Laure Pecquerie

Integrating dynamic energy budget (DEB) theory with traditional bioenergetic models

Summary Dynamic energy budget (DEB) theory offers a systematic, though abstract, way to describe how an organism acquires and uses energy and essential elements for physiological processes, in addition to how physiological performance is influenced by environmental variables such as food density and temperature. A ‘standard’ DEB model describes the performance (growth, development, reproduction, respiration, etc.) of all life stages of an animal (embryo to adult), and predicts both intraspecific and interspecific variation in physiological rates. This approach contrasts with a long tradition of more phenomenological and parameter-rich bioenergetic models that are used to make predictions from species-specific rate measurements. These less abstract models are widely used in fisheries studies; they are more readily interpretable than DEB models, but lack the generality of DEB models. We review the interconnections between the two approaches and present formulae relating the state variables and fluxes in the standard DEB model to measured bioenergetic rate processes. We illustrate this synthesis for two large fishes: Pacific bluefin tuna (Thunnus orientalis) and Pacific salmon (Oncorhynchus spp.). For each, we have a parameter-sparse, full-life-cycle DEB model that requires adding only a few species-specific features to the standard model. Both models allow powerful integration of knowledge derived from data restricted to certain life stages, processes and environments.

Shedding light on fish otolith biomineralization using a bioenergetic approach.

Otoliths are biocalcified bodies connected to the sensory system in the inner ears of fish. Their layered, biorhythm-following formation provides individual records of the age, the individual history and the natural environment of extinct and living fish species. Such data are critical for ecosystem and fisheries monitoring. They however often lack validation and the poor understanding of biomineralization mechanisms has led to striking examples of misinterpretations and subsequent erroneous conclusions in fish ecology and fisheries management. Here we develop and validate a numerical model of otolith biomineralization. Based on a general bioenergetic theory, it disentangles the complex interplay between metabolic and temperature effects on biomineralization. This model resolves controversial issues and explains poorly understood observations of otolith formation. It represents a unique simulation tool to improve otolith interpretation and applications, and, beyond, to address the effects of both climate change and ocean acidification on other biomineralizing organisms such as corals and bivalves.

The impact of metabolism on stable isotope dynamics: a theoretical framework

Stable isotope analysis is a powerful tool used for reconstructing individual life histories, identifying food-web structures and tracking flow of elemental matter through ecosystems. The mechanisms determining isotopic incorporation rates and discrimination factors are, however, poorly understood which hinders a reliable interpretation of field data when no experimental data are available. Here, we extend dynamic energy budget (DEB) theory with a limited set of new assumptions and rules in order to study the impact of metabolism on stable isotope dynamics in a mechanistic way. We calculate fluxes of stable isotopes within an organism by following fluxes of molecules involved in a limited number of macrochemical reactions: assimilation, growth but also structure turnover that is here explicitly treated. Two mechanisms are involved in the discrimination of isotopes: (i) selection of molecules occurs at the partitioning of assimilation, growth and turnover into anabolic and catabolic sub-fluxes and (ii) reshuffling of atoms occurs during transformations. Such a framework allows for isotopic routing which is known as a key, but poorly studied, mechanism. As DEB theory specifies the impact of environmental conditions and individual state on molecule fluxes, we discuss how scenario analysis within this framework could help reveal common mechanisms across taxa.

Bayesian inference for bioenergetic models

Dynamic energy budget (DEB) theory provides a sophisticated, mechanistic framework for understanding the full life cycles of individuals within a complex environment. By relating environmental conditions, notably food availability, to individual life histories, DEB theory makes it possible, in principle, to make predictions for individuals and populations that extend beyond the conditions used to develop and parameterize the model. However, for this approach to reach its full potential as a predictive theory, we need methods of similar sophistication to link unobservable modeled quantities to data and to infer model parameters. Here, we develop such a method in a Bayesian framework. We offer a rigorous methodology for modeling the link between underlying unobservable states and observable quantities and for parameter inference. The methodology is introduced and its effectiveness as applied to data simulated under various dynamic food regimes is demonstrated. We also examine how parameter estimates can be affected by misspecification of the food model, specifically by assuming a constant food level when the true underlying dynamics are variable. This is critical as many published applications of DEB theory assume constant food when estimating parameter values. The effectiveness of the approach for data on the growth and reproduction of the water flea Daphnia is also discussed.

DEBSe@: an e-learning platform to introduce the Dynamic Energy Budget (DEB) theory for marine ecology, fisheries sciences and aquaculture applications

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. DEBSe@: an e-learning platform to introduce the Dynamic Energy Budget (DEB) theory for marine ecology, fisheries sciences and aquaculture applications Yoann Thomas, Fred Jean, Laure Pecquerie, Gonçalo Marques, Sébastien Hervé, Valérie Dantec, Jonathan Flye-Sainte-Marie