The AmP project: Comparing species on the basis of dynamic energy budget parameters.
The AmP project: Comparing species on the basis of dynamic energy budget parameters.
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DOI：
10.1371/journal.pcbi.1006100
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发表时间：
2018-05
影响因子：
4.3
通讯作者：
Kooijman SALM
中科院分区：
文献类型：
--
作者：
Marques GM;Augustine S;Lika K;Pecquerie L;Domingos T;Kooijman SALM
我们开发了新的参数估计方法，并在125位作者的帮助下，建立了动态能量预算（DEB）模型，参数和动物参考基础数据的AmP（Add-my-Pet）数据库，其中每个物种构成一个数据库条目。DEB参数的组合涵盖了整个生物体生命周期中能量学的所有方面，从胚胎发育开始到衰老死亡。物种特异性参数值捕获生物多样性，现在可以第一次在动物物种之间进行比较。AmP项目带来的一个重要见解是根据一系列相关的DEB模型对动物能量学进行分类，这些模型是基于代谢加速模式构建的，与幼虫阶段的发育有关。我们讨论在这种情况下，在一般动物，特别是鳍鱼，软体动物和甲壳类动物的新陈代谢的演变。新的DEBtool代码估计DEB参数的数据已被写入。还创建了用于分析参数值模式的AmPtool代码。新的Web界面支持多种方式来可视化整个集合中的数据、参数和隐含属性，以及逐个条目的数据。DEB模型被证明能够很好地拟合数据，对于2018/03/12的1035种动物物种，包括一些灭绝的物种，来自所有大型门和所有脊索动物目，跨越16个数量级的体重范围，相对误差中位数仅为0.07。这项研究是将进化方面纳入参数估计的第一步，可以推断出知之甚少的物种特性。我们发现，动态能量收支（DEB）模型的参数可以估计从一组简单的数据，动物的生活史方面，生长和繁殖，如果组合处理。除了拟合优度作为估计标准外，与其他物种的参数值的关系也很重要，因为DEB参数具有明确的生理学解释，并且由于错误的原因而良好拟合总是要考虑的风险。我们开发并优化了这种类型的参数估计方法，并在开放访问的Add-my-Pet（AmP）数据库中组织了1000多种动物物种的结果，到目前为止，已有125位作者对此做出了贡献。我们还开发了软件包AmPtool来比较集合中的参数值，该软件包基于DEBtool来辅助DEB理论的应用。一个家庭的相关DEB模型，结构相对于代谢加速的模式，捕捉生物多样性，包括不同的生命阶段。我们讨论了DEB模型在进化背景下的家族结构的一些特征。AmP收集的数据在研究生物多样性在生态系统结构和功能中的作用方面具有巨大潜力，随着数据库的规模不断扩大，这方面的研究也将不断增加。
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. We discovered that parameters of Dynamic Energy Budget (DEB) models can be estimated from a set of simple data on animal life history aspects, growth and reproduction, if treated in combination. Apart from goodness-of-fit as an estimation criterion, relations with parameter values of other species are important, since DEB parameters have a clear physiological interpretation and a good fit for the wrong reasons is always a risk to consider. We developed and optimized methods for this type of parameter estimation-in-context and organized the results of over 1000 animal species in the open-access Add-my-Pet (AmP) database, to which 125 authors contributed so far. We also developed software package AmPtool to compare parameter values in the collection, that builds on DEBtool to assist applications of DEB theory. A family of related DEB models, structured with respect to the modes of metabolic acceleration, captures biodiversity, including various life stages. We discuss some features of the family structure of DEB models in an evolutionary context. The AmP collection has a great potential for research on the role of biodiversity in ecosystem structure and functioning, which will grow with the size of the database.
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影响因子：
2
作者：
KOOIJMAN, SALM
通讯作者：
KOOIJMAN, SALM
DOI：
10.1098/rstb.2000.0771
发表时间：
2001-03-29
影响因子：
6.3
作者：
Kooijman, SALM
通讯作者：
Kooijman, SALM
影响因子：
1.9
作者：
Kooijman, S. A. L. M.
通讯作者：
Kooijman, S. A. L. M.
影响因子：
2
作者：
Lika, Konstadia;Kearney, Michael R.;Kooijman, Sebastiaan A. L. M.
通讯作者：
Kooijman, Sebastiaan A. L. M.
影响因子：
10
作者：
Kooijman, S. A. L. M.;Sousa, T.;Jager, T.
通讯作者：
Jager, T.