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Making sense of ecotoxicity test results



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DEBtox information

Publications / DEBkiss applications

Explanation


The papers here are organised by year of publication. Each paper gets a few keys to facilitate searching by topic. Each paper has a DigitalObject Identifier (DOI), that uniquely identifies it on the internet. Clicking the link provides the abstract, and also the PDF if you have access rights to that journal. Inclusion of a paper in this list does not mean an endorsement or a quality mark of any kind.

Requirements to be included


My initial plan was to collect here all applications of the DEBkiss framework. However, I soon realised that that would be too narrow: there are just too many very-closely-related models that should be of interest in this context. I will now include all kappa-models without an initial reserve compartment, so models where the assimilation flux is split immediately into a somatic and a maturation/reproduction flux. I will be including PhD theses and work that is submitted and in advanced preparation (as far as I know about them). Papers that deal with toxicants will also be included in the DEBtox list.

I start with a list of papers that appeared before DEBkiss, which apply (variations on) the Kooijman-Metz model (which is very similar to DEBkiss). The graph also includes these papers that appeared pre-DEBkiss.



Essential reading


Download of accepted versions


On this page, I will try to include downloadable PDF versions of my papers. These will be the my version of the paper; the last submitted version that was accepted (post peer review, but pre formatting by the journal). I will only offer that version for download below when the publisher/journal allows this, and adding the license information as prescribed by the publisher/journal. Furthermore, I am only offering downloads for papers on which I am the first author. It will take some time before all papers are added ... Note that there may be (small) differences with the published version.


Pre-DEBkiss models; most based on the Kooijman-Metz formulation.


  • Kooijman SALM and Metz JAJ (1984). On the dynamics of chemically stressed populations: the deduction of population consequences from effects on individuals. Ecotoxicol Environ Saf 8(3): 254-274. http://dx.doi.org/10.1016/0147-6513(84)90029-0 
  • De Roos AM et al. (1992). Studying the dynamics of structured population models: a versatile technique and its application to Daphnia. Am Nat 139(1): 123-147. http://www.jstor.org/stable/2462588   
  • Baveco JM and De Roos AM (1996). Assessing the impact of pesticides on lumbricid populations: an individual-based modelling approach. J Appl Ecol 33: 1451-1468. http://www.jstor.org/stable/2404784 
  • Klok C. and De Roos AM (1996). Population level consequences of toxicological influences on individual growth and reproduction in Lumbricus rubellus (Lumbricidae, Oligochaeta). Ecotox Environ Saf 33: 118-127. http://dx.doi.org/10.1006/eesa.1996.0015 
  • Klok C et al. (1997). Assessing the effects of abiotic environmental stress on population growth in Lumbricus rubellus (Lubricidae, Oligochaeta). Soil Biol Biochem 29(3-4): 287-293. http://dx.doi.org/10.1016/s0038-0717(96)00050-8 
  • Rinke K and Vijverberg J (2005). A model approach to evaluate the effect of temperature and food concentration on individual life-history and population dynamics of Daphnia. Ecol Mod 186(3): 326-344. http://dx.doi.org/10.1016/j.ecolmodel.2005.01.031 
  • Klok C et al. (2006). Population growth and development of the earthworm Lumbricus rubellus in a polluted field soil: Possible consequences for the godwit (Limosa limosa). Environ Toxicol Chem 25(1): 213-219. http://dx.doi.org/10.1897/05-286r.1 
  • Klok C et al. (2006). Does reproductive plasticity in Lumbricus rubellus improve the recovery of populations in frequently inundated river floodplains? Soil Biol Biochem. 38:611-618. http://dx.doi.org/10.1016/j.soilbio.2005.06.013 
  • Klok C et al. (2007). Extending a combined dynamic energy budget matrix population model with a bayesian approach to assess variation in the intrinsic rate of population increase. An example in the earthworm Dendrobaena octaedra. Environ Toxicol Chem 26(11): 2383-2388. http://dx.doi.org/10.1897/07-223R.1 
  • Klok C (2008). Gaining insight in the interaction of zinc and population density with a combined dynamic energy budget and population model. Environ Sci Technol 42: 8803-8808. http://dx.doi.org/10.1021/es8016599 
  • Jager T and Klok C (2010). Extrapolating toxic effects on individuals to the population level: the role of dynamic energy budgets. Phil Trans Royal Soc B 365: 3531-3540. http://dx.doi.org/10.1098/rstb.2010.0137

DEBkiss models (and later models that are closely related). Full list by year


2013

2014

  • Barsi A, Jager T, Collinet M, Lagadic L and Ducrot V (2014). Considerations for test design to accommodate energy-budget models in ecotoxicology: a case study for acetone in the pond snail Lymnaea stagnalis. Environ Toxicol Chem 33(7):1466-1475 http://dx.doi.org/10.1002/etc.2399
  • Hamda NT (2014). Mechanistic models to explore combined effects of toxic chemicals and natural stressing factors: case study on springtails. PhD thesis (Ch. 5 and 6 are DEBkiss applications).
  • Jager T, Barsi A, Hamda NT, Martin BT, Zimmer EI and Ducrot V. (2014). Dynamic energy budgets in population ecotoxicology: applications and outlook. Ecol Mod 280:140-147 http://dx.doi.org/10.1016/j.ecolmodel.2013.06.024  accepted version. (Not directly an application, but reserveless DEB models are mentioned as a potential building block for population models).
  • Jager T, Gudmundsdóttir EM and Cedergreen N (2014). Dynamic modeling of sub-lethal mixture toxicity in the nematode Caenorhabditis elegans. Environ Sci Technol 48:7026-7033 http://dx.doi.org/10.1021/es501306t accepted version and SI.
2015

  • Barsi A (2015). Towards understanding the effects of putative endocrine disruptors in the great pond snail Lymnaea stagnalis: experimental and toxicokinetic-toxicodynamic modelling approaches. PhD thesis (Ch. 3 and 4 are DEBkiss applications).
  • Fiechter J, Huff DD, Martin BT, Jackson DW, Edwards CA, Rose KA, Curchitser EN, Hedstrom KS, Lindley ST and Wells BK (2015). Environmental conditions impacting juvenile Chinook salmon growth off central California: an ecosystem model analysis. Geophysical Research Letters 42(8):2910–2917 http://dx.doi.org/10.1002/2015GL063046
  • Groeneveld J, Johst K, Kawaguchi S, Meyer B, Teschke M and Grimm V (2015). How biological clocks and changing environmental conditions determine local population growth and species distribution in Antarctic krill (Euphausia superba): a conceptual model. Ecol Mod 303:78-86. http://dx.doi.org/10.1016/j.ecolmodel.2015.02.009 
  • Jager T and Ravagnan E (2015). Parameterising a generic model for the dynamic energy budget of Antarctic krill, Euphausia superba. Mar Ecol Progr Ser 519:115-128 http://dx.doi.org/ 10.3354/meps11098. accepted version and SI.
  • Jager T, Salaberria I and Hansen BH (2015). Capturing the life history of the marine copepod Calanus sinicus into a generic bioenergetics framework. Ecol Mod 299:114-120. http://dx.doi.org/10.1016/j.ecolmodel.2014.12.011. accepted version.

2016


2017

  • Desforges JPW, Sonne C and Dietz R (2017). Using energy budgets to combine ecology and toxicology in a mammalian sentinel species. Scientific Reports 7:46267. http://dx.doi.org/10.1038/srep46267 (Open Acces, first application for mammals)
  • Jager T, Salaberria I, Altin D, Nordtug T and Hansen BH (2017). Modelling the dynamics of growth, development and lipid storage in the marine copepod Calanus finmarchicus. Marine Biology 164:1. http://dx.doi.org/10.1007/s00227-016-3030-8 (Open Access)
  • Martin BT, Heintz R, Danner EM and Nisbet RM (2017). Integrating lipid storage into general representations of fish energetics. J Animal Ecol 86:812-825 http://dx.doi.org/10.1111/1365-2656.12667 (closely related, but different from DEBkiss: removes maturity entirely, and replaces it with a storage).
  • Smallegange IM, Caswell H, Toorians MEM and De Roos AM (2017). Mechanistic description of population dynamics using dynamic energy budget theory incorporated into integral projection models. Methods in Ecology and Evolution 8(2):146-154. http://dx.doi.org/10.1111/2041-210X.12675 (more Kooijman-Metz than DEBkiss)  
2018

2019


  • Boersch-Supan PH and LR Johnson (2019). Two case studies detailing Bayesian parameter inference for dynamic energy budget models. Journal of Sea Research 143:57-69. https://doi.org/10.1016/j.seares.2018.07.014
  • Hamda NT, B Martin, JB Poletto, DE Cocherell, NA Fangue, J Van Eenennaam, EA Mora and E Danner (2019). Applying a simplified energy-budget model to explore the effects of temperature and food availability on the life history of green sturgeon (Acipenser medirostris). Ecological Modelling 395:1-10. https://doi.org/10.1016/j.ecolmodel.2019.01.005
  • Martin T, H Thompson, P Thorbek and R Ashauer (2019). Toxicokinetic−toxicodynamic modeling of the effects of pesticides on growth of Rattus norvegicus. Chem Res Toxicol 32(11):2281-2294. http://dx.doi.org/10.1021/acs.chemrestox.9b00294 (mammal, growth only)
  • Martin T, P Thorbek and R Ashauer (2019). Common ground between growth models of rival theories: a useful illustration for beginners. Ecological Modelling 407:108712. https://doi.org/10.1016/j.ecolmodel.2019.05.017 (not really an application, but DEBkiss is discussed i.r.t. MTE)
  • Smallegange IM and MP Berg (2019). A functional trait approach to identifying life history patterns in stochastic environments. Ecology and Evolution 9(16):9350-9361. https://doi.org/10.1002/ece3.5485 (Based on Kooijman-Metz)

2020


  • Chaparro‐Pedraza, PC and AM de Roos (2020), Density‐dependent effects of mortality on the optimal body size to shift habitat: why smaller is better despite increased mortality risk. Evolution 74: 831-841. https://doi-org.vu-nl.idm.oclc.org/10.1111/evo.13957  
  • De Roos, AM (2020). A general approach for analysis of physiologically structured population models: the R package 'PSPManalysis'. bioRxiv 2020.06.27.174722. https://doi.org/10.1101/2020.06.27.174722  
  • Goussen B, C Rendal, D Sheffield, E Butler, OR Price and R Ashauer (2020). Bioenergetics modelling to analyse and predict the joint effects of multiple stressors: meta-analysis and model corroboration. Sci Total Environ 749:141509. https://doi.org/10.1016/j.scitotenv.2020.141509 (Open Access)
  • Jager T (2020). Revisiting simplified DEBtox models for analysing ecotoxicity data. Ecol Modell 416:108904. https://doi.org/10.1016/j.ecolmodel.2019.108904. accepted version and SI.
  • Pfab F, GV DiRenzo, A Gershman, CJ Briggs and RM Nisbet (2020). Energy budgets for tadpoles approaching metamorphosis. Ecol Modell 436:109261. https://doi.org/10.1016/j.ecolmodel.2020.109261 (compares DEBkiss to standard DEB)
  • Sherborne N and N Galic (2020). Modelling sublethal effects of chemicals: application of a simplified dynamic energy budget model to standard ecotoxicity data. Environ Sci Technol. 54(12):7420-7429. https://doi.org/10.1021/acs.est.0c00140 
  • Sherborne N, N Galic and R Ashauer (2020). Sublethal effect modelling for environmental risk assessment of chemicals: problem definition, model variants, application and challenges. Sci Total Environ 745:141027. https://doi.org/10.1016/j.scitotenv.2020.141027
  • Smallegange IM, M Flotats Avilés, K Eustache (2020). Unusually paced life history strategies of marine megafauna drive atypical sensitivities to environmental variability. Frontiers in Marine Science 7:1065. https://doi.org/10.3389/fmars.2020.597492 (based on Kooijman-Metz)
  • ...

2021


  • Bahlburg D, B Meyer and U Berger (2021). The impact of seasonal regulation of metabolism on the life history of Antarctic krill. Ecol Modell 442:109427. https://doi.org/10.1016/j.ecolmodel.2021.109427.
  • Chaparro‐Pedraza PC and AM de Roos (2021). Individual energy dynamics reveal nonlinear interaction of stressors threatening migratory fish populations. Funct Ecol 35:727-738. https://doi.org/10.1111/1365-2435.13751 (uses the model version of Martin et al 2017
  • Jager T, J Heuschele, T Lode and K Borgå (2021). Analysing individual growth curves for the copepod Tigriopus brevicornis, while considering changes in shape. J Sea Res 174:102075. https://doi.org/10.1016/j.seares.2021.102075 (Open Access) (not really an application, but preparatory work for DEBkiss analysis, and links nicely to the previous copepod work)
  • Svendheim LH, PA Olsvik, IB Øverjordet, T Jager, TM Ciesielski, T Nordtug, T Kristensen, BH Hansen, B Kvæstad, D Altin and J Farkas (2021). Investigating the effects of marine tailing exposure on the development, growth, and lipid accumulation of Calanus finmarchicus. Chemosphere 282:131051. https://doi.org/10.1016/j.chemosphere.2021.131051  
  • ...



The DEBtox information site, www.debtox.info, since July 2011