The AmP project: Comparing species on the basis of dynamic energy budget parameters

Abstract

We developed new methods for parameter estimation-in-context and, with the help of 125 authors, built the AmP (Add-my-Pet) database of Dynamic Energy Budget (DEB) models, parameters and referenced underlying data for animals, where each species constitutes one database entry. The combination of DEB parameters covers all aspects of energetics throughout the full organism’s life cycle, from the start of embryo development to death by aging. The species-specific parameter values capture biodiversity and can now, for the first time, be compared between animals species. An important insight brought by the AmP project is the classification of animal energetics according to a family of related DEB models that is structured on the basis of the mode of metabolic acceleration, which links up with the development of larval stages. We discuss the evolution of metabolism in this context, among animals in general, and ray-finned fish, mollusks and crustaceans in particular. New DEBtool code for estimating DEB parameters from data has been written. AmPtool code for analyzing patterns in parameter values has also been created. A new web-interface supports multiple ways to visualize data, parameters, and implied properties from the entire collection as well as on an entry by entry basis. The DEB models proved to fit data well, the median relative error is only 0.07, for the 1035 animal species at 2018/03/12, including some extinct ones, from all large phyla and all chordate orders, spanning a range of body masses of 16 orders of magnitude. This study is a first step to include evolutionary aspects into parameter estimation, allowing to infer properties of species for which very little is known.

Field tests of a general ectotherm niche model show how water can limit lizard activity and distribution

“…, b, Marques et al. ), based on parameters derived from the detailed observations of growth and reproduction from the ongoing captive colony previously described. In addition to the single‐observation (“zero‐variate”) data (Table ), we included univariate data on length vs. age ( n = 14 individuals), mass vs. age ( n = 8), and length vs. mass ( n = 33) derived from the captive colony.…”

A mechanistic theory of personality‐dependent movement behaviour based on dynamic energy budgets

“…Nevertheless, some shortcuts have been proposed (see Table 11.1 in Kooijman ), and, recently, the procedures for estimating DEB parameters have been substantially improved (Marques et al . ). Moreover, estimating the full range of DEB parameters from empirical data is not always required, and many bioenergetics parameters can be extrapolated from one species to another (Kooijman et al .…”

Dynamic Energy Budget (DEB) modelBlue mussels (Mytilus edulis) : technical report INNOPRO project

“…The Add_My_Pet routine (Kooijman, 2009;Marques et al, 2018) allows to estimate the species specific DEB parameters simultaneously using the co-variation method (Lika et al, 2011a). The covariation method is an iterative optimisation routine based on the Nelder-Meads simplex algorithms.…”

“…The parameter estimation is done using the Add_My_Pet software (Kooijman, 2009;Lika et al, 2011b;Marques et al, 2018) (Kooijman, 1986;Kooijman, 2000;Kooijman, 2010) describes the individual growth, energy dynamics and reproduction as a function of environmental conditions such as temperature and food. The DEB theory is a generic theory that can be applied to different species and life stages by using species specific parameters (Kooijman, 2001).…”