James J, Anderson

University of Washington Seattle | UW · School of Aquatic and Fishery Sciences

Variation in the recruitment of salmon is often found to be correlated with marine climate indices, but mechanisms behind environment-recruitment relationships remain unclear and correlations often break down over time. We used an ecosystem model-ing approach to explore bottom-up and top-down mechanisms linking a variable environment to salmon recr...

Climate change and impoundment increase river temperatures, shifting the bioclimatic envelope in which freshwater biota have evolved and increasing salmonid egg mortality. To mitigate this, conservation flows from reservoirs are often implemented to maintain favourable water temperatures downstream from impoundments throughout salmonid embryo devel...

Decision triggers, used in adaptive management frameworks to decide when a specific management action will be implemented, are often informed by monitoring data. The identification and application of decision triggers is highly relevant to endangered fishes migrating through regulated rivers, as examined in the current study. The main goal was to d...

Background Severe COVID-19 T-cell lymphopenia is more common among older adults and entails poor prognosis. Offsetting the decline in T-cell count during COVID-19 demands fast and massive T-cell clonal expansion, which is telomere length (TL)-dependent. Methods We developed a model of TL-dependent T-cell clonal expansion capacity with age and virt...

Allocating reservoir flows to meet societal and ecosystem needs under increasing water demands and climatic variability presents challenges to resource managers. Often, rivers have been regulated to meet flow and temperature compliance points or mimic historical patterns. Because it is difficult to assess if this approach is efficient, process‐base...

Determining which factors are most effective for mitigative strategies in conservation management can be difficult for species with complex life cycles. Salmon (Oncorhynchus spp.) migrating through a hydroelectric power system experience conditions that can affect their survival directly within a life stage and indirectly in subsequent life stages...

The slow pace of global vaccination and the rapid emergence of SARS-CoV-2 variants suggest recurrent waves of COVID-19 in coming years. Therefore, understanding why deaths from COVID-19 are highly concentrated among older adults is essential for global health. Severe COVID-19 T-cell lymphopenia is more common among older adults, and it entails poor...

Population vital rates, such as stage-specific survival, are influenced by individual behavior and movement patterns. Yet few methods exist to incorporate behavior into predator-prey models, omitting a potentially important source of variability in population dynamics. Here were combine results from an acoustic telemetry study of juvenile Chinook s...

Allocating reservoir flows to meet societal and ecosystem needs under increasing demands for water and increasing climatic variability presents challenges to resource managers. Often, regulated rivers have been operated to meet flow and temperature compliance points that mimic historical patterns. Because it is difficult to assess if this approach...

While survivorship curves typically exhibit smooth declines over time, step-patterned curves can occur with multiple stressors within a life stage. To explore this process, we examined the effects of heat (24°C) and food restriction on juvenile rainbow trout (Oncorhynchus mykiss Walbaum) in challenge experiments. We observed step-patterned survivor...

A mechanistic model based on first principles of growth and predator-prey behavior introduces the effects of a predator size distribution on the survival of rapidly growing prey. The model, fit to Chinook salmon data, can explain the observed increase in ocean survival with smolt ocean entrance length using different predator size-frequency distrib...

Juvenile to adult survival of fish is modeled by the rate at which prey progressively escape the size distribution of gape-limited predators through growth. The model characterizes adult survival as a function of the mean and standard deviation of the predator population gape sizes, the ratio of mortality and growth rates and a compensatory growth...

Abstract Telomere length (TL) in offspring is positively correlated with paternal age at the time of the offspring conception. The paternal-age-at-conception (PAC) effect on TL is puzzling, and its biological implication at the population level is unknown. Using a probabilistic model of transgenerational TL and population dynamics, we simulated the...

A model describes the relationship between mammal body mass and survivorship by combining replicative senescence theory postulating a cellular basis of aging, metabolic theory relating metabolism to body mass, and vitality theory relating survival to vitality loss and extrinsic mortality. In the combined framework, intrinsic mortality results from...

Allocating reservoir flows to societal and ecosystem needs under increasing demands for water and increasing variability in climate presents challenges to resource managers. In the past, managers have operated reservoirs to achieve flow and temperature compliance points based on qualitative predictions of competing needs. Because it is difficult, i...

When introduced to exotic ecosystems, feral cats can inflict irreversible harm on native fauna. This is especially true in insular ecosystems because endemic vertebrate species often lack predator defenses. Feral cat control programs have been implemented on islands throughout the world with varied success. Effective and responsible management of p...

Experiences of migratory species in one habitat may affect their survival in the next habitat, in what is known as carryover effects. These effects are especially relevant for understanding how freshwater experience affects survival in anadromous fishes. Here, we study the carryover effects of juvenile salmon passage through a hydropower system (Sn...

Experiences of migratory species in one habitat may affect their survival in the next habitat, in what is known as carryover effects. These effects are especially relevant for understanding how freshwater experience affects survival in anadromous fishes. Here, we study the carryover effects of juvenile salmon passage through a hydropower system (Sn...

We examined delayed effects (or carryover effects) on marine survival from the freshwater experiences of migrating Chinook Salmon Oncorhynchus tshawytscha. Juvenile Chinook Salmon that differed in their freshwater experience in passing hydroelectric power dams of the Columbia and Snake rivers (Pacific Northwest) as run-of-the-river or barged fish w...

The relationship between body mass and survivorship is explained by a model that merges metabolic theory relating metabolism to body mass, and vitality theory relating survival to vitality loss and extrinsic mortality. The resulting metabolic-vitality framework hypothesizes mortality results from replicative senescence of the hematopoietic system a...

Individuals with short telomeres should be at increased risk for cancer, since short telomeres lead to genomic instability – a hallmark of cancer. However, individuals with long telomeres also display an increased risk for major cancers, thus creating a cancer-telomere length (TL) paradox. The two-stage clonal expansion model we propose is based on...

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Process point of view (POV) models of mortality, such as the Strehler-Mildvan and stochastic vitality models, represent death in terms of the loss of survival capacity through challenges and dissipation. Drawing on hallmarks of aging, we link these concepts to candidate biological mechanisms through a framework that defines death as challenges to v...

The rise in human life expectancy has involved declines in intrinsic and extrinsic mortality processes associated, respectively, with senescence and environmental challenges. To better understand the factors driving this rise, we apply a two-process vitality model to data from the Human Mortality Database. Model parameters yield intrinsic and extri...

Process point of view models of mortality, such as the Strehler-Mildvan and stochastic vitality models, represent death in terms of the loss of survival capacity through challenges and dissipation. Drawing on hallmarks of aging, we link these concepts to candidate biological mechanisms through a framework that defines death as challenges to vitalit...

The rise in human life expectancy has involved declines in intrinsic and extrinsic mortality processes associated, respectively, with senescence and environmental challenges. To better understand the factors driving this rise, we apply a two-process vitality model to data from the Human Mortality Database. Model parameters yield intrinsic and extri...

Ocean currents or temperature may substantially influence migration behavior in many marine species. However, high-resolution data on animal movement in the marine environment are scarce; therefore, analysts and managers must typically rely on unvalidated assumptions regarding movement, behavior, and habitat use. We used a spatially explicit, indiv...

Feral cats (Felis catus) have been shown to be a main contributor to species decline throughout the world and are especially threatening to insular species that lack appropriate defense characteristics. To mitigate the impact of feral cats on threatened species, space-use data are commonly used to design control strategies. In this article we repor...

Twin studies that focus on the correlation in age-at-death between twin pairs have yielded important insights into the heritability and role of genetic factors in determining lifespan, but less attention is paid to the biological and social role of zygosity itself in determining survival across the entire life course. Using data from the Danish Twi...

Two-process vitality model bias correction formulas. (PDF)

Certain herbivores and their predators undergo high amplitude periodic fluctuations in abundance in northern latitudes but exhibit damped cyclic dynamics in their respective southern ranges. Generalist predators and habitat disturbance have been identified as two features of southern habitats that may contribute to the attenuation of cycles in sout...

A vitality framework partitions mortality into intrinsic and extrinsic parts representing age-dependent loss of survival capacity and environmental challenges to the capacity. We extend a previous 4-parameter model suitable to modeling adult mortality to a 6-parameter form that includes vitality challenges to early life and thus is suitable for mod...

The Strehler and Mildvan (SM) general theory of ageing and mortality provides a mechanism-based explanation of Gompertz's law and predicts a log-linear relationship between the two Gompertz coefficients, known as the SM correlation. While the SM correlation is supported by data from developed countries before the second half of the twentieth centur...

Scope and Intent of Review: This report presents findings and opinions of the Independent Review Panel (IRP) assembled by the Delta Science Program to inform the National Marine Fisheries Service (NMFS) and the U.S. Fish & Wildlife Service (USFWS) as to the efficacy of water operations and certain regulatory actions prescribed by their respective L...

To mitigate negative impacts of delayed migration it is necessary to understand the causes of avoidance exhibited by animals at behavioural barriers. For downstream migrating juvenile salmon, avoidance of velocity gradients at anthropogenic structures may compromise fitness. Building on previous experimental investigations on salmonid response to v...

Significance Whereas adult salmon swimming upstream through a ladder visibly illustrates the challenge a dam presents to fish returning home to spawn, the downstream passage of juveniles swimming toward the ocean is often a greater, although more unseen, challenge to their survival. Decades of work have identified many factors that affect fish beha...

To study the complex coastal migrations patterns exhibited by juvenile Columbia River Chinook salmon as they enter and move through the marine environment, we created an individual-based model in a coupled Eulerian-Lagrangian framework. We modeled five distinct migration strategies and compared the resulting spatial distributions to catch data coll...

Determining when resource competition increases survivorship can reveal processes underlying population dynamics and reinforce the importance of heterogeneity among individuals in conservation. We ran an experiment mimicking the effects of competition in a growing season on survivorship during a selection event (e.g., overwinter starvation, drought...

Migrating animals rely on a variety of cues to guide them, but the relative importance of those signals may vary with size, life stage, or location. During their initial ocean migration, yearling Chinook salmon (Oncorhynchus tshawytcha) from the Columbia River have stock-specific spatial distributions that shift through time. We used a two-process...

The choice titration procedure presents a subject with a repeated choice between a standard option that always provides the same reward and an adjusting option for which the reward schedule is adjusted based on the subjects previous choices. The procedure is designed to determine the point of indifference between the two schedules which is then use...

Deviations from the Gompertz law of exponential mortality increases in late-middle and early-old age are commonly neglected in overall mortality analyses. In this study, we examined mortality increase patterns between ages 40 and 85 in 16 low-mortality countries and demonstrated sex differences in these patterns, which also changed across period an...

We projected effects of mid-21(st) century climate on the early-life growth of Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) in western United States streams. Air temperature and snowpack trends projected from climate models and observed 20(th) century trends were used to predict future seasonal stream temperatures. Fish growt...

Evidence is accumulating that ocean conditions affects survival of juvenile salmon and steelhead in the first year of residence in the ocean. A hypothesized mechanism is that early ocean survival depends on fish length which is determined by the length at ocean entrance and growth during the first year in the ocean. In turn, first year growth is in...

The age of first reproduction is known to correlate with economic- and longevity-related factors and a general pattern emerges in which reproduction timing is advanced when expected lifespan is shorter and timing is delayed with increased wealth and education. While these patterns have been considered with economic models, quantitative models based...

Proceedings of the workshop are available online as the NPAFC (North Pacific Anadromous Fish Commission) Technical Report #9 (2013): http://www.npafc.org/new/pub_technical9.html The specific link to this paper is: http://www.npafc.org/new/publications/Technical%20Report/TR9/Burke%20et%20al.pdf

Animals are capable of enhanced decision making through cooperation, whereby accurate decisions can occur quickly through decentralized consensus. These interactions often depend upon reliable social cues, which can result in highly coordinated activities in uncertain environments. Yet information within a crowd may be lost in translation, generati...

The oceanic distribution of Columbia River spring-summer Chinook Salmon Oncorhynchus tshawytscha is essentially unknown, as they are first detected in the fishery at the mouth of the river and then at Bonneville Dam, located 235 km upstream of the river mouth. Although the composite run timing to Bonneville Dam varies interannually, earlier studies...

Abstract BACKGROUND While historical declines in human mortality are clearly shaped by lifestyle and environmental improvements, modeling patterns is difficult because intrinsic and extrinsic processes shape mortality through complex stochastic interactions. OBJECTIVE To develop a stochastic model describing intrinsic and extrinsic mortality rates...

Juvenile yearling Chinook salmon emigrating from the Columbia River, USA, tend to migrate north towards British Columbia and Alaska. However, coastal currents in this area generally flow southward during spring and summer. Do salmon initiate an energetically-expensive positive rheotactic migration with the genetic ‘knowledge’ that feeding condition...

Background/Question/Methods The effects of variability in mass on survival have remained elusive, despite the well demonstrated increased survival caused by increased mean size or mean growth in fish populations. In this study, we examined the effects of food competition on variability in body masses and vitality, which is an abstract measure of...

This report is a postseason analysis of the accuracy of the 2011 predictions from Escapement Forecaster / Adult Upstream Model. The effectiveness of these modeling efforts are compared to observations of passage and river conditions at the end of the season. A pattern matching routine forecasts total run-size and run timing (daily passage) by op...

Anderson, J. Decadal climate cycles and declining Columbia River salmon. Sustainable Fisheries Conference Proceedings, p. 22(1998). http://www.cqs.washington.edu/papers/jim/victoria.html.

Behavioural devices that attract or deflect migrating fish to preferred routes are used to enhance the efficiency of mechanical structures (e.g. screens at turbine and other intakes) or as an alternative to them when their application is deemed unviable. Fish response to stimuli (signals) encountered, and consequently the efficiency of these behavi...

Evidence suggests that the year-class strength of salmon populations is related to decadal scale climatic/ocean fluctuations. The interactions have complex latitudinal patterns and appear to involve the major food web and current structures of the North Pacific. To understand the effect of climate on Columbia River salmon the North Pacific system m...

Migratory and resident fish species have evolved inherent flight responses to avoid potentially harmful situations. At many dams, fish screens or other structures have been installed to guide fish away from turbines or attract them to routes that will result in higher survival. Avoidance responses of fish to rapidly decelerating and accelerating fl...

Although evidence indicates that salmon could use geomagnetic cues in their high seas homing migration, the underlying behavioral strategy salmon apply to navigation cues is poorly understood. In one hypothesis, salmon imprint on the magnetic field when entering the ocean as juveniles and use the difference between the local and imprinted fields to...

Pavlovian conditioning and foraging theory are foundational topics in psychology and ecology that both study the behavior of animals in obtaining rewards and avoiding punishment. However, their approaches, vocabularies and theories are very different. For example, psychology considers conditioning animals to respond to stimuli, response extinction...

Little stills our thoughts more than gazing at schools of fish as they dart and wheel beneath the surface, providing us with impressive displays of coordination and presumed solidarity in the process. Yet conflict exists within schools, as members have competing interests, such as balancing social information to enhance resource discovery rate with...

Behavioural devices used to attract or repel migrating fish to preferred routes of passage are increasingly employed to enhance the efficiency of mechanical mitigation structures (e.g. screens that divert fish away from turbine intakes), or as an alternative to traditional approaches when their application is deemed unviable. Fish response to stimu...

We studied the effect of food competition on heterogeneity in growth and survival capacity. In a two-stage experimental protocol, four groups of juvenile guppies (Poecilia reticulata) were first treated with differing amounts of food and foraging competition for 21 days and then challenged with increased water temperature and starvation. Fitting th...

Seasonal temperature and bioenergetic models were coupled to explore the impacts on juvenile salmonid growth of possible climate-induced changes to mean annual water temperature and snowpack in four characteristic ecoregions. Increasing mean temperature increases juvenile growth in streams that currently experience cool spring temperatures. In stre...

We explore mechanisms associated with collective animal motion by drawing on the neurobiological bases of sensory information processing and decision-making. The model uses simplified retinal processes to translate neighbor movement patterns into information through spatial signal integration and threshold responses. The structure provides a mechan...

Functional forms of predator-prey interactions are developed for predators optimally foraging on prey distributed in patches. The model uses mean free-path-length theory to develop functional forms for two idealized behaviors of prey in patches. For congregating prey that maintain a fixed density, for example, fish schools, the predation rate has a...

As recently as 2002, nearly 1.5 million Sacrament River fall Chinook (SRFC) were caught in fisheries or returned to the Sacramento River basin to spawn. Only 66,000 spawners returned to natural areas and hatcheries in 2008. As a result of this dramatic decline, fisheries for Chinook salmon off California and Oregon were closed to protect SRFC in 20...

Migrating salmonids often return to their spawning habitats in overlapping timing patterns of multiple stocks (populations) collectively called a run that varies in its genetic makeup across and within years. Managers, tasked with developing harvest strategies on these runs, may have preseason estimates of total run size but little information on r...

Behavioral heterogeneity among individuals is a universal feature of natural populations. Most diffusion-based models of animal dispersal, however, implicitly assume homogeneous movement parameters within a population. Recent attempts to consider the effect of heterogeneous populations on dispersal distributions have been somewhat limited by the hi...