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Traditionally, the terms altricial and precocial are used to described the state at birth of birds and mammals. We suggest an explanation for why birds evolved from precocial to altricial and mammals from altricial to precocial. However, the concept is not confined to these groups alone and is an important pattern underlying all animal metabolism. Being able to quantify it, helps position species in multi-dimensional diversity trait space. We here argue that a quantification of the state of development of an individual at birth, in the context of its life cycle, can best be done by comparison with the state at puberty. Two natural quantifiers for the altricial-precocial spectrum exist in the context of the Dynamic Energy Budget (DEB) theory that are applicable to the whole animal kingdom: maturity and maturity density at birth divided by that at puberty. These quantities have been estimated, in combination with other parameters, for some 875 species belonging to all large phyla. We study how taxa are ranked according to both the maturity and maturity density ratios. We conclude that only the maturity ratio qualifies as quantifier for the altricial-precocial spectrum. We were able to retrieve known patterns in altriciality for birds and mammals, while the concept is now applicable to all animal taxa. This new quantifier for animal altriciality can be linked quantitatively to other properties. These linkages are studied by examining how maturity parameters interact with other DEB parameters and implied properties. With the exception of mammals, cartilaginous fish and insects, bigger-bodied species show a clear tendency for to be more frequently altricial. We discuss possible explanations. Age at birth as fraction of age at puberty was found to be proportional to the maturity ratio to the power 1/3; this is consistent with DEB's co-variation rules, but does not follow from them. Maturity at puberty follows a Weibull distribution with great accuracy while that at birth does not, which is consistent with the idea that Weibull distributions can be expected when many factors contribute. We found that species from all taxa with a very high allocation fraction to soma, tend to have low maturities at birth and puberty. We discuss the possible implications of these patterns.

Finfish aquaculture in the Mediterranean Sea faces increasing challenges due to climate change while potential adaptation requires a robust assessment of the arising threats and opportunities. This paper presents an approach developed to investigate effects of climate drivers on Greek aquaculture, a representative Mediterranean country with a leading role in the sector. Using a farm level approach, Dynamic Energy Budget models for European seabass and meagre were developed and environmental forcing was used to simulate changes in production and farm profitability under IPCC scenarios RCP45 and RCP85. The effects of temperature and extreme weather events at the individual and farm level were considered along with that of husbandry parameters such as stocking timing, market size, and farm location (inshore, offshore) for nine regions. The simulations suggest that at the individual level fish may benefit from warmer temperatures in the future in terms of growth, thus reaching commercial sizes faster, while the husbandry parameters may have as large an effect on growth as the projected shifts in climatic cues. However, this benefit will be largely offset by the adverse effects of extreme weather events at the population level. Such events will be more frequent in the future and, depending on the intensity one assigns to them, they could cause losses in biomass and farm profits that range from mild to detrimental for the industry. Overall, these results provide quantification of some of the potential threats for an important aquaculture sector while suggesting possibilities to benefit from emerging opportunities. Therefore, they could contribute to improving the sector’s readiness for tackling important challenges in the future.

The method of multidimensional scaling (MDS) has long existed, but could only recently be applied to animal traits in the context of dynamic energy budget (DEB) theory. The application became possible because of the following: (i) the Add-my-Pet (AmP) collection of DEB parameters and traits (approximately 280) recently reached 3000 animal species with 45000 data sets of measurements; (ii) we found a natural distance measure for species based on their traits as a side result of our research on parameter estimation in DEB context; and (iii) we developed plotting code for visualization that allows labelling of taxonomic relationships. Traits, here defined as DEB parameters or any function of these parameters, have different dimensions, which hamper application of many popular distance measures since they (implicitly) assume that all traits have the same dimensions. The AmP collection follows the workflow that measured data determine parameters and parameters determine trait values. In this way we could fill up the species traits table completely, which we could not do by using measured values only, as data availability varies considerably between species and is typically poor. The goodness of fit of predictions for all data sets is generally excellent. This paper discusses links between the MDS method and parameter estimation and illustrates the application of MDS for the AmP collection to five taxa, three ectothermic and two endothermic, which we consider to be ‘complete’, in the sense that we expect that it will be difficult to find more species with data in the open literature. This application of MDS shows links between traits and taxonomy that supplements our efforts to find patterns in the co-variation of parameter values. Knowledge about metabolic performance is key to conservation biology, sustainable management and environmental risk assessment, which are seen as interlinked fields.

We propose an extension of a parameter-free loss function for the estimation of Dynamic Energy Budget parameters for a set of related species that is symmetric in the role of data and predictions. The extension allows that particular parameters might vary, but not by much, among species, while the degree of variation is controlled by weight coefficients. We discuss the choice of these coefficients and illustrate the application with an example of two species of catfish, with their mutual hybrids. In our simultaneous parameter estimation for this example, we could reduce the variation in a parameter, here the energy conductance, substantially with a minor effect on the goodness of fit. We selected this parameter among the ones that varied, because its value was poorly determined by the data. We discuss this example in some detail. The software for implementing this augmented loss function has been implemented in the available software DEBtool_M on Github ( www.github.com/add-my-pet/DEBtool_M ).

Population growth, and other population characteristics, have been computed and made available online for over 2000 animal species in the Add-my-Pet (AmP) collection, assuming constant food and temperature environments. The AmP collection – online database of Dynamic Energy Budget model parameters, implied properties and referenced underlying data – provides an unique opportunity to study how energetics of individuals relates to population growth. For the comparisons of traits, we assume that the background hazard rate is zero, but aging applies to all species and ‘thinning’ to species with high reproduction rates. The new concept ‘thinning’ is a state-dependent hazard rate such that the feeding rate of a cohort does not change in time: the increase of individual feeding rates due to growth is exactly compensated by a reduction in numbers. Thinning affects population growth rate, but the impact differs substantially between species. Some 11% of species do not survive thinning, even at abundant food. The population growth rate relates to the underlying energetics; we discuss and suggest explanations for how population growth rates fit into all known patterns in the co-variation of parameter values: body size-scaling, metabolic acceleration, waste-to-hurry, supply-demand spectrum and altricial-precocial spectrum. We show that, after reproduction, age at puberty dominates population growth. The specific population growth rate scales with maximum body weight in the same way as the weight-specific respiration scales with body weight. DEB theory, which explains both, shows, however, that no direct relationship exists between the population growth rate and respiration. We suggest that the similarity in scaling results from the equality between specific population growth and specific growth rate at maximum growth of structure, and might be an evolutionary relict from times that life consisted of dividing unicellulars; population and body growth are directly connected for unicellulars. We show that the specific growth rate at maximum growth equals 1.5 times the von Bertalanffy growth rate, in a DEB context, which is a new interpretation of the latter growth rate. We expected the population growth rate to co-vary with specific somatic maintenance rate, based on a previously discovered pattern, called the waste-to-hurry strategy, where growth and reproduction are increased by simultaneously increasing assimilation and somatic maintenance in species that live off temporarily abundant food supplies. We did find this effect in ecdysozoa and spiralia, which comprise roughly 95% of animal species, but hardly so in tetrapods. The reason might be that specific somatic maintenance also co-varies with specific maturity levels at puberty for tetrapods. The scaled functional response at which the population growth rate is zero is very close to that at which puberty can just be reached in absence of thinning, and somewhat higher in presence of thinning. The specific population growth rate at abundant food correlates negatively with the functional response for which population growth rate is zero. It also correlates negatively with the precociality index, i.e. the ratio of maturity levels at puberty and birth: the more precocial, the larger neonate size, the smaller reproduction rate, especially in restricted taxa such as mammals and cartilaginous fish. Like other traits, the population growth rate shows considerable segregation among taxa, where mammals have a relatively low rate, glires a relatively high rate among mammals, followed by marsupials; afrotherians have the lowest population growth rates.

WOS:000453497600006; Dynamic Energy Budget (DEB) theory constitutes a coherent set of universal biological processes that have been used as building blocks for modeling biological systems over the last 40 years in many applied disciplines. In the context of extracting parameters for DEB models from data, we discuss the methodology of fitting multiple models, which share parameters, to multiple data sets in a single parameter estimation. This problem is not specific to DEB models, and is (or should be) really general in biology. We discovered that a lot of estimation problems that we suffered from in the past originated from the use of a loss function that was not symmetric in the role of data and predictions. We here propose two much better symmetric candidates, that proved to work well in practice. We illustrate estimation problems and their solutions with a Monte-Carlo case study for increasing amount of scatter, which decreased the amount of information in the data about one or more parameter values. We here validate the method using a set of models with known parameters and different scatter structures. We compare the loss functions on the basis of convergence, point and interval estimates. We also discuss the use of pseudo-data, i.e. realistic values for parameters that we treat as data from which predictions can differ. These pseudo-data are used to avoid that a good fit results in parameter values that make no biological sense. We discuss our new method for estimating confidence intervals and present a list of concrete recommendations for parameter estimation. We conclude that the proposed method performs very well in recovering parameter values of a set of models, applied to a set of data. This is consistent with our large-scale applications in practice.

Reserve capacity quantifies the ability of an animal to smooth out fluctuations in food availability. It is defined as the maximum reserve density, and can be quantified through the application of the Dynamic Energy Budget (DEB) theory. In this study, we analyze inter-specific patterns in DEB parameters of 1041 animal species, focusing on those that control reserve capacity (maximum specific assimilation and energy conductance) and maintenance. The co-variation rules of DEB theory expect that specific somatic maintenance and energy conductance are independent of maximum structural length, with the implication that reserve capacity is proportional to maximum structural length among species and independent of somatic maintenance. We found however that the reserve density increases with somatic maintenance among all large animal taxa in the collection: invertebrates, fish and amphibians, sauropsids and mammals. The waste-to-hurry phenomenon implies that small-bodied species frequently have both a higher specific maintenance and higher specific assimilation (with respect to larger species) allowing them to boost growth and reproduction. If waste-to-hurry strategists would increase both parameters in proportion, maximum structural length would not be affected, reserve capacity would become proportional to somatic maintenance and its relationship with maximum structural length would depend on quantitative details. We did find a positive relationship between reserve capacity and specific somatic maintenance, but the increase (as an average over all taxa) is less than proportional. The reason is that specific assimilation is less than proportional to specific somatic maintenance, the scaling parameter roughly being 0.8, while energy conductance hardly depends on somatic maintenance. The implication is that maximum assimilation is proportional to structural length to the power − 0.7, which explains why the waste-to-hurry strategy is not a viable route for big-bodied species: they would need more assimilates than small-bodied ones, not less. We discuss applications of these findings in the context of parameter estimation. As a side-result we also found that birds have a higher specific somatic maintenance and also a higher (mean) energy conductance, compared to other sauropsids at the same body temperature. The first is to be expected because they are demand species, the latter might be an adaptation to flight: reserve density increases for decreasing energy conductance, while it contributes to weight.

Mixotrophic nanoflagellates (MNF) play a key role in the carbon flux within aquatic ecosystems. They contribute significantly to primary production while, at the same time, they are important consumers of bacteria. MNF comprise a diverse assemblage with a whole range of photosynthetic and feeding potential and with various metabolic responses to environmental drivers, such as light, nutrients and prey availability. However, in most cases MNF are modelled as a single functional group with no reference to the distinct nutritional strategies and constraints of the different types of MNF. Here we develop a mathematical framework for the distinct functional responses of four types of MNF. Our approach is based on the Dynamic Energy Budget (DEB) theory and the concept of Synthesing Unit (SU), which is used to merge phototrophic and phagotrophic nutrition into mixotrophic growth. The resulting models describe explicitly the functional diversity of the MNF group taking into account the dynamic interaction of phototrophy and phagotrophy within the four types of MNF. Our results are in agreement with theoretical expectations and a wide range of experimental observations for the different types of MNF. Our simulations suggest that the growth dynamics of the four types of MNF are affected differently by the availability of resources. Moreover, using our models to compare the rates of organic carbon production and prey consumption by the various MNF types, we show that their net ecosystem role, as producers or consumers, depends on the mixotrophic strategy and it can vary as a function of the prevailing environmental conditions. Overall, our study highlights the importance of mechanistically modelling the distinct metabolic responses of the different types of MNF to environmental drivers in order to better understand their role in the carbon cycle in anticipation of global environmental changes.

Extracellular release of dissolved organic matter (DOM) by phytoplankton is a significant process that drives the microbial loop, providing energy and nutrients to bacteria. In this paper, a dynamic energy budget model is proposed for describing DOM release by phytoplankton under nitrogen and phosphorus limiting conditions. The model allows for the distinction of the two major mechanisms of DOM release; passive diffusion related to growth and lysis of the cells and active exudation related to rejection of unprocessed substrates due to stoichiometric constraints. Model results suggest that phosphorus deficiency has less severe effect on phytoplankton growth and primary production (PP) rate than nitrogen deficiency, while co-limitation by both nutrients has the most severe effect. The dependence of dissolved organic carbon (DOC) release rate on the cellular carbohydrates concentration is also highlighted by the model. Furthermore, model predictions resolve the relationship between PP and DOC release under different nutrient availability scenarios, providing a possible explanation for the deviations from 1 : 1 linear relationship between PP and DOC release, often observed in oligotrophic systems. This deviation is a result of the prevalence of the active exudation mechanism and the reduction of the PP rate due to nutrient limitation. Conversely, passive diffusion is more important under nutrient-replete conditions. The different relative contributions of the two mechanisms result in different qualities of DOM produced by phytoplankton in terms of elemental and molecular composition and size fractions, with potential implications for the bioavailability of the produced DOM for bacteria and the coupling of phytoplankton-bacteria dynamics.

The recent finding that the Greenland shark, Somniosus microcephalus, reaches a life-span of almost 4 centuries and attains sexual maturity around 1.5 centuries, made us wonder what metabolic differences were responsible for these seemingly extreme values, compared to the related and better known spurdog Squalus acanthias. We studied this in the context of the dynamic energy budget (DEB) theory for metabolic organisation, which was applied to some 700 animal species from all large phyla and all chordate orders. The referenced data, estimated parameters and implied properties for all these species are published in the online Add-my-Pet collection, which provides a frame of reference for metabolic and life history properties. Given the few known data on S. microcephalus, we were able to estimate ageing parameters and gestation time, by application of the standard DEB model. We inferred that a recently estimated life-span of 392 years is probably too short for life at 2 °C, rather than too long. The ageing acceleration is only slightly smaller than that of the spurdog, and the gestation time is very likely between 8 and 18 years with the implication of around 200–700 pups per life-time. The low body temperature and high maximum reserve density of S. microcephalus could be identified as the causes of its long life-span. We see the latter cause as an adaptation to a life in the deep sea sporadically preying on big carcasses, where it is necessary to survive long spells of starvation. This application of the standard DEB model shows that it can be applied in situations where few data are available and how implied properties (gestation) can be used to constrain parameter values. The methods used here could be further developed by fisheries biologists working with deep sea species for which very little is known.

The framework provided by the Dynamic Energy Budget (DEB) theory allows the quantification of metabolic processes and the associated biological rates that are of interest for aquaculture, such as growth and feeding. The DEB parameters were estimated for farmed European sea bass (Dicentrarchus labrax), a species of major importance for the Mediterranean aquaculture, using zero- and uni-variate literature data and achieving an overall good fit. The obtained parameter set was used to validate the model on sites representatively covering the geographic distribution of the aquaculture activity in Greece via comparison of model predictions to observations. Inter-individual variability of farmed fish was introduced through: 1) an individual initial weight and 2) a factor that acts as an individual-specific multiplier for some of the model parameters and produces scatter in maximum size, and age and size at puberty. Growth of E. sea bass was adequately predicted by the model while feeding tended to be underestimated, particularly during the period following the summer months when warmer temperatures promote high growth rates. The results suggest robustness of the model since it is able to simulate growth and food intake in several independent aquaculture production units, using a common parameter set. The accuracy of growth predictions supports the applicability of the model in variable environmental conditions in the context of climate change. Reconstruction of the feeding history from growth data revealed variations in the scaled functional response (f), i.e., the feeding rate as fraction of maximum possible one of an individual of a given size, throughout the production cycle. However, model simulations with constant f result in reasonably good predictions for growth and feeding in variable environmental conditions. Tendency of the model to underestimate the feeding process revealed both model weaknesses associated with higher temperatures as well as irregularities in the feeding protocols applied at the farm level. Our work demonstrates the capacity and potential of DEB theory for further development of tools that contribute to the assessment and improvement of feeding practices in aquaculture.