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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.

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.

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.

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.

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.

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.

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...

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.

We used a variety of modeling approaches to assess the effects of fire on the demography and population viability of scrub buckwheat (Eriogonum longifoliumvar. gna- phalifolium), a threatened herb endemic to periodically burned xeric uplands in central Florida, USA. We compared the management implications of different approaches. Using demographic data from ten years including five fires, we constructed Lefkovitch matrix models of scrub buckwheat populations in unburned habitats for populations experiencing a burn and for populations one year after burning. Deterministic analysis of the unburned matrices predicted relatively stable populations in unburned habitats using optimistic fertility estimates ( l5 1.002, 95% CI 0.975-1.033), but almost certain decline given pessimistic fertility estimates ( l5 0.981, 0.962-1.003). Burned populations are always predicted to increase (CI on l. 1.08). Numerical calculations of single-year growth rates based on the expected stable stage distribution of an unburned population yielded positive, but lower, growth rates. The l's calculated for periodically burned populations had confidence intervals entirely above 1 for fire return intervals shorter than 20 yr (optimistic) or 5 yr (pessimistic). Stochastic simulations yielded highly uncertain estimates of the probability of quasi-extinction over 250 yr, with only fire return intervals shorter than 20 yr (optimistic) or 5 yr (pessimistic) yielding quasi- extinction confidence intervals entirely below 1. Population growth rates in partially burned areas increased linearly with the proportion burned. The results of these density-independent simulations remained virtually unchanged (maximum difference of 5.2%) by introducing plausible population ceilings. Regression and stasis transitions had the highest elasticities for unburned populations, while fecundity elasticities were relatively greater for burn years. Transient elasticity analysis on total population size of simulated single-year post-fire growth and on the population vector five years in the future showed broadly similar patterns to standard elasticities, although the standard analysis assigned higher elasticity values to tran- sitions contributing to future reproductive potential. Fire management is important to en- couraging viable populations. Our analysis suggests minimum fire return intervals of 20 yr (optimistic) or 5 yr (pessimistic). These fire return intervals are consistent with those often used in the sandhill and oak-hickory scrub habitats of scrub buckwheat.

Among-individual heterogeneity in growth is a commonly observed phenomenon that has clear consequences for population and community dynamics yet has proved difficult to quantify in practice. In particular, observed among-individual variation in growth can be difficult to link to any given mechanism. Here, we develop a Bayesian state-space framework for modeling growth that bridges the complexity of bioenergetic models and the statistical simplicity of phenomenological growth models. The model allows for intrinsic individual variation in traits, a shared environment, process stochasticity, and measurement error. We apply the model to two populations of steelhead trout (Oncorhynchus mykiss) grown under common but temporally varying food conditions. Models allowing for individual variation match available data better than models that assume a single shared trait for all individuals. Estimated individual variation translated into a roughly twofold range in realized growth rates within populations. Comparisons between populations showed strong differences in trait means, trait variability, and responses to a shared environment. Together, individual- and population-level variation have substantial implications for variation in size and growth rates among and within populations. State-dependent life-history models predict that this variation can lead to differences in individual life-history expression, lifetime reproductive output, and population life-history diversity.

Conservationists are continually seeking new strategies to reverse population declines and safeguard against species extinctions. Here we evaluate the potential efficacy of a recently proposed approach to offset a major anthropogenic threat to many marine vertebrates: incidental bycatch in commercial fisheries operations. This new approach, compensatory mitigation for marine bycatch (CMMB), is conceived as a way to replace or reduce mandated restrictions on fishing activities with compensatory activities (e.g., removal of introduced predators from islands) funded by levies placed on fishers. While efforts are underway to bring CMMB into policy discussions, to date there has not been a detailed evaluation of CMMB's potential as a conservation tool, and in particular, a list of necessary and sufficient criteria that CMMB must meet to be an effective conservation strategy. Here we present a list of criteria to assess CMMB that are tied to critical ecological aspects of the species targeted for conservation, the range of possible mitigation activities, and the multi-species impact of fisheries bycatch. We conclude that, overall, CMMB has little potential for benefit and a substantial potential for harm if implemented to solve most fisheries bycatch problems. In particular, CMMB is likely to be effective only when applied to short-lived and highly-fecund species (not the characteristics of most bycatch-impacted species) and to fisheries that take few non-target species, and especially few non-seabird species (not the characteristics of most fisheries). Thus, CMMB appears to have limited application and should only be implemented after rigorous appraisal on a case-specific basis; otherwise it has the potential to accelerate declines of marine species currently threatened by fisheries bycatch.