The effect of growth-dependent mortality, external environment and internal dynamics on larval fish otolith growth: an individual-based modelling approach

The daily otolith increment growth of individuals in a cohort of fish larvae was simulated by a simple individual-based model over 30 days. The daily otolith growth of an individual larva was dependent on past growth, within fixed limits common to all larvae. The survival of a larva at the end of each day was either a linear function of larval growth or a random outcome, simulating growth-dependent and growth-independent mortality, respectively, The combined effect of the external environment on growth was also studied. Eleven environmental scenarios, favouring or hindering growth at different stages, were tested and compared to runs with no environmental effect on growth. Growth-dependent mortality induced an increase in the average otolith daily increment width amongst surviving larvae. Such an outcome, however, could be negated by an unfavourable environment. The increase in mean growth rate of the population generated by growth-dependent mortality was directly related to the inherent variability in daily otolith growth. With increased variability, the influence of the environment became relatively less important. The effect of the environment on growth was more critical during the early stages of development. A comparison of results generated by the model with patterns observed in data from a field survey of larval herring was consistent with the occurrence of growth-dependent mortality in the sea. The simulation model provided a useful insight into the way in which various processes controlling larval growth interact.     

Effects of piscivore-mediated habitat use on growth, diet and zooplankton consumption of roach: an individual-based modelling approach

SUMMARY 1. We used an individual based modelling approach for roach to (i) simulate observed diel habitat shifts between the pelagic and littoral zone of a mesotrophic lake; (ii) analyse the relevance of these habitat shifts for the diet, activity costs and growth of roach; and (iii) quantify the effects of a hypothetical piscivore-mediated (presence of pikeperch) confinement of roach to the littoral zone on roach diet, activity costs and growth.
2. The model suggests that in the presence of pikeperch, roach shifts from zooplankton as the primary diet to increased consumption of less nutritious food items such as macrophytes, filamentous algae and detritus.
3. The growth of roach between May and October was predicted to be significantly higher in the absence of pikeperch, although the net activity costs were about 60% higher compared with the scenario where pikeperch were present.
4. These modelling results provide quantitative information for interpreting diel horizontal migrations of roach as a result from a trade-off between food availability and predation risk in different habitats of a lake.
5. Altering the habitat selection mode of planktivorous roach by piscivore stocking has the potential to reduce zooplankton consumption by fish substantially, and could therefore be used as a biomanipulation technique complementing the reduction of zooplanktivorous fish.     

Effect of size-selective mortality on growth of coastal cod illustrated by tagging data and an individual-based growth and mortality model

In a release experiment with cod in Norway, the apparent mean growth rates of 3+ cod, calculated by sampling the released cohorts at different ages, were very slow (<0·08 mm day⁻¹). However, when individual growth rates of individual tagged cod of the same size range were measured, the mean growth rates were much faster (0·24 mm day⁻¹). These observations were attributed to size-selective fishing mortality and were illustrated by an individual based simulation model of a cohort of cod with variable individual growth rates. The effects on mean length at age of the surviving cohort of increasing fishing intensity were demonstrated. The model showed that size-selective fishing with the observed individual growth variation, removed the fastest-growing individuals at proportionally higher rates than the slower-growing ones, leading to decreased apparent mean growth rate. The fishing pattern which gave the optimum yield, changed when individual variation was included, and when the apparent growth rate was used in the model the yield per recruit reduced dramatically. This study has shown that individual growth heterogeneity and size-selective mortality are factors which should be considered in future fisheries management models.     

Plastic inducible morphologies are not always adaptive: The importance of time delays in a stochastic environment

Summary We present a mathematical model for predicting the expected fitness of phenotypically plastic organisms experiencing a variable environment. We assume that individuals experience two discrete environments probabilistically in time (as a Markov process) and that there are two different phenotypic states, each yielding the highest fitness in one of the two environments. We compare the expected fitness of a phenotypically fixed individual to that of an individual whose phenotype is induced to produce the better phenotype in each environment with a time lag between experiencing a new environment and realization of the new phenotype. Such time lags are common in organisms where phenotypically plastic, inducible traits have been documented. We find that although plasticity is generally adaptive when time lags are short (relative to the time scale of environmental variability), plasticity can be disadvantageous for longer lag times. Asymmetries in environmental change probabilities and/or the relative fitnesses of each phenotype strongly influence whether plasticity is favoured. In contrast to other models, our model does not require costs for plasticity to be disadvantageous; costs affect the results quantitatively, not qualitatively.     

Temperature, growth and dietary effects on fish mercury dynamics in two Ontario lakes

A bioenergetics-based model was used to investigate the effects of temperature, growth and dietary exposure on methylmercury dynamics in walleye (Stizostedion vitreum) and yellow perch (Perca flavescens) from two lakes sampled in northwestern Ontario. Orange Lake was smaller, warmer, had slower fish growth and higher mercury concentrations in yearling yellow perch and walleye (three fold difference in 40 cm walleye) than Trout Lake. The model was applied to test the hypothesis that higher water temperatures in Orange Lake increased metabolic needs, food consumption and mercury uptake in fish. The effects of different growths rates in the lakes were also considered. Temperature/metabolic effects and growth effects on internal methylmercury dynamics in walleye and perch were predicted to occur but be of secondary importance. Different dietary exposure to methylmercury was likely the dominant source of variation in fish mercury concentrations between the two lakes.     

Recruitment variation in a stream galaxiid fish: multiple influences on fry dynamics in a heterogeneous environment

1. The relative importance of density‐dependent and density‐independent processes in explaining fluctuations in natural populations has been widely debated. In particular, the importance of larval supply and whether it may control the type of regulatory processes a population experiences has proved contentious. 2. Using surveys and field experiments conducted in streams in Canterbury, New Zealand, we investigated how variation in the survival of non‐migratory Galaxias vulgaris fry was affected by density‐dependent and density‐independent processes and how this variation influenced recruitment dynamics. 3. Fry populations with high settlement densities experienced a 70–80% reduction in population size from density‐related mortality during the first fourteen days after peak settlement but thereafter the influence of density‐dependent processes on fry was weak. The impact of environmental conditions on fry populations was dependent on fry size and the magnitude of the perturbation, such that flooding effects on fry survival were most severe when fry were small. 4. In streams not affected by flooding, the size and density of introduced trout (Salmo trutta and Oncorhynchus mykiss) were the most significant factors determining the abundance of eventual recruits. A field experiment manipulating brown trout access to fry populations revealed that trout as small as 110 mm may be capable of greatly reducing and possibly preventing galaxiid recruitment. 5. Overall, the results indicated density‐dependent population regulation was only possible at sites with high native fish densities because trout were likely to be suppressing the number of potential recruits at sites with low native fish numbers. Whilst density‐dependent processes had a strong effect on fry survival following the period of peak fry abundance, density‐independent processes associated with flow and predatory trout influences on fry survival largely determined recruitment variability among galaxiid populations. Focusing conservation efforts on improving habitat to increase fry retention and reducing the impacts of trout on galaxiids would ensure more native fish populations reached their potential abundance.     

Density distribution and size sorting in fish schools: an individual-based model

In fish schools the density varies per location and often individualsare sorted according to familiarity and/or body size. High densityis considered advantageous for protection against predatorsand this sorting is believed to be advantageous not only toavoid predators but also for finding food. In this paper, welist a number of mechanisms and we study, with the help of anindividual-based model of schooling agents, which spatial patternsmay result from them. In our model, schooling is regulated bythe following rules: avoiding those that are close by, aligningto those at intermediate distances, and moving towards othersfurther off. Regarding kinship/familiarity, we study patternsthat come about when agents actively choose to be close to relatedagents (i.e., ‘active sorting’). Regarding bodysize, we study what happens when agents merely differ in sizebut behave according to the usual schooling rules (‘sizedifference model’), when agents choose to be close tothose of similar size, and when small agents avoid larger ones(‘risk avoidance’). Several spatial configurationsresult: during ‘active sorting’ familiar agentsgroup together anywhere in the shoal, but agents of differentsize group concentrically, whereby the small agents occupy thecenter and the large ones the periphery (‘size differencemodel’ and ‘active sorting’). If small agentsavoid the risk of being close to large ones, however, smallagents end up at the periphery and large ones occupy the center(‘risk avoidance’). Spatial configurations are alsoinfluenced by the composition of the group, namely the percentageof agents of each type. Furthermore, schools are usually oblongand their density is always greatest near the front. We explainthe way in which these patterns emerge and indicate how resultsof our model may guide the study of spatial patterns in realanimals.     

Gyro-scope: an individual-based computer model to forecast gyrodactylid infections on fish hosts

Individual-based computer models (IBM) feature prominently in current theoretical ecology but have only been applied in a small number of parasitological studies. Here we designed an IBM to simulate the infection dynamics of gyrodactylid parasites and immune defence of na?ve hosts (i.e. fish previously not exposed to these parasites). We compared the results of the model with empirical data from guppies (Poecilia reticulata) infected with Gyrodactylus parasites. The laboratory experiments on guppies showed that larger fish acquired a heavier parasite load at the peak of the infection. The survival probability declined with increased body size and no fish survived a parasite load of 80 or more worms in this experiment (i.e. lethal load). The model was a good predictor of the Gyrodactylus infection dynamics of guppies and the model output was congruent with previously published data on Gyrodactylus salaris infections of salmon (Salmo salar). Computer simulations indicated that the infections persisted longer on larger hosts and that the parasite load increased exponentially with the body size of the host. Simulations furthermore predicted that the parasite load of fish with a standard length in excess of 17mm (i.e. the size of adult guppies) reached a lethal load. This suggests that in the conditions of the experiment, the immune defence of na?ve guppies can offer moderate protection against gyrodactylid infections to juveniles, but not to na?ve adult guppies. The model is a useful tool to forecast the development of gyrodactylid infections on single hosts and make predictions about optimal life history strategies of parasites.     

Influence of diet shifts in underyearling fish on phosphorus recycling in a hypertrophic biomanipulated reservoir

1. In addition to effects of direct predation by planktivorous fish, nutrient recycling by fish may also contribute to structuring foodwebs in lakes. There is little evidence, however, about whether underyearling fish undergoing several ontogenetic diet shifts may have a comparable bottom-up impact. 2. This study examined seasonal patterns of phosphorus (P) concentration and external load, phytoplankton, zooplankton and benthos, and diet shifts in three underyearling fish [perch (Perca fluviatilis), roach (Rutilus rutilus) and ruffe (Gymnocephalus cernuus)] in the shallow, hypertrophic biomanipulated Bautzen reservoir, Germany. Phosphorus metabolism of fish was calculated by a balanced bioenergetics model on the basis of fish diet, growth and water temperature. 3. The fish showed several shifts from planktivory to other food sources during the sampling period from May to September. These shifts were probably caused by the seasonal succession of the zooplankton community, mainly the midsummer decline of Daphnia galeata. 4. The diet shifts in fish also had consequences for the amount of P consumed and released. During periods of dominant zooplanktivory, the excretion of P did not exceed the removal of P stored in pelagic prey. By contrast, if benthivory dominated, fish subsidized the pelagic P pool by excreting more P from benthic prey than had been removed from the pelagic area. This occurred predominantly in perch and ruffe during periods of low zooplankton biomass, whereas the roach ate more algae and therefore excreted less P of benthic origin. 5. Phosphorus release by underyearling fish was estimated at a maximum of 0.1 mg m^–3 JY day^–1. This value was negligible compared with both the external load of P to Bautzen reservoir and the concentration of P in the pelagic area during summer. It is therefore concluded that both the predominance of underyearling zooplanktivorous fish and the high Daphnia biomass during certain periods of the year in the Bautzen reservoir may be the reason that nutrient release by the fish structured the foodweb only marginally. 6. This study suggests that biomanipulation has altered both top-down and bottom-up impacts of fish in Bautzen reservoir. The highest efficiency of foodweb manipulations may be obtained after reduction of the external P loading below a certain threshold. In turn, if external restoration of eutrophied lakes is not accompanied by changes in fish community, then the combined forces of strong zooplanktivory and high P recycling of dense stocks of zooplanktivorous and benthivorous fish may hold the water in a eutrophic-like stage, even if external load has been significantly reduced.     

An ecomorphological framework for the coexistence of two cyprinid fish and their hybrids in a novel environment

Niche variation between hybrid taxa and their parental species has been deemed imperative to the persistence of hybrid populations in nature. However, the ecological factors promoting hybrid establishment remain poorly understood. Through the application of a multidisciplinary approach integrating genetics, morphometry, life‐history, and trophic ecology, we studied the hybrids of roach (Rutilus rutilus L.) and bream (Abramis brama L.), and their parental species inhabiting an Irish lake. The roach × bream hybrid exhibited a body shape intermediate of that of the parental species. Diet analyses depicted the hybrid as a generalist, feeding on all prey items consumed by either parental species. Stable isotope data confirm the trophic niche breadth of hybrids. A significant correlation between body shape and diet was detected, suggesting that the intermediate phenotype of hybrids might play a role in their feeding abilities, resulting in the utilization of a broader trophic spectrum than the parental species. Growth and age class structure analyses also yielded a scenario that is consistent with the ecological success of hybrids. Genetic analyses suggest that the majority of hybrids result from first‐generation crosses between the parental species; however, a potentially significant proportion of back‐crosses with bream were also detected. The recent introduction of roach and bream into Irish waters, as well as the climatic and ecological features of the colonized habitats, can explain the remarkable success of the roach × bream hybrid in Ireland. The adaptive significance of hybridization and its demographic consequences for the parental species are discussed. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 768–783.     

General response patterns of fish populations to stress: an evaluation using an individual-based simulation model

General response patterns of fish populations tostress, originally proposed by Colby for fisheriesrehabilitation and later adapted by Munkittrick forcontaminants, were evaluated using an individual-basedsimulation model. General response patterns relatechanges in population-level variables to the type ofstress. The model follows the daily growth,mortality, and spawning of individual yellow perch andwalleye through their lifetime, and was corroboratedusing Oneida Lake data. Two versions of the model wereused: population (yellow perch only) and community(dynamic predation on yellow perch by walleye). Eightstresses were imposed on the population and communityversions of the model and 100-year simulations wereperformed. Response patterns were defined by changesin predicted yellow perch mean population abundance,mean age of adults, and mean adult growth (representedby mean length at age-7). Proposed response patternswere similar to those predicted using the populationversion of the model. Simulations using the communityversion of the model distorted the response patterns,either causing amplification, dampening, or reversalof many of the patterns. Predicted response patternsbecame unique when additional variables were included.Our model results suggest that caution is appropriatein interpreting general response patterns based onmean age, or when the population of interest plays amajor role in a relatively simple food web. The responsepattern approach may be better at identifying the lifestage impacted rather than the mechanism of the stress.     

Evolution of cell motility in an individual-based model of tumour growth

Tumour invasion is driven by proliferation and importantly migration into the surrounding tissue. Cancer cell motility is also critical in the formation of metastases and is therefore a fundamental issue in cancer research. In this paper we investigate the emergence of cancer cell motility in an evolving tumour population using an individual-based modelling approach. In this model of tumour growth each cell is equipped with a micro-environment response network that determines the behaviour or phenotype of the cell based on the local environment. The response network is modelled using a feed-forward neural network, which is subject to mutations when the cells divide. With this model we have investigated the impact of the micro-environment on the emergence of a motile invasive phenotype. The results show that when a motile phenotype emerges the dynamics of the model are radically changed and we observe faster growing tumours exhibiting diffuse morphologies. Further we observe that the emergence of a motile subclone can occur in a wide range of micro-environmental growth conditions. Iterated simulations showed that in identical growth conditions the evolutionary dynamics either converge to a proliferating or migratory phenotype, which suggests that the introduction of cell motility into the model changes the shape of fitness landscape on which the cancer cell population evolves and that it now contains several local maxima. This could have important implications for cancer treatments which focus on the gene level, as our results show that several distinct genotypes and critically distinct phenotypes can emerge and become dominant in the same micro-environment.     

Home-cage activity in heterogeneous stock (HS) mice as a model of baseline activity

Behavioral genetic work in humans indicates that clinical hyperactivity is best viewed as the extreme end of activity levels in the population. However, current animal models of hyperactivity are not studied as quantitative traits as they are either knockout models or inbred strains. Furthermore, these animal models generally demonstrate elevated locomotion in novel environments, but not in their home-cages. This is the opposite of the symptoms seen in the human condition where childhood hyperactivity is generally more pronounced in constant, unstimulating situations. In this study we filmed an outbred population of 44 heterogeneous stock (HS) mice under red light during their active phase, to assess the reliability of individual differences in home-cage behavior and extract an index of home-cage activity (HCA) level. We then compared this measure to locomotor behavior in a novel environment — the open-field. Reliable individual differences in home-cage behaviors such as running, swinging on bars, and burrowing were found, and principal component factor analysis yielded a general activity factor, which accounted for 32% of the variance and correlated 0.90 with a subjective impression of activity level. The correlation between HCA and locomotor activity in the open-field was 0.23, which was non-significant. However, the association with HCA level appeared to increase over the five minutes of the open-field, presumably as the mice habituated. Furthermore, although mice displaying particularly high and low HCA were indistinguishable early in the open-field task, they became significantly differentiated over time. We conclude that home-cage behaviors and the open-field, after habituation, display good face and construct validity, and may provide a good model of baseline activity for quantitative trait loci (QTL) discovery and functional genomics in the HS mice.     

Population dynamics of mosquito-borne disease: persistence in a completely heterogeneous environment

We investigate the persistence of a mosquito-borne disease (malaria) in a system where mosquitoes and hosts are grouped in patches containing any number of individuals. A mosquito from any one of vector patches can bite, and take blood meals, in any one of m host patches. We confirm our earlier result (C. Dye and G. Hasibeder, 1986, Trans. R. Soc. Trop. Med. Hyg. 80, 69-77) that nonhomogeneous host selection by mosquitoes leads to basic reproductive rates (which measure the persistence of infection in the system) greater than or equal to those obtained under uniform host selection. We find, in addition, that strong associations between particular groups of mosquitoes and hosts lead to still higher basic reproductive rates. Exacting fieldwork would be required to find out how much higher.     

A test for the genetic basis of natural selection: an individual-based longitudinal study in a stream-dwelling fish

In addition to the well-studied evolutionary parameters of (1) phenotype-fitness covariance and (2) the genetic basis of phenotypic variation, adaptive evolution by natural selection requires that (3) fitness variation is effected by heritable genetic differences among individuals and (4) phenotype-fitness covariances must be, at least in part, underlain by genetic covariances. These latter two requirements for adaptive evolutionary change are relatively unstudied in natural populations. Absence of the latter requirements could explain stasis of apparently directionally selected heritable traits. We provide complementary analyses of selection and variation at phenotypic and genetic levels for juvenile growth rate in brook charr Salvelinus fontinalis in Freshwater River, Newfoundland, Canada. Contrary to the vast majority of reports in fish, we found very little viability selection of juvenile body size. Large body size appears nonetheless to be selectively advantageous via a relationship with early maturity. Genetic patterns in evolutionary parameters largely reflected phenotypic patterns. We have provided inference of selection based on longitudinal data, which are uncommon in high fecundity organisms. Furthermore we have provided a practicable framework for further studies of the genetic basis of natural selection.     

Influence of hydrological fluctuations on the growth and nutrient dynamics ofPhalaris arundinacea L. in a riparian environment

Seasonal changes in aboveground and belowground tissues ofPhalaris arundinacea L. were studied in a population colonizing an ancient meander of the Garonne river (France) submitted to important fluctuations of the permanent water table. Waterlogged conditions in spring stopped the growth of rhizomes and promoted the translocation of nutrient to the shoots. The early senescence of plants after flowering could be related to the withdrawal of the water table. It was characterized by a distribution of nutrients in belowground tissues and a release in litter and soil. Aerated conditions in late summer permitted the growth of belowground tissues. At this time a partition of resources between aboveground and belowground biomass of a new generation of plants was observed. Rising water and decreasing temperatures in winter induced the death of aboveground parts. Reconstitution of nutrient stocks in rhizomes and losses by leaching then occured. Beside a very high primary production this strategy confers toPhalaris arundinacea a great interest in different uses, especially in the removal of nutrients from water in riparian zones as in artificial sites.