Modifying and parameterizing the individual-based model inSTREAM for Atlantic salmon and brown trout in the regulated Gullspång River, Sweden

We modified, parameterized, and applied the individual-based model inSTREAM version 6.1 for lake-migrating populations of landlocked Atlantic salmon (Salmo salar) and brown trout (S. trutta) in a residual flow stretch of the hydropower-regulated Gullspång River, Sweden. This model description is structured according to the TRACE model description framework. Our aim was to model responses in salmonid recruitment to alternative scenarios of flow release and other environmental alterations. The main response variable was the number of large out-migrating juvenile fish per year, with the assumption that individuals are more inclined to out-migrate the larger they get, and that migration is an obligatory strategy. Population and species-specific parameters were set based on local electrofishing surveys, redd surveys, physical habitat surveys, broodstock data as well as scientific literature.•Simulations were set to run over 10 years, with sub-daily time steps, in this spatially and temporally explicit model.•Model calibration and validation of fish growth was done using data on juvenile fish from electrofishing.•The results were found to be sensitive to parameter values for aggregated fish, i.e., "superindividuals" and for the high temperature limit to spawning.

Suboptimal foraging theory: How inaccurate predictions and approximations can make better models of adaptive behavior

Optimal foraging theory (OFT) is based on the ecological concept that organisms select behaviors that convey future fitness, and on the mathematical concept of optimization: finding the alternative that provides the best value of a fitness measure. As implemented in, e.g., state-based dynamic modeling, OFT is powerful for one key problem of modern ecology: modeling behavior as a tradeoff among competing fitness elements such as growth, risk avoidance, and reproductive output. However, OFT is not useful for other modern problems such as representing feedbacks within systems of interacting, unique individuals: when we need to model foraging by each of many individuals that interact competitively or synergistically, optimization is impractical or impossible-there are no optimal behaviors. For such problems we can, however, still use the concept of future fitness to model behavior, by replacing optimization with less precise (but perhaps more realistic) techniques for ranking alternatives. Instead of simplifying the systems we model until we can find "optimal" behavior, we can use theory based on inaccurate predictions, coarse approximations, and updating to produce good behavior in more complex and realistic contexts. This "state- and prediction-based theory" (SPT) can, for example, produce realistic foraging decisions by each of many unique, interacting individuals when growth rates and predation risks vary over space and time. Because SPT lets us address more natural complexity and more realistic problems, it is more easily tested against more kinds of observation and more useful in management ecology. A simple foraging model illustrates how SPT readily accommodates complexities that make optimization intractable. Other models use SPT to represent contingent decisions (whether to feed or hide, in what patch) that are tradeoffs between growth and predation risk, when both growth and risk vary among hundreds of patches, vary unpredictably over time, depend on characteristics of the individuals, are subject to feedbacks from competition, and change over the daily light cycle. Modern ecology demands theory for tradeoff behaviors in complex contexts that produce feedbacks; when optimization is infeasible, we should not be afraid to use approximate fitness-seeking methods instead.

Incorporating the life stages of fish into habitat assessment frameworks: A case study in the Baihetan Reservoir

Although it is widely accepted that the construction of dams may alter fish habitats, few studies have followed the life cycles of fish and combined the environmental conditions with the ecological behaviors and habit preferences of fish during reproductive processes to assess its effects of dam construction. In this study, we call for more sophisticated and holistic assessment framework, including effectiveness of technologies intended to mitigate environmental impacts in different life stages. An assessment framework that considers the swimming ability, perception ability of water flow and environmental preference of different fish species during migration, spawning and hatching was proposed. We used the Baihetan Reservoir as an example environment to assess the impoundment effect on the habitat of a tributary upstream of the reservoir. We observed shifts in the habitats of target fish in different life stages which is dominated by reservoir operation of the Baihetan Dam. Combined with the response of fish activities to impoundment, the selection of suitable positions for artificial breeding and release projects and the outlet of the fish transportation system were recommended measures to improve the migration possibilities. Our reassessment results also demonstrated the theoretical possibility and feasibility of joint improvements in spawning and hatching periods using instream structures. Our framework provides a complete set of "assessment-solution" processes for developers and managers to address the aquatic ecological degradation caused by resource development, and its use is strongly recommended for assessments or assessments of damming effects in other regions and on other fish species.

Incorporating thermodynamics in predator-prey games predicts the diel foraging patterns of poikilothermic predators

Models of foraging behaviour typically assume that prey do not adapt to temporal variation in predation risk, such as by avoiding foraging at certain times of the day. When this behavioural plasticity is considered-such as in predator-prey games-the role of abiotic factors is usually ignored. An abiotic factor that exerts strong influence on the physiology and behaviour of many animals is ambient temperature, although it is often ignored from game models as it is implicitly assumed that both predators and prey are homothermic. However, poikilotherms' performance may be reduced in cold conditions due to reduced muscle function, limiting the prey-capture ability of predators and the predator-avoidance and foraging abilities of prey. Here, we use a game-theoretic predator-prey model in which diel temperature changes influence foraging gains and costs to predict the evolutionarily stable diel activity of predators. Our model predicts the range of patterns observed in nature, including nocturnal, diurnal, crepuscular and a previously unexplained post-sunset crepuscular pattern observed in some sharks. In general, smaller predators are predicted to be more diurnal than larger ones. The safety of prey when not foraging is critical, explaining why predators in coral reef systems (with safe refuges) may often have different foraging patterns to pelagic predators. We make a range of testable predictions that will enable the further evaluation of this theoretical framework for understanding diel foraging patterns in poikilotherms.

Contingent trade-off decisions with feedbacks in cyclical environments: testing alternative theories

Many animals make contingent decisions, such as when and where to feed, as trade-offs between growth and risk when these vary not only with activity and location but also 1) in cycles such as the daily light cycle and 2) with feedbacks due to competition. Theory can assume an individual decides whether and where to feed, at any point in the light cycle and under any new conditions, by predicting future conditions and maximizing an approximate measure of future fitness. We develop four such theories for stream trout and evaluate them by their ability to reproduce, in an individual-based model, seven patterns observed in real trout. The patterns concern how feeding in four circadian phases—dawn, day, dusk, and night—varies with predation risk, food availability, temperature, trout density, physical habitat, day length, and circadian cycles in food availability. We found that theory must consider the full circadian cycle: decisions at one phase must consider what happens in other phases. Three theories that do so could reproduce almost all the patterns, and their ability to let individuals adapt decisions over time produced higher average fitness than any fixed behavior cycle. Because individuals could adapt by selecting among habitat patches as well as activity, multiple behaviors produced similar fitness. Our most successful theories base selection of habitat and activity at each phase on memory of survival probabilities and growth rates experienced 1) in the three previous phases of the current day or 2) in each phase of several previous days.

Use of a mechanistic growth model in evaluating post-restoration habitat quality for juvenile salmonids

Individual growth data are useful in assessing relative habitat quality, but this approach is less common when evaluating the efficacy of habitat restoration. Furthermore, available models describing growth are infrequently combined with computational approaches capable of handling large data sets. We apply a mechanistic model to evaluate whether selection of restored habitat can affect individual growth. We used mark-recapture to collect size and growth data on sub-yearling Chinook salmon and steelhead in restored and unrestored habitat in five sampling years (2009, 2010, 2012, 2013, 2016). Modeling strategies differed for the two species: For Chinook, we compared growth patterns of individuals recaptured in restored habitat over 15-60 d with those not recaptured regardless of initial habitat at marking. For steelhead, we had enough recaptured fish in each habitat type to use the model to directly compare habitats. The model generated spatially explicit growth parameters describing size of fish over the growing season in restored vs. unrestored habitat. Model parameters showed benefits of restoration for both species, but that varied by year and time of season, consistent with known patterns of habitat partitioning among them. The model was also supported by direct measurement of growth rates in steelhead and by known patterns of spatio-temporal partitioning of habitat between these two species. Model parameters described not only the rate of growth, but the timing of size increases, and is spatially explicit, accounting for habitat differences, making it widely applicable across taxa. The model usually supported data on density differences among habitat types in Chinook, but only in a couple of cases in steelhead. Modeling growth can thus prevent overconfidence in distributional data, which are commonly used as the metric of restoration success.

The role of detritivory as a feeding tactic in a harsh environment - a case study of weatherfish (Misgurnus fossilis)

The weatherfish (Misgurnus fossilis) is a species that is tolerant of unfavourable environmental conditions and can survive low dissolved oxygen concentrations and high water temperatures. Although this species occurs across almost the whole of Europe, and is protected in many countries, relatively little is known regarding its ecology. To determine the diet of weatherfish, 120 individuals from an artificial drainage canal in central Poland were collected in two seasons (spring and late summer) with contrasting abiotic condition (oxygen concentration, water temperature and transparency). Analysis of gut fullness showed that weatherfish consumed a greater quantity of food in spring (0.92 ± 0.90) compared with summer (0.20 ± 0.26). Contrary to other cobitid taxa, weatherfish fed actively during daytime in both seasons. An estimate of the importance of each dietary component indicated that the most important food categories were chironomids, copepods, Asellus aquaticus and detritus. SIMPER analysis indicated that these four categories together constituted over 65.8% of cumulative dissimilarity in the diet between seasons. Additionally, trophic niche breadth differed significantly between seasons. The study demonstrated that the weatherfish is an opportunistic feeder, consuming large quantities of detritus despite possessing a gut morphology that is atypical of a detritivore. The quantity of detritus in the gut of weatherfish was positively associated with fish total length and varied seasonally, with a greater quantity of detritus in the diet in late summer. These results demonstrate the importance of detritus as a source of energy, particularly during periods of scarcity of alternative prey categories.

Inactive trout come out at night: behavioral variation, circadian activity, and fitness in the wild

Theory suggests that high activity levels in animals increase growth at the cost of increased mortality. This growth-mortality tradeoff has recently been incorporated into the wider framework of the pace-of-life syndrome (POLS) hypothesis. However, activity is often quantified only in the laboratory and on a diurnal basis, leaving open the possibility that animals manage predation risk and feeding efficiency in the wild by modulating their circadian activity rhythms. Here we investigate how laboratory activity in wild brown trout parr (Salmo trutta L.) associates with circadian activity, growth, and mortality in their natal stream. We found that individuals with high activity in the laboratory displayed high dispersal and cathemeral activity in their natal stream. In contrast, trout with low laboratory activity showed variation of activity in the wild, which was negatively related to the light intensity. Our results do not support the growth-mortality trade-off of the POLS hypothesis as highly active, fast-growing individuals showed higher survival than inactive conspecifics. These novel results show for the first time that active and inactive individuals, as scored in the lab, can show different circadian patterns of behavior in the wild driven by light intensity. This implies that studies conducted under a narrow range of light conditions can bias our understanding of individual behavioral variation and its fitness consequences in the wild.

Diversity and Resistance to Change: Macro Conditions for Marginalization in Post-industrial Societies

We argue that two society-level properties—resistance to change and diversity within a culture—significantly affect agents' degrees of marginalization, which is here defined as access to cultural knowledge and institutional means for accomplishing cultural goals. We develop an agent-based model using findings from Norasakkunkit et al. (Norasakkunkit and Uchida, 2011, 2014; Norasakkunkit et al., 2012). We found that varying the degrees of resistance to change and diversity affected similarities between the mainstream subculture and other subcultures, changes in subcultures over time, and the relative population proportion of each subculture. In particular, we found that high diversity and low resistance to change created the greatest cultural changes within the marginalized subculture over time and allowed for maximal growth of rebellious subcultures. Also, low diversity and high resistance to change allowed for maximal growth of the marginalized subcultures and the greatest overlap between the marginalized and mainstream subcultures. These have important implications for understanding the emergence and maintenance of marginalization in post-industrial societies.

Using the shuttlebox experimental design to determine temperature preference for juvenile Westslope Cutthroat Trout (Oncorhynchus clarkii lewisi)

Temperature preference for various fishes has often been used as a proxy of optimal temperature for growth and metabolism due to the ease of obtaining preferred temperature zones in laboratory experiments. Several laboratory designs and methods have been proposed to examine preferred temperature zones, however, differences between them (i.e. thermal gradients vs. static temperatures in chambers and duration of acclimation/experimental periods) have led to varying measurements, precluding comparisons between experiments, species and/or life-stages. Juvenile Westslope Cutthroat Trout (Oncorhynchus clarkii lewisi), a species listed as threatened in Alberta and of special concern in British Columbia, were tested in an automated shuttlebox experimental design (Loligo® Systems) to determine average and ranges of temperature preference (T_pref) and occupied temperatures. Previous lab studies suggested that Westslope Cutthroat Trout (WCT) prefer temperatures around 15°C, however, we found that average daytime T_pref for lab-reared juvenile WCT was substantially higher at 18.6°C, with occupied temperatures ranging between 11.9°C and 26.0°C throughout the duration of trials. This seems to indicate that despite constant lab-rearing conditions of 12°C, juvenile WCT may tolerate and even prefer warmer water temperatures. The duration of the acclimation period (1h, 12 h and 24 h) did not have an effect on T_pref, however, T_pref differed significantly for variable trial durations (12 h, 24 h and 36 h). A closer look at thermal trends throughout trials revealed that photoperiod significantly influenced T_pref, as nighttime temperature preference reached consistently 26°C. Collectively, these results suggest that shuttlebox experiments on WCT need to take into account the photoperiod, as behaviour may drive T_pref more so than the duration of acclimation periods.

Diet Composition, Feeding Periodicity, and Prey Selection of Slimy Sculpin During Winter

Slimy Sculpin Cottus cognatus is an important component of the benthic ichthyofauna of many lakes and streams in the northern latitudes of North America. Although considerable information exists on the feeding ecology of this species, there is essentially no information available on winter feeding. Consequently, we examined the winter feeding ecology of Slimy Sculpins in a central New York stream. Ephemeropterans (37.8%) and trichopterans (31.2%) were the primary prey taxa consumed in January. There was evidence of diel variation in diet composition, with ephemeropterans making up 24.1% of the diet at 0400 hours and 46.7% at 1600 hours and trichopterans contributing 22.7% at 1200 hours and 43.8% at 2000 hours. During winter, Slimy Sculpins selected chironomids (0.46) and trichopterans (0.43) and avoided coleopterans (−0.84) and nonchironomid dipterans (−0.67). Peak food consumption of Slimy Sculpins occurred at night. Winter feeding patterns of Slimy Sculpins in Grout Brook, a second-order tributary of Skaneateles Lake in central New York, contrasted sharply with observations from other studies carried out during other seasons. Our findings are a significant contribution on the winter feeding ecology of this important benthic species and illustrate the need for both diel and winter studies to fully understand life history characteristics.

Feeding Ecology of Brook Silverside, Golden Shiner, and Subyearling Pumpkinseed in a Lake Ontario Embayment

Fish feeding ecology has been shown to vary over a 24-h period in terms of the prey consumed and feeding intensity. Consequently, in order to best determine the interspecific feeding associations within a fish community, examination of the diet at multiple times over a 24-h period is often necessary. We examined the diel feeding ecology of three fish species that were numerically dominant in a Lake Ontario embayment during summer. The diet of each of the three species, young-of-year Pumpkinseed Lepomis gibbosus, Golden Shiner Notemigonus crysoleucas, and Brook Silverside Labidesthes sicculus, was distinct with no significant overlap in diet composition occurring within any of the 4-h time intervals. The diet composition of each species suggested that Brook Silverside were feeding at the surface (terrestrial invertebrates and aquatic surface dwelling hemipterans), whereas young-of-year Pumpkinseed (amphipods) and Golden Shiner (tipulids) were feeding on different benthic prey. Differences in feeding periodicity were most pronounced for young-of-year Pumpkinseed. Our findings provide valuable insights on interspecific feeding associations among these three fish species during summer in a Lake Ontario embayment.

Making Predictions in a Changing World: The Benefits of Individual-Based Ecology

Ecologists urgently need a better ability to predict how environmental change affects biodiversity. We examine individual-based ecology (IBE), a research paradigm that promises better a predictive ability by using individual-based models (IBMs) to represent ecological dynamics as arising from how individuals interact with their environment and with each other. A key advantage of IBMs is that the basis for predictions—fitness maximization by individual organisms—is more general and reliable than the empirical relationships that other models depend on. Case studies illustrate the usefulness and predictive success of long-term IBE programs. The pioneering programs had three phases: conceptualization, implementation, and diversification. Continued validation of models runs throughout these phases. The breakthroughs that make IBE more productive include standards for describing and validating IBMs, improved and standardized theory for individual traits and behavior, software tools, and generalized instead of system-specific IBMs. We provide guidelines for pursuing IBE and a vision for future IBE research.

Alternative responses to predation in two headwater stream minnows is reflected in their contrasting diel activity patterns

Animals exhibit diel periodicity in their activity in part to meet energy requirements whilst evading predation. A competing hypothesis suggests that partitioning of diel activities is less important because animals capitalise on opportunity. To test these hypotheses we examined the diel activity patterns for two cyprinid minnows, chubbyhead barb Barbus anoplus and the Eastern Cape redfin minnow Pseudobarbus afer that both occur within headwater streams in the Eastern Cape, South Africa. Chubbyhead barbs exhibited consistent nocturnal activity based on both field and laboratory observations. Due to the absence of fish predators within its habitat, its nocturnal behaviour suggests a response to the cost associated with diurnal activity, such as predation risk by diving and wading birds. In contrast, redfin minnows showed high diurnal activity and a shoaling behaviour in the wild, whereas, in the laboratory, they showed high refuge use during the diel cycle. Despite their preference for refuge in the laboratory, they were diurnally active, a behaviour that was consistent with observations in the wild. The diurnal activity of this species suggests a response to the cost associated with nocturnal activity. Such a cost could be inferred from the presence of the longfin eel, a native predator that was active at night, whereas the daytime shoaling behaviour suggests an anti-predator mechanism to diurnal visual predators. The implications of these findings relate to the impacts associated with the potential invasions by non-native piscivores that occur in the mainstem sections. Diurnal activity patterns for redfin minnows, that are IUCN-listed as endangered, may, in part, explain their susceptibility to high predation by visual non-native piscivores, such as bass and trout. In contrast, the nocturnal habits of chubbyhead barbs suggest a probable pre-adaptation to visual predation. The likelihood of invasion by nocturnally-active sharptooth catfish Clarias gariepinus, however, may compromise this prior advantage.

Diversity of movements by individual anadromous coastal cutthroat trout Oncorhynchus clarkii clarkii

Wild, downstream-migrating cutthroat trout, Oncorhynchus clarkii clarkii, smolts and adults were captured at a weir in Big Beef Creek, Hood Canal, Washington, surgically implanted with acoustic tags and tracked to identify spring and summer movements using stationary receivers in order to test the assumption that the species moves little while in marine waters. Overall, 93-96% migrated from the stream into the east side of the long narrow fjord, where they dispersed north and south along the shoreline. Most O. c. clarkii were detected nearshore within 10 km of the release site, with declining detection rates to 77 km. Over one-third (36%) crossed c. 2-4 km of deep water to the other side but only one O. c. clarkii left the Hood Canal basin. Movements and behaviour patterns did not differ between smolts and adults but cluster analysis revealed two modes of distribution, here categorized as residents and migrants. Within these categories of overall distribution, a range of finer-scale behaviour patterns was observed, including sedentary individuals, daily moving between proximate sites and more continuous long-distance travel. Diel movement patterns varied markedly among individuals but overall activity increased near dawn, peaked around mid-day and declined but continued at night. These patterns contrast with sympatric and closely related steelhead trout, Oncorhynchus mykiss, providing new insights into the diversity of salmonid behaviour.

Rain reverses diel activity rhythms in an estuarine teleost

Activity rhythms are ubiquitous in nature, and generally synchronized with the day-night cycle. Several taxa have been shown to switch between nocturnal and diurnal activity in response to environmental variability, and these relatively uncommon switches provide a basis for greater understanding of the mechanisms and adaptive significance of circadian (approx. 24 h) rhythms. Plasticity of activity rhythms has been identified in association with a variety of factors, from changes in predation pressure to an altered nutritional or social status. Here, we report a switch in activity rhythm that is associated with rainfall. Outside periods of rain, the estuarine-associated teleost Acanthopagrus australis was most active and in shallower depths during the day, but this activity and depth pattern was reversed in the days following rain, with diurnality restored as estuarine conductivity and turbidity levels returned to pre-rain levels. Although representing the first example of a rain-induced reversal of activity rhythm in an aquatic animal of which we are aware, our results are consistent with established models on the trade-offs between predation risk and foraging efficiency.

Trait-mediated trophic interactions: is foraging theory keeping up?

Many ecologists believe that there is a lack of foraging theory that works in community contexts, for populations of unique individuals each making trade-offs between food and risk that are subject to feedbacks from behavior of others. Such theory is necessary to reproduce the trait-mediated trophic interactions now recognized as widespread and strong. Game theory can address feedbacks but does not provide foraging theory for unique individuals in variable environments. 'State- and prediction-based theory' (SPT) is a new approach that combines existing trade-off methods with routine updating: individuals regularly predict future food availability and risk from current conditions to optimize a fitness measure. SPT can reproduce a variety of realistic foraging behaviors and trait-mediated trophic interactions with feedbacks, even when the environment is unpredictable.

Importance of fish behaviour in modelling conservation problems: food limitation as an example

Simulation experiments using the inSTREAM individual-based brown trout Salmo trutta population model explored the role of individual adaptive behaviour in food limitation, as an example of how behaviour can affect managers' understanding of conservation problems. The model includes many natural complexities in habitat (spatial and temporal variation in characteristics such as depth and velocity, temperature, hiding and feeding cover, drift-food supply and predation risk), fish physiology (especially, how food intake and growth vary with hydrodynamics, cover, fish size and temperature) and behaviour. When drift-food concentration was increased over a wide range in 7 year simulations, the simulated population was always food limited. In fact, as food supply increased, the population increased at an increasing rate and consumed a higher percentage of the food supply, apparently because higher food concentrations make more stream area energetically profitable for drift feeders. The behaviour most responsible for this response was activity selection: when food was abundant, fish chose to feed less frequently and more nocturnally, thereby reducing predation mortality so more fish survived longer. These results indicate that the traditional concept of food limitation, that food availability stops limiting population size when it exceeds some threshold level, may not be useful and can be misleading. Results also strongly contradict the concept that a salmonid population is not food limited if the total food supply is greater than the population's consumption. Explicit consideration of adaptive behaviour produced a novel but believable understanding of food effects on salmonid populations. Published 2011. This article is a U.S. Government work and is in the public domain in the USA.