonal timing of water conditions necessary for juvenile fish to use nursery habitats and (2) inform management decisions about (a) mitigating climate‐mediated stress on nursery habitat function and (b) conserving heat‐constrained species in warming environments. Cool, wet winters deposited snow and cold water into mountains and reservoirs, which kept the lower watershed adequately cool for juveniles through the spring despite the region approaching its hot, dry summers. For every 1°C waters in April were colder, the juvenile fish population (1) inhabited the watershed 4–7 d longer and (2) entered marine waters, where survival is size selective, at maximum sizes 2.1 mm larger. Climate therefore appeared to constrain the nursery functions of this system by determining seasonal windows of tolerable rearing conditions, and cold water appeared to be a vital ecosystem component that promoted juvenile rearing. Fish in this system inhabit the southernmost extent of their range and already rear during the coolest part of the year, suggesting that a warming climate will truncate rather than shift their annual presence. Our findings are concerning for coldwater diadromous species in general because warming climates may constrain watershed use and diminish viability of life histories (e.g., late springtime rearing) and associated portfolio benefits over the long term. Lower watershed nurseries for coldwater fish in warming climates may be enhanced through allocating coldwater reservoir releases to prolong juvenile rearing periods downstream or restorations that facilitate colder conditions.

Biocomplexity contributes to asynchronous population dynamics, buffering stock complexes in temporally variable environments, a phenomenon referred to as a “portfolio effect”. We previously revealed a weakened but persistent portfolio effect in California’s Central Valley fall-run Chinook salmon (Oncorhynchus tshawytscha), despite considerable degradation and loss of habitat. Here, we further explore the timing of changes in variability and synchrony and relate these changes to factors hypothesized to influence variability in adult abundance, including hatchery release practices and environmental variables. We found evidence for increasing synchrony among fall-run populations that coincided temporally with increased off-site hatchery releases into the estuary but not with increased North Pacific environmental variability (measured by North Pacific Gyre Oscillation), nor were common trends well explained by a suite of environmental covariates. Moreover, we did not observe a simultaneous increase in synchrony in the nearby Klamath–Trinity system, where nearly all hatchery releases are on-site. Wavelet analysis revealed that variability in production was higher and at a longer time period later in the time series, consistent with increased environmental forcing and a shift away from dynamics driven by natural spawners.

We evaluated the scope for improving abundance forecasts for fishery management using Sacramento River fall Chinook salmon (Oncorhynchus tshawytscha) as a case study. A range of forecast models that related the Sacramento Index (SI; an index of adult ocean abundance) to jack (estimated age 2) spawning escapement the previous year were considered. Alternative models incorporated effects of density dependence, local environmental conditions, the abundance of the previous cohort, and trends or autocorrelation in the jack-to-SI relationship. Forecast performance was assessed in terms of bias, accuracy, ability to track trends in the SI, and management objectives. Several models achieved higher accuracy than the model used for management, but no single model performed best across all criteria, and substantial forecast error remained across all approaches considered. Environmental models generally performed better than the management model, but there were differences in the relative importance of individual environmental variables over time and among model formulations. Accounting for model selection uncertainty in environmental models decreased their forecast performance. Simpler models often had similar or better performance than environmental models. In particular, the model incorporating temporally autocorrelated errors demonstrated potential for modest forecast improvement with relatively little additional model complexity.

Author(s): O'Farrell, Michael R.; Satterthwaite, William H.; Hendrix, Albert N.; Mohr, Michael S. | Abstract: https://doi.org/10.15447/sfews.2018v16iss4art4 Sacramento River winter-run Chinook salmon are listed under the Endangered Species Act as Endangered and there are substantial efforts to estimate, predict, and limit mortalities at various stages of their life cycle. One such effort is the annual forecast of the number of juvenile winter-run entering the Sacramento-San Joaquin Delta. The natural-origin Juvenile Production Estimate (JPE) is defined as the number of winter-run juveniles produced from natural spawning areas that enter the Delta, and its forecast is used to determine the allowable level of winter-run incidental take at the state and federal pumping facilities located in the south Delta. Current monitoring programs in the Sacramento Basin do not allow for direct estimation of the JPE and thus various methods have been used to forecast this value annually. Here we describe three alternative methods for forecasting the natural-origin JPE. The methods range from the status quo approach (Method 1), which expresses the JPE forecast only as a point estimate, to two other methods that account for forecast uncertainty to various degrees. A comparison of JPE forecasts for 2018 across the three methods indicates that relative to Method 1, Methods 2 and 3 result in lower JPE forecasts, by 24 and 18 percent, respectively, primarily owing to lower forecasts of the fry-to-smolt transition and the smolt survival rate occurring downstream of Red Bluff Diversion Dam. Because post-hoc estimates of juvenile winter-run abundance at the entrance to the Delta do not currently exist, we are unable to evaluate forecast skill among the three methods.

Author(s): Satterthwaite, William H.; Cordoleani, Flora; O'Farrell, Michael R.; Kormos, Brett; Mohr, Michael S. | Abstract: Central Valley spring-run Chinook Salmon (CVSC) are designated threatened by state and federal authorities. Although CVSC are caught in ocean fisheries, their harvest is not actively managed, because it is assumed that measures currently in place to protect endangered Sacramento River winter-run Chinook Salmon (SWRC) will also sufficiently protect CVSC. Recoveries of tags and genetically-identified CVSC suggest these fish have a more northerly distribution than SRWC. Further, escapement data and cohort reconstructions suggest that CVSC mature later than SRWC. Thus, regulations (time/area restrictions and minimum size limits) crafted to protect SRWC alone may not adequately protect CVSC; on the other hand, regulations to constrain impacts on Klamath River and California coastal Chinook Salmon populations may also reduce impacts on CVSC. Trends in CVSC escapement were deemed acceptable in recent status updates, but concerns remain because of the negative effects caused by recent drought and ocean conditions. Should more active management of CVC be desired, current options are limited. The most promising approach is based on estimating age-specific ocean fishing mortality rates by using cohort reconstructions applied to tagged Chinook Salmon that originate from the Feather River Hatchery. At a minimum, ocean fishing mortality rates could be monitored and compared to proxy thresholds. If reference harvest rates were established, harvest models could be developed to predict how CVSC would be affected by fishing regulations, similar to the way fall-run Chinook Salmon fisheries are evaluated. Abundance forecasts would require improved juvenile production data (e.g., from genetic sampling of juvenile emigrants), since sibling-based forecasts commonly used for fall-run Chinook Salmon would not be available in time for pre-season planning. It is unclear if ocean fishing mortality rate estimates derived from hatchery proxies for natural-origin fish are truly representative, but existing data do not demonstrate obvious differences in ocean distribution or size-at-age fish. Substantial new investments in tagging or sampling would be needed to directly estimate ocean fishing mortality rates for natural-origin CVSC. Establishing specific harvest targets or limits for CVSC requires an improved understanding of production throughout their life cycle through juvenile production estimates and long-term information on spawner age structure.

The match-mismatch hypothesis suggests there is an optimal window for organisms to undergo key life cycle events. Here, we test the importance of match-mismatch dynamics in the timing of salmon arrival to the ocean, relative to ecosystem phenology, for the ocean survival rates of hatchery-origin fall run Chinook salmon originating from California's Central Valley. Specifi- cally, we considered tag recovery data for releases of coded-wire tagged fish released into the San Francisco Estuary during the years 1978 to 2010. We determined a time lag for each release relative to the local spring transition date (initiation of net upwelling). Additionally, we obtained information on fish condition and size at release, the number of fish released corresponding to distinct tag codes, and yearly stock-specific harvest rate estimates. We used generalized linear models, generalized additive models, and cross-validation to identify the best-supported models for the effects of release timing and other covariates on age-3 ocean fishery recovery rates, a proxy of ocean survival rates. Release time is a useful predictor of within-year variation in survival rates, above and beyond the effects of size at release, presence of disease, and the use of net pens, and the lag relative to spring transition was a slightly better predictor than year-day. The optimal release timing appeared to occur around the end of May, and the optimal time lag appeared to be approximately 70 to 115 d after the spring transition date. However, timing is only one of many factors that affected within- and among-year variation in survival.

An eco-genetic model tuned on a population of marble trout Salmo marmoratus subject to periodic flood events was used to explore how the evolution of growth rates interacting with density-dependent processes can modify size at age and population structure and in turn influence the resilience of populations. Fish with greater growth potential were assumed to have higher mortality rates. The results of simulations were compared between two scenarios, one in which populations may evolve growth rates and the other one in which the distribution of growth rates within a population is kept fixed. Evolving populations had a greater proportion of age 1 year individuals in the population, greater median length at age 3 years (the typical age at sexual maturity for S. marmoratus) and lower population sizes. The slightly smaller population sizes did not affect realized extinction risk. Resilience, defined as the number of years necessary to rebound from flood-induced population collapse, was on average from 2 to 3 years in both scenarios, with no significant difference between them. Moderate heritability of growth, relaxation of density-dependent processes at low densities and rapid recovery to a safe population size combine to limit the capacity to evolve faster recovery after flood-induced population collapses via changing growth rates.

Managing weak stocks in mixed-stock fisheries often relies on proxies derived from data-rich indicator stocks, although there have been limited tests of the appropriateness of such proxies. For example, full cohort reconstruction of tagged Klamath River fall-run Chinook Salmon Oncorhynchus tshawytscha of northern California enables the use of detailed models to inform management. Information gained from this stock is also used in the management of the untagged, threatened California Coastal Chinook Salmon (CCC) stock, where it is assumed that a cap on Klamath harvest rates effectively constrains impacts on CCC to acceptable levels. To evaluate use of this proxy, we used a novel approach based on genetic stock identification (GSI) data to compare the two stocks’ size at age and ocean distribution (as inferred from spatial variation in CPUE), two key factors influencing fishery exposure. We developed broadly applicable methods to account for both sampling and genetic assignment uncertainty in estima...

Avian predation on juvenile salmonids is an important source of mortality in freshwater and estuarine habitats when birds and salmonids overlap spatially and temporally. We assessed the potential impact of avian predation upon juvenile steelhead Oncorhynchus mykiss in a coastal watershed in central California. We conducted stream surveys between 2008 and 2010 to determine the composition, distribution, and density of piscivorous birds in areas that provide rearing habitat for juvenile steelhead. The most commonly sighted bird species were common mergansers Mergus merganser and belted kingfishers Megacyrle alcyon. The density of avian predators varied spatially and temporally but was greatest in the estuary regardless of season and decreased with increasing distance from the estuary. In the absence of local predator diet data, we applied a bioenergetics model to estimate the potential predation on juvenile steelhead by mergansers and kingfishers in the Scott Creek estuary. Model parameters include...

We adapt methods from the stochastic theory of invasions – for which a key question is whether a propagule will grow to an established population or fail – to show how monitoring early participation in a social collaboration network allows prediction of success. Social collaboration networks have become ubiquitous and can now be found in widely diverse situations. However, there are currently no methods to predict whether a social collaboration network will succeed or not, where success is defined as growing to a specified number of active participants before falling to zero active participants. We illustrate a suitable methodology with Wikipedia. In general, wikis are web-based software that allows collaborative efforts in which all viewers of a page can edit its contents online, thus encouraging cooperative efforts on text and hypertext. The English language Wikipedia is one of the most spectacular successes, but not all wikis succeed and there have been some major failures. Using these new methods, we derive detailed predictions for the English language Wikipedia and in summary for more than 250 other language Wikipedias. We thus show how ideas from population biology can inform aspects of technology in new and insightful ways.

Cohort reconstructions (CR) currently applied in Pacific salmon management estimate temporally variant exploitation, maturation, and juvenile natural mortality rates but require an assumed (typically invariant) adult natural mortality rate (dA), resulting in unknown biases in the remaining vital rates. We explored the sensitivity of CR results to misspecification of the mean and/or variability of dA, as well as the potential to estimate dA directly using models that assumed separable year and age/cohort effects on vital rates (separable cohort reconstruction, SCR). For CR, given the commonly assumed dA = 0.2, the error (RMSE) in estimated vital rates is generally small (≤ 0.05) when annual values of dA are low to moderate (≤ 0.4). The greatest absolute errors are in maturation rates, with large relative error in the juvenile survival rate. The ability of CR estimates to track temporal trends in the juvenile natural mortality rate is adequate (Pearson's correlation coefficient > 0.75) except for high dA (≥ 0.6) and high variability (CV > 0.35). The alternative SCR models allowing estimation of time-varying dA by assuming additive effects in natural mortality, fishing mortality, and/or maturation rates did not outperform CR across all simulated scenarios, and are less accurate when additivity assumptions are violated. Nevertheless an SCR model assuming additive effects on fishing and natural (juvenile and adult) mortality rates led to nearly unbiased estimates of all quantities estimated using CR, along with borderline acceptable estimates of the mean dA under multiple sets of conditions conducive to CR. Adding an assumption of additive effects on the maturation rates allowed nearly unbiased estimates of the mean dA as well. The SCR models performed slightly better than CR when the vital rates covaried as assumed. These separable models could serve as a partial check on the validity of CR assumptions about the adult natural mortality rate, or even a preferred alternative if there is strong reason to believe the vital rates, including juvenile and adult natural mortality rates, covary strongly across years or age classes as assumed.

In this paper, we lay out the theoretical framework for using modeling approaches from behavioral ecology (in particular, state-dependent and game theoretical models) to predict the behavioral responses of central place foragers to changes in their food environment. We develop individual-based models of the state-dependent behavior of individual central place foragers over the course of a breeding season and show how our approach provides a framework for the prediction of trip lengths, foraging location, food delivery, and reproductive success. We formulate a common framework of models for northern fur seals (Callorhinus ursinus), black-legged kittiwakes (Rissa tridactyla), and thickbilled murres (Uria lomvia), and provide worked examples parameterized to represent fur seals and murres. We then develop a game theoretic model at the colony-level for predicting the distribution of multiple individuals across space in the face of potential interference or facilitation, providing a worked example for kittiwakes. We demonstrate how these models can be used to predict near-term aspects of foraging behavior such as diet choice and trip destinations and durations at the individual and colony level. We show how (i) behavioral predictions can be translated into predictions of foraging success, (ii) foraging success can be scaled up to demographically relevant parameters such as survival and reproduction, and (iii) this approach can help predict impacts of environmental change on top-level predators.

We examined the reproductive ecology of black-legged kittiwakes Rissa tridactyla in several breeding colonies in the North Pacific to test if inter-annual changes in the Pacific Decadal Oscillation (PDO), Winter Ice Cover (ICI), or local sea-surface temperature (SST) predict changes in productivity (fledglings per nest) or nutritional stress (corticosterone). We explored the implica- tions of the observed variation in productivity and stress for projected population dynamics based on a previously demonstrated corticosterone−survival relationship. Although productivity was highly variable (0 to 0.9 fledglings nest −1 ), the relationships between productivity and environ- mental indices were weak, with local SST providing slightly more explanatory power than PDO or ICI, suggesting that local factors rather than large-scale climate variability may determine varia- tion in productivity. The relationships between stress and environmental indices were stronger than the relationship between productivity and environment. The measured response of stress to environment showed opposite signs between the southern and northern colonies, and typically implied annual mortality rates varying from 11 to 17%. The observed relationships between cli- mate and stress indicate that anticipated warming might bring at least short-term demographic benefits for kittiwakes in the Bering shelf region, while having negative impacts on birds breeding in the Gulf of Alaska and western Aleutians. We predict decline (without immigration) for colonies with the lowest productivity and conclude that climate variability is likely to affect survival of North Pacific kittiwakes on a region-specific basis. Longevity of these birds may not always be sufficient to buffer their populations from low reproductive performance.

Oncorhynchus mykiss exhibit high plasticity in their life history patterns. Individual life history decisions are hypothesized to result from genetic thresholds shaped by local adaptation, with variation in environmental factors influencing the trajectories of growth and condition (e.g., Fulton's K, lipid content). We compared growth rates and life history patterns in two coastal creeks (Scott and Soquel) and two Central Valley (CV) rivers (American and Mokelumne) in California. The two regions differed markedly in habitat and physical factors, including hydrograph timing and amplitude, temperature regime, and food availability (measured as drift). Growth rates of coastal age-0 fish averaged 0.1 mm/d in summer–fall and 0.2 mm/d in winter–spring. Growth rates of CV fish were up to 10 times faster than those of fish on the coast and had the opposite seasonal pattern, in which growth in summer–fall was faster than that in winter–spring. Fish growth also differed between CV rivers; the mean growth ra...

Anadromous salmonids vary considerably in their age at ocean entry, their timing of ocean entry within a year, and the extent to which they use multiple habitat types within freshwater. To better understand habitat use and movement timing, we developed a broadly applicable model of state-dependent movements among multiple habitats, which was parameterized based on a case study of steelhead Oncorhynchus mykiss in a California coastal watershed with a seasonally closed lagoonal estuary. The model correctly predicted population-level patterns, including predominance of anadromy and a dominant smolt age of 2 years. In addition, the new model predicted the occurrence of small, lagoon-rearing fish (displaying smoltlike migratory behavior) that returned upstream and did not enter the ocean until the next year, whereas large fish emigrated from the lagoon into the ocean. The new model predicted all-or-nothing habitat use for fish of a given size, but we observed a mix of strategies for fish of the same s...

Biological control (the importation of enemies from an invader's native range) is often considered our best chance of controlling the most widespread invaders. Ideally, the agent reduces invader abundance to some acceptably low level, and the two coexist at low density with the agent providing continuous control over the long-term. But the outcome may be complicated when the agent is attacked by native predators and parasites. We used a spatially explicit, discrete-time, individual-based, coupled plant-seed predator-parasitoid model to estimate the impact of the biocontrol agent Eustenopus villosus (a seed predator) on the invasive, annual weed Centaurea solstitialis, both with and without the generalist parasitoid Pyemotes tritici. We estimated the agent's ability to reduce plant density, spread rate, and population growth rate over 50 years. We used long-term demographic data from two sites in central California, USA, to parameterize the model and assess how populations in different climatic zones might respond differently to the agent and the parasitoid. We found that the biocontrol agent reduced plant density (relative to predictions for an uncontrolled invasion), but its impact on the invader's spread rate was modest and inconsistent. The agent had no long-term impact on population growth rate (lambda). Parasitism caused a trophic cascade, the strength of which varied between sites. At our coastal site, the parasitoid entirely eliminated the impact of the agent on the plant. At our Central Valley site, even when parasitized, the agent significantly reduced plant density and spread rate over several decades (although to a lesser degree than when it was not parasitized), but not invader lambda. Surprisingly, we also found that the length of time the invader was allowed to spread across the landscape prior to introducing the agent (5, 25, or 50 years) had little influence over its ability to control the weed in the long-term. This is encouraging news for land managers attempting to control invasive plants that have already established widespread, high-density populations. Unfortunately, our results also show that attack by the native generalist parasitoid had a larger influence over how effectively the agent reduced invader performance.

Density-dependent variations in body growth and size have important consequences for the population dynamics of stream-dwelling salmonid populations, since body size is related to a variety of ecologically relevant characteristics. These include survival and fecundity, competitive and predatory abilities, and foraging behavior. However, little work has been done to understand how density-dependent body growth varies across temporal and spatial scales and when this compensatory process is relevant for recruitment and population dynamics of stream- dwelling salmonids. Increased intra- or inter-cohort competition reduces growth rates of juveniles. Both within- and among-cohort differences at the juvenile stage are likely to be maintained through the lifetime. Limited movement or dispersal can lead to subdivision of a population into several local populations with independent dynamics. The spatial and temporal variation in movement and the patchy distribution of resources make fish likely to experience density- dependence across location, life-stage, and season. The relaxation of density-dependent suppression of body growth at low densities constitutes a potential mechanism for salmonids to persist in the face of environmental perturbation and may contribute to explaining the peculiar resilience to population col- lapses often showed by salmonids. The inclusion of density-dependent growth in population models may increase the usefulness of model predictions in management contexts. Models not accounting for density-dependent growth may underestimate the recovery potential of resident salmonid populations when they collapse to low densities.

Optimal life histories in a fluctuating environment are likely to differ from those that are optimal in a constant environment, but we have little understanding of the consequences of bounded fluctuations versus episodic massive mortality events. Catastrophic disturbances, such as floods, droughts, landslides and fires, substantially alter the population dynamics of affected populations, but little has been done to investigate how catastrophes may act as a selective agent for life-history traits. We use an individual-based model of population dynamics of the stream-dwelling salmonid marble trout (Salmo marmoratus) to investigate how trade-offs between the growth and mortality of individuals and density-dependent body growth can lead to the maintenance of a wide or narrow range of individual variation in body growth rates in environments that are constant (i.e., only demographic stochasticity), variable (i.e., environmental stochasticity), or variable with catastrophic events that cause massive mortalities (e.g., flash floods). We find that occasional episodes of massive mortality can substantially reduce persistent variability in individual growth rates. Lowering the population density reduces density dependence and allows for higher fitness of more opportunistic strategies (rapid growth and early maturation) during the recovery period.

The confounding effects of difficult sampling and dynamic systems make uncertainty the norm for managers of marine ecosystems. Thus managers need approaches that use relatively small amounts of information and account for a wide suite of biological and physical influences. here we use a case study approach to review the use of several possible techniques for making decisions about marine ecosystems despite uncertainty. we describe the use of expert judgment in the rebuilding plans for data-poor us fisheries, models to manage the krill fishery in the southern ocean to account for both the impacts of climate change and the resource needs of krill predators, an integrated risk assessment framework to prioritize shark management in the atlantic ocean despite severe data limitations, and models to account for climate impacts on salmonid populations in california. Through this review, we show that with limited information, managers can use models to explore how highly variable systems might respond to management options under different scenarios. expert judgment can help shape the assumptions that form the basis for those models and propose sensible boundaries within which management options can be developed. a weight of evidence approach can take advantage of small amounts of information from multiple sources, including models and expert judgment. although none of these approaches is perfect, they can help provide a logical starting point for conservation and management, despite the certainty of uncertainty.

We tested the effect of temporal patterns in food supply on life history decisions in coastal steelhead Oncorhynchus mykiss irideus from a Central California coastal (CCC) population (Scott Creek) and a Northern California Central Valley (NCCV) population (upper Sacramento River basin). We manipulated growth through feeding experiments conducted from May to the following March using warm (2006 cohort) and cool (2007 cohort) temperature regimes. Survival in seawater challenges just before the time of typical juvenile emigration provided an index of steelhead smolt versus nonsmolt life history pathways. Survival varied significantly with fish size (with larger fish being more likely to survive than smaller fish) and by source population (with CCC steelhead being more likely to survive than NCCV steelhead of the same size). The timing of increased food supply (treatment group) did not significantly affect seawater survival rates in either NCCV or CCC steelhead. For both strains, the eventual survivo...

I present a model for the evolution of a seed bank in the absence of externally driven environmental variation. I use Evolutionarily Stable Strategy (ESS) analyses of both analytic and simulation models to assess the conditions under which a dormant genotype can invade and resist invasion. In my models, plant seeds compete through lottery for discrete safe sites holding one individual each. Analyzing the conditions under which a dormant genotype can invade when rare and resist invasion once established, I conclude that dormancy can be an ESS when some fraction of seeds is retained locally, seed bank survival is high, and mortality in the seed bank is low. The advantage of dormancy stems from the ability of dormant seeds to recapture a lost site and the fact that a plant’s offspring are more likely to win the lottery in its own site than in any new site. The advantage of dormancy does not depend on individual fecundity or on low relatedness with the offspring of kin, making this mechanism distinct from earlier models of sib competition.

We use a state dependent life history model to predict the life history strategies of female steelhead trout (Oncorhynchus mykiss) in altered environments. As a case study of a broadly applicable approach, we applied this model to the American and Mokelumne Rivers in central California, where steelhead are listed as threatened. Both rivers have been drastically altered, with highly regulated flows and translocations that may have diluted local adaptation. Nevertheless, evolutionary optimization models could successfully predict the life history displayed by fish on the American River (all anadromous, with young smolts) and on the Mokelumne River (a mix of anadromy and residency). The similar fitness of the two strategies for the Mokelumne suggested that a mixed strategy could be favored in a variable environment. We advance the management utility of this framework by explicitly modeling growth as a function of environmental conditions and using sensitivity analyses to predict likely evolutionary endpoints under changed environments. We conclude that the greatest management concern with respect to preserving anadromy is reduced survival of emigrating smolts, although large changes in freshwater survival or growth rates are potentially also important. We also demonstrate the importance of considering asymptotic size along with maximum growth rate.

Steelhead Oncorhynchus mykiss display a dizzying array of life history variation (including the purely resident form, rainbow trout). We developed a model for female steelhead in coastal California (close to the southern boundary of their range) in small coastal streams. We combined proximate (physiological) and ultimate (expected reproductive success) considerations to generalize the notion of a threshold size for emigration or maturity through the development of a state-dependent life history theory. The model involves strategies that depend on age, size or condition, and recent rates of change in size or condition during specific periods (decision windows) in advance of the actual smolting or spawning event. This is the first study in which such a model is fully parameterized based on data collected entirely from California steelhead populations, the majority of data coming from two watersheds the mouths of whose rivers are separated by less than 8 km along the coast of Santa Cruz County. We p...

Although conservation and restoration practitioners have focused on maximizing aboveground population size and seed set of rare plants, a clear understanding of seed bank dynamics is crucial to managing these species. Santa Cruz tarplant (Holocarpha macradenia) is a threatened annual forb restricted to coastal prairie habitats in central California. Holocarpha produces disk achenes germinating within a year of production and ray achenes forming a persistent seed bank. We constructed both deterministic and stochastic demographic models for a restored Holocarpha population, using demographic rates measured separately for unmanipulated plants and plants growing in plots where vegetation was clipped. The deterministic models indicated that regardless of germination from the seed bank, the population would decline without clipping or similar treatments that enhance survival and reproductive output. Deterministic models showed only a slight positive effect of increased ray seed germination rates on population growth, which would need to be balanced against a potential loss of buffering against environmental variation as the dormant seed bank was reduced. Our stochastic simulations suggested that extinction risk for Holocarpha populations would be minimized by intermediate levels of ray seed germination. Thus, managers should focus on improving the performance of aboveground plants before considering actions to stimulate germination, since the former will yield a greater increase in deterministic population growth and not sacrifice any buffering effect of the seed bank. This case study emphasizes the importance of considering dormant seeds and seed banks in designing successful restoration and management strategies for plant species at risk of extinction.

The traditional dichotomy of seed versus safe site limitation of plant populations is an oversimplification. While most plant models implicitly assume that the number of safe sites colonized will increase directly with increased seed production by each plant, the number of sites colonized may also strongly depend on patterns of seed dispersal relative to the parent plant, since the majority of a plant’s seeds are deposited very close to it and so not all safe sites are equally accessible. I created a series of spatially explicit individual based plant population models exploring how seed versus safe site limitation is jointly affected by the number of seeds produced per plant and mean dispersal distances. While increased dispersal distance led to reduced seed limitation (more saturation of available safe sites) when a parent plant’s site was temporarily unsuitable following its death, increased dispersal distances could increase seed limitation, especially at low per-plant fecundities, if safe sites did not turn over through time. Models comparing localized to global seed dispersal indicated substantially different degrees of seed limitation for constant per-plant fecundities. Thus seed addition experiments need to be designed to add seeds in realistic spatial patterns to yield meaningful results.