{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T02:00:03Z","timestamp":1773280803050,"version":"3.50.1"},"reference-count":53,"publisher":"Oxford University Press (OUP)","issue":"1","funder":[{"name":"Norwegian Science Council","award":["NFR 255295"],"award-info":[{"award-number":["NFR 255295"]}]},{"DOI":"10.13039\/501100004488","name":"Croatian science foundation","doi-asserted-by":"crossref","award":["IP-2018-01-3150"],"award-info":[{"award-number":["IP-2018-01-3150"]}],"id":[{"id":"10.13039\/501100004488","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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 \u2018complete\u2019, 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.<\/jats:p>","DOI":"10.1093\/conphys\/coab086","type":"journal-article","created":{"date-parts":[[2021,12,9]],"date-time":"2021-12-09T13:13:30Z","timestamp":1639055610000},"source":"Crossref","is-referenced-by-count":11,"title":["Multidimensional scaling for animal traits in the context of dynamic energy budget theory"],"prefix":"10.1093","volume":"9","author":[{"given":"Sebastiaan A L M","family":"Kooijman","sequence":"first","affiliation":[{"name":"Department of Theoretical Biology, VU University Amsterdam, de Boelelaan 1087, 1081 HV Amsterdam, The Netherlands"}]},{"given":"Konstadia","family":"Lika","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Crete, 70013, Heraklion, Greece"}]},{"given":"Starrlight","family":"Augustine","sequence":"additional","affiliation":[{"name":"Akvaplan-niva AS, Fram High North Research Centre for Climate and the Environment, 9296 Troms\u00f8, Norway"}]},{"given":"Nina","family":"Marn","sequence":"additional","affiliation":[{"name":"Division for Environmental and Marine Research, Rudjer Bo\u0161kovi\u0107 Institute, 10000 Zagreb, Croatia"}]}],"member":"286","published-online":{"date-parts":[[2021,12,15]]},"reference":[{"key":"2021121700370491500_ref1","volume-title":"AmP collection","author":"AmP","year":"2021"},{"key":"2021121700370491500_ref2","volume-title":"Software package AmPtool","author":"AmPtool","year":"2021"},{"key":"2021121700370491500_ref3","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.seares.2018.04.006","article-title":"Life in the slow lane? A dynamic energy budget model for the western swamp turtle, Pseudemydura umbrina","volume":"143","author":"Arnall","year":"2019","journal-title":"J Sea Res"},{"key":"2021121700370491500_ref4","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.seares.2018.03.006","article-title":"Altricial-precocial spectra in animal kingdom","volume":"143","author":"Augustine","year":"2019","journal-title":"J Sea Res"},{"key":"2021121700370491500_ref5","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.seares.2018.06.002","article-title":"Why big-bodied animal species cannot evolve a waste-to-hurry strategy","volume":"143","author":"Augustine","year":"2019","journal-title":"J Sea Res"},{"key":"2021121700370491500_ref6","doi-asserted-by":"crossref","first-page":"109077","DOI":"10.1016\/j.ecolmodel.2020.109077","article-title":"Comparing loss functions and interval estimates for survival data","volume":"430","author":"Augustine","year":"2020","journal-title":"Ecol Model"},{"key":"2021121700370491500_ref7","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1007\/s10646-014-1413-5","article-title":"Sensitivity of animals to chemical compounds links to metabolic rate","volume":"24","author":"Baas","year":"2015","journal-title":"Ecotoxicology"},{"key":"2021121700370491500_ref8","doi-asserted-by":"crossref","first-page":"3309","DOI":"10.3390\/su13063309","article-title":"Testing a model of pacific oysters\u2019 (Crassostrea gigas) growth in the Adriatic Sea: implications for aquaculture spatial planning","volume":"13","author":"Bertolini","year":"2021","journal-title":"Sustainability"},{"key":"2021121700370491500_ref9","volume-title":"Size, Function and Life History","author":"Calder","year":"1984"},{"key":"2021121700370491500_ref10","doi-asserted-by":"crossref","first-page":"734621","DOI":"10.1016\/j.aquaculture.2019.734621","article-title":"Integrated multi-trophic aquaculture of red drum (Sciaenops ocellatus) and sea cucumber (Holothuria scabra): assessing bioremediation and life-cycle impacts","volume":"516","author":"Chary","year":"2020","journal-title":"Aquaculture"},{"key":"2021121700370491500_ref11","author":"DEBtool","year":"2021"},{"key":"2021121700370491500_ref12","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1002\/jmor.1051900408","article-title":"Relationships of lungfishes","volume":"1","author":"Forey","year":"1986","journal-title":"J Morphol"},{"key":"2021121700370491500_ref13","volume-title":"Improving representations of higher trophic-level species in models: using individual-based modelling and dynamic energy budget theory to project population trajectories of southern elephant seals","author":"Goedegebuure","year":"2018"},{"key":"2021121700370491500_ref14","doi-asserted-by":"crossref","first-page":"109207","DOI":"10.1016\/j.ecolmodel.2020.109207","article-title":"Dynamic energy budget of endemic and critically endangered bivalve Pinna nobilis: a mechanistic model for informed conservation","volume":"434","author":"Haberle","year":"2020","journal-title":"Ecol Model"},{"key":"2021121700370491500_ref15","article-title":"TimeTree","author":"Hedges","year":"2021"},{"key":"2021121700370491500_ref16","volume-title":"The GREAT-ER model as a tool for chemical risk assessment and management for Chinese river catchments","author":"Jackson","year":"2018"},{"key":"2021121700370491500_ref17","doi-asserted-by":"crossref","DOI":"10.1007\/978-981-13-9447-8_16","article-title":"Transforming environmental chemistry and toxicology to meet the anthropocene sustainability challenges beyond silent spring","volume-title":"A New Paradigm for Environmental Chemistry and Toxicology: From Concepts to Insights","author":"Jin","year":"2020"},{"key":"2021121700370491500_ref18","doi-asserted-by":"crossref","first-page":"1385","DOI":"10.1111\/1365-2435.13829","article-title":"Where do functional traits come from? The role of theory and models","volume":"35","author":"Kearney","year":"2021","journal-title":"Funct Ecol"},{"key":"2021121700370491500_ref19","doi-asserted-by":"crossref","first-page":"315","DOI":"10.3733\/hilg.v06n11p315","article-title":"Body size and metabolism","volume":"6","author":"Kleiber","year":"1932","journal-title":"Hilgardia"},{"key":"2021121700370491500_ref20","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/S0022-5193(86)80107-2","article-title":"Energy budgets can explain body size relations","volume":"121","author":"Kooijman","year":"1986","journal-title":"J Theor Biol"},{"key":"2021121700370491500_ref21","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511805400","volume-title":"Dynamic Energy Budget theory for metabolic organisation","author":"Kooijman","year":"2009"},{"key":"2021121700370491500_ref22","author":"Kooijman","year":"2010"},{"key":"2021121700370491500_ref23","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1111\/j.1600-0706.2012.00098.x","article-title":"Waste to hurry: dynamic energy budgets explain the need of wasting to fully exploit blooming resources","volume":"122","author":"Kooijman","year":"2013","journal-title":"Oikos"},{"key":"2021121700370491500_ref24","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/j.seares.2014.06.005","article-title":"Metabolic acceleration in animal ontogeny: an evolutionary perspective","volume":"94","author":"Kooijman","year":"2014","journal-title":"J Sea Res"},{"key":"2021121700370491500_ref25","doi-asserted-by":"crossref","first-page":"109052","DOI":"10.1016\/j.ecolmodel.2020.109052","article-title":"The comparative energetics of petrels and penguins","volume":"427","author":"Kooijman","year":"2020","journal-title":"Ecol Model"},{"key":"2021121700370491500_ref26","doi-asserted-by":"crossref","first-page":"109106","DOI":"10.1016\/j.ecolmodel.2020.109106","article-title":"The standard dynamic energy budget model has no plausible alternatives","volume":"428","author":"Kooijman","year":"2020","journal-title":"Ecol Model"},{"key":"2021121700370491500_ref27","volume-title":"The Analysis of Aquatic Toxicity Data","author":"Kooijman","year":"1996"},{"key":"2021121700370491500_ref28","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1016\/0147-6513(84)90029-0","article-title":"On the dynamics of chemically stressed populations; the deduction of population consequences from effects on individuals","volume":"8","author":"Kooijman","year":"1984","journal-title":"Ecotoxicol Environ Saf"},{"key":"2021121700370491500_ref29","volume-title":"Numerical Ecology","author":"Legendre","year":"1998"},{"key":"2021121700370491500_ref30","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.seares.2018.04.005","article-title":"Body size as emergent property of metabolism","volume":"143","author":"Lika","year":"2019","journal-title":"J Sea Res"},{"key":"2021121700370491500_ref31","doi-asserted-by":"crossref","first-page":"109110","DOI":"10.1016\/j.ecolmodel.2020.109110","article-title":"The use of augmented loss functions for estimating dynamic energy budget parameters","volume":"428","author":"Lika","year":"2020","journal-title":"Ecol Model"},{"key":"2021121700370491500_ref32","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.jtbi.2014.03.025","article-title":"The bijection from data to parameter space with the standard deb model quantifies the supply-demand spectrum","volume":"354","author":"Lika","year":"2014","journal-title":"J Theor Biol"},{"key":"2021121700370491500_ref33","volume-title":"Multivariate Analysis","author":"Mardia","year":"1982"},{"key":"2021121700370491500_ref34","doi-asserted-by":"crossref","first-page":"1479","DOI":"10.1111\/ele.13574","article-title":"Quantifying impacts of plastic debris on marine wildlife identifies ecological breakpoints","volume":"23","author":"Marn","year":"2020","journal-title":"Ecol Lett"},{"key":"2021121700370491500_ref35","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/j.ecolmodel.2017.07.001","article-title":"Environmental effects on growth, reproduction, and life-history traits of loggerhead turtles","volume":"360","author":"Marn","year":"2017","journal-title":"Ecol Model"},{"key":"2021121700370491500_ref36","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1006100","article-title":"The AmP project: comparing species on the basis of Dynamic Energy Budget parameters","volume":"14","author":"Marques","year":"2018","journal-title":"PLoS Comput Biol"},{"key":"2021121700370491500_ref37","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1016\/j.seares.2018.07.004","article-title":"Fitting multiple models to multiple data sets","volume":"143","author":"Marques","year":"2019","journal-title":"J Sea Res"},{"key":"2021121700370491500_ref38","first-page":"1","article-title":"Conservation physiology of marine fishes: state of the art and prospects for policy","volume":"4","author":"McKenzie1","year":"2016","journal-title":"Conserv Physiol"},{"key":"2021121700370491500_ref39","doi-asserted-by":"crossref","first-page":"1612","DOI":"10.1016\/j.biocon.2010.04.004","article-title":"Predicting survival, reproduction and abundance of polar bears under climate change","volume":"143","author":"Moln\u00e1r","year":"2010","journal-title":"Biol Conserv"},{"key":"2021121700370491500_ref40","article-title":"Traitbank: practical semantics for organism attribute data","volume":"7","author":"Parra","year":"2015","journal-title":"Semantic Web"},{"key":"2021121700370491500_ref41","doi-asserted-by":"crossref","first-page":"109049","DOI":"10.1016\/j.ecolmodel.2020.109049","article-title":"A box-model of carrying capacity of the Thau lagoon in the context of ecological status regulations and sustainable shellfish cultures","volume":"426","author":"Pete","year":"2020","journal-title":"Ecol Model"},{"key":"2021121700370491500_ref42","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511608551","volume-title":"The Ecological Implications of Body Size","author":"Peters","year":"1983"},{"key":"2021121700370491500_ref43","doi-asserted-by":"crossref","first-page":"109006","DOI":"10.1016\/j.ecolmodel.2020.109006","article-title":"Impact of environmental variability on Pinctada margaritifera life-history traits: a full life cycle DEB modeling approach","volume":"423","author":"Sangare","year":"2020","journal-title":"Ecol Model"},{"key":"2021121700370491500_ref44","doi-asserted-by":"crossref","first-page":"3654","DOI":"10.1111\/gcb.14296","article-title":"Predicting shifting sustainability trade-offs in marine finfish aquaculture under climate change","author":"Sar\u00e0","year":"2018","journal-title":"Glob Change Biol"},{"key":"2021121700370491500_ref45","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1111\/maec.12106","article-title":"Thinking beyond organism energy use: a trait-based bioenergetic mechanistic approach for predictions of life history traits in marine organisms","volume":"35","author":"Sar\u00e0","year":"2014","journal-title":"Mar Ecol"},{"key":"2021121700370491500_ref46","first-page":"49","article-title":"43 genes support the lungfish-coelacanth grouping related to the closest living relative of tetrapods with the Bayesian method under the coalescence model","volume-title":"BMC Res Notes","author":"Shan","year":"2011"},{"issue":"12","key":"2021121700370491500_ref47","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0144059","article-title":"A comparison study on similarity and dissimilarity measures in clustering continuous data","volume":"10","author":"Shirkhorshidi","year":"2015","journal-title":"PLoS One"},{"key":"2021121700370491500_ref48","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1007\/s10584-021-03096-y","article-title":"Projecting climate change impacts on mediterranean finfish production: a case study in greece","volume":"165","author":"Stavrakidis-Zachou","year":"2021","journal-title":"Clim Change"},{"key":"2021121700370491500_ref49","doi-asserted-by":"crossref","first-page":"1512","DOI":"10.1093\/molbev\/msh150","article-title":"The phylogenetic relationship of tetrapod, coelacanth, and lungfish revealed by the sequences of forty-four nuclear genes","volume":"21","author":"Takezaki","year":"2004","journal-title":"Mol Biol Evol"},{"key":"2021121700370491500_ref50","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1007\/s10750-019-04066-3","article-title":"Towards a cohesive strategy for the conservation of the united states\u2019 diverse and highly endemic crayfish fauna","volume":"846","author":"Taylor","year":"2019","journal-title":"Hydrobiologia"},{"key":"2021121700370491500_ref51","volume-title":"Application of dynamic energy budget theory for conservation relevant modelling of bird life histories","author":"Teixeira","year":"2016"},{"key":"2021121700370491500_ref52","doi-asserted-by":"crossref","first-page":"109186","DOI":"10.1016\/j.ecolmodel.2020.109186","article-title":"A dynamic energy budget model of Fenneropenaeus chinensis with applications for aquaculture and stock enhancement","volume":"431","author":"Yang","year":"2020","journal-title":"Ecol Model"},{"key":"2021121700370491500_ref53","first-page":"5449","article-title":"Evolutionary relationships of the coelacanth, lungfishes, and tetrapods based on the 28s ribosomal RNA gene","volume-title":"Proc Natl Acad Sci U S A","author":"Zardoya","year":"1996"}],"container-title":["Conservation Physiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/conphys\/article-pdf\/9\/1\/coab086\/41780048\/coab086.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/conphys\/article-pdf\/9\/1\/coab086\/41780048\/coab086.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,12,17]],"date-time":"2021-12-17T00:37:39Z","timestamp":1639701459000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/conphys\/article\/doi\/10.1093\/conphys\/coab086\/6463315"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,1,1]]},"references-count":53,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/conphys\/coab086","relation":{},"ISSN":["2051-1434"],"issn-type":[{"value":"2051-1434","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021]]},"published":{"date-parts":[[2021,1,1]]},"article-number":"coab086"}}